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All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

aa(String) - Method in class org.snpeff.codons.CodonTable
Translate codons to an amino acid sequence
aa(String, boolean) - Method in class org.snpeff.codons.CodonTable
 
aa(String, Genome, String) - Method in class org.snpeff.codons.CodonTables
Translate a codon into an amino acid for a given genome+chromosome
AA_TO_CODE - Static variable in class org.snpeff.util.GprSeq
 
aa1 - Variable in class org.snpeff.pdb.DistanceResult
 
aa2 - Variable in class org.snpeff.pdb.DistanceResult
 
aa2Code(char) - Static method in class org.snpeff.util.GprSeq
Convert from AA char to code
aa2Code(String) - Static method in class org.snpeff.util.GprSeq
Convert from AA sequence to codes
aaAlt - Variable in class org.snpeff.snpEffect.VariantEffect
 
aaCode(char) - Method in class org.snpeff.snpEffect.HgvsProtein
 
aaCode(String) - Method in class org.snpeff.snpEffect.HgvsProtein
Use one letter / three letter AA codes Most times we want to vonvert to 3 letter code HGVS: the three-letter amino acid code is prefered (see Discussion), with "*" designating a translation termination codon; for clarity we this page describes changes using the three-letter amino acid
aaNumber2Pos() - Method in class org.snpeff.interval.Transcript
Calculate chromosome position as function of Amino Acid number Note that returns the chromosomal position of the first base for each Amino Acid
aaNumber2Pos(int) - Method in class org.snpeff.interval.Transcript
Find a genomic position of the first base in a Amino Acid 'aaNum'
aaPairCode(byte, byte) - Static method in class org.snpeff.util.GprSeq
Code an AA-pair
aaPairCode(char, char) - Static method in class org.snpeff.util.GprSeq
Code an AA-pair
aaPos1 - Variable in class org.snpeff.pdb.DistanceResult
 
aaPos2 - Variable in class org.snpeff.pdb.DistanceResult
 
aaRef - Variable in class org.snpeff.snpEffect.VariantEffect
 
aasAroundNew - Variable in class org.snpeff.snpEffect.VariantEffect
 
aasAroundOld - Variable in class org.snpeff.snpEffect.VariantEffect
 
aaThreeLetterCode(char) - Method in class org.snpeff.codons.CodonTable
 
aaThreeLetterCode(String) - Method in class org.snpeff.codons.CodonTable
Convert 1-letter code to 3-letter code (amino acids) Reference: http://www.hgvs.org/mutnomen/standards.html#aalist
ACAT - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
 
accession - Variable in class org.snpeff.nextProt.CvTerm
 
accession - Variable in class org.snpeff.nextProt.LocationTargetIsoform
 
AcgtTree - Class in org.snpeff.spliceSites
ACGT tree
AcgtTree() - Constructor for class org.snpeff.spliceSites.AcgtTree
 
AcgtTree(String, AcgtTree) - Constructor for class org.snpeff.spliceSites.AcgtTree
 
add(double) - Method in class org.snpeff.gsa.PvaluesList
Add a p-value to the list
add(double) - Method in class org.snpeff.gsa.ScoreList
Add a p-value to the list
add(double) - Method in class org.snpeff.gtex.GtexExperiment
 
add(double) - Method in class org.snpeff.stats.Average
 
add(double) - Method in class org.snpeff.stats.AverageInt
 
add(double) - Method in class org.snpeff.stats.CounterDouble
 
add(long) - Method in class org.snpeff.stats.Counter
 
add(long) - Method in class org.snpeff.stats.CounterDouble
 
add(String) - Method in class org.snpeff.geneSets.GeneSets
Add a gene and aliases
add(String) - Method in class org.snpeff.spliceSites.AcgtTree
 
add(String, int) - Method in class org.snpeff.geneSets.GeneSetsRanked
Add a 'ranked' gene (to every corresponding GeneSet in this collection)
add(String, String) - Method in class org.snpeff.gtex.IdMap
Add a mapping id <-> name
add(String, String) - Method in class org.snpeff.interval.GffMarker
Add key value pair
add(String, String) - Method in class org.snpeff.logStatsServer.LogStats
Add a 'name=value' pair
add(String, String) - Method in class org.snpeff.nextProt.NextProtSequenceConservation
 
add(String, String) - Method in class org.snpeff.vcf.VcfGenotype
Add a name=value pair WARNING: This method does NOT change the FORMAT field.
add(String, GeneSet) - Method in class org.snpeff.geneSets.GeneSets
Add a gene and it's corresponding gene set
add(Collection<? extends Marker>) - Method in class org.snpeff.interval.tree.IntervalForest
Add all intervals
add(Collection<T>) - Method in class org.snpeff.binseq.indexer.SequenceIndexer
Add a collection of sequences
add(K, Collection<V>) - Method in class org.snpeff.collections.MultivalueHashMap
Add multiple values
add(K, V) - Method in class org.snpeff.collections.MultivalueHashMap
Add a single value
add(CodonTable) - Method in class org.snpeff.codons.CodonTables
Add a codon table
add(FeatureCoordinates) - Method in class org.snpeff.genBank.Feature
 
add(GoTerm) - Method in class org.snpeff.geneOntology.GoTerms
Add a GOTerm (if not already in this GOTerms) WARNING: Creates 'fake' symbolNames based on symbolIds.
add(GeneSet) - Method in class org.snpeff.geneSets.GeneSets
Add a gene set
add(Cds) - Method in class org.snpeff.interval.Transcript
Add a CDS
add(Cds) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
add(Chromosome) - Method in class org.snpeff.interval.Genome
Add a chromosome
add(Chromosome) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
add(Chromosome, int, int, double) - Method in class org.snpeff.gsa.ChrPosScoreList
 
add(Exon) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Add an exon
add(Gene) - Method in class org.snpeff.geneSets.GeneStats
 
add(Gene) - Method in class org.snpeff.interval.Genes
Add a gene interval to this collection
add(Gene) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Add a Gene
add(Gene) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Add a gene interval
add(Gene, boolean) - Method in class org.snpeff.geneSets.GeneStats
Add a gene, update statistics
add(Intron) - Method in class org.snpeff.interval.Transcript
Add an intron
add(Marker) - Method in class org.snpeff.interval.CytoBands
 
add(Marker) - Method in class org.snpeff.interval.Markers
Add an interval to the collection
add(Marker) - Method in class org.snpeff.interval.tree.IntervalForest
Add an interval
add(Marker) - Method in class org.snpeff.interval.tree.IntervalTree
Add an interval object to the interval tree's list Note: Marks the tree as 'not inSync', but will not rebuild the tree until the next query or call to build
add(Marker) - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
add(Marker) - Method in class org.snpeff.interval.tree.IntervalTreeOri
Add an interval object to the interval tree's list Note: Marks the tree as 'not inSync', but will not rebuild the tree until the next query or call to build
add(Marker) - Method in interface org.snpeff.interval.tree.Itree
Add an interval object to the interval tree's list
add(Marker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Add a generic Marker
add(Marker) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Add a marker
add(Marker) - Method in class org.snpeff.snpEffect.testCases.unity.TestGenome
Add markers to SnpEffPredictor
add(Markers) - Method in class org.snpeff.interval.Markers
Add all intervals
add(Markers) - Method in class org.snpeff.interval.tree.IntervalForest
Add all intervals
add(Markers) - Method in class org.snpeff.interval.tree.IntervalTree
Add all intervals to interval tree's list Note: Marks the tree as 'not inSync', but will not rebuild the tree until the next query or call to build
add(Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
add(Markers) - Method in class org.snpeff.interval.tree.IntervalTreeOri
Add all intervals to interval tree's list Note: Marks the tree as 'not inSync', but will not rebuild the tree until the next query or call to build
add(Markers) - Method in interface org.snpeff.interval.tree.Itree
Add all intervals to interval tree's list
add(SpliceSite) - Method in class org.snpeff.interval.Exon
Add a splice site to the collection
add(SpliceSite) - Method in class org.snpeff.interval.Intron
Add a splice site to the collection
add(SpliceSite) - Method in class org.snpeff.interval.Transcript
Add a SpliceSite
add(Transcript) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Add a transcript
add(Utr) - Method in class org.snpeff.interval.Transcript
Add a UTR
add(Variant, Marker, EffectType, String) - Method in class org.snpeff.snpEffect.VariantEffects
Add an effect
add(Variant, Marker, EffectType, VariantEffect.EffectImpact, String) - Method in class org.snpeff.snpEffect.VariantEffects
Add an effect
add(NextProtXmlAnnotation) - Method in class org.snpeff.nextProt.NextProtXmlEntry
Add an annotation
add(OsCmdRunner) - Method in class org.snpeff.osCmd.OsCmdQueue
Add command to be executed
add(OsCmdRunner, String) - Method in class org.snpeff.osCmd.OsCmdQueue
Add command to be executed, only if 'outputFile' does not exist
add(IdMapperEntry) - Method in class org.snpeff.pdb.IdMapper
 
add(TfamEntry) - Method in class org.snpeff.ped.PedFamily
Add an entry t this family
add(TfamEntry) - Method in class org.snpeff.ped.PedPedigree
Add an entry to this pedigree
add(Entity) - Method in class org.snpeff.reactome.events.Complex
 
add(Entity) - Method in class org.snpeff.reactome.Monitor
 
add(Entity, String) - Method in class org.snpeff.reactome.Reactome
Add an entity <-> geneId
add(Event) - Method in class org.snpeff.reactome.events.Pathway
 
add(SamHeaderRecord) - Method in class org.snpeff.sam.SamHeader
Add a record to the header
add(EffectType) - Method in class org.snpeff.filter.VariantEffectFilter
 
add(VariantEffect) - Method in class org.snpeff.outputFormatter.OutputFormatter
Add effects to list
add(VariantEffect) - Method in class org.snpeff.snpEffect.VariantEffects
Add an effect
add(VcfAnnotator) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
Add a new annotator
add(VcfHeader) - Method in class org.snpeff.vcf.VcfHeader
Add all missing lines from 'vcfHeader'
add(VcfHeaderEntry) - Method in class org.snpeff.vcf.VcfHeader
Add header line
add(T) - Method in class org.snpeff.binseq.indexer.SequenceIndexer
Add a sequence to this index
add(T) - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
Add a sequence to this index
add(T) - Method in class org.snpeff.interval.IntervalAndSubIntervals
Add a subinterval
addAll(Iterable<T>) - Method in class org.snpeff.interval.IntervalAndSubIntervals
Add all intervals
addAll(Collection<? extends Marker>) - Method in class org.snpeff.interval.Markers
Add all markers in this collection
addAll(Collection<IdMapperEntry>) - Method in class org.snpeff.pdb.IdMapper
 
addAll(Markers) - Method in class org.snpeff.interval.IntervalAndSubIntervals
Add all markers
addAll(Markers) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Add a set of markers
addBestU12Score(Transcript, String, String, int, int) - Method in class org.snpeff.spliceSites.SpliceTypes
Calculate the best U12 score.
addCatalyst(Entity) - Method in class org.snpeff.reactome.events.Reaction
 
addChild(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
Add a goTermId as a child of this GOTerm Also adds 'this' as parent of 'goTerm'
addChromosomeSequence(String, String) - Method in class org.snpeff.binseq.GenomicSequences
Create a sequence for the whole chromsome (mostly used in test cases)
addColumn(String, int[]) - Method in class org.snpeff.stats.plot.GoogleLineChart
 
addColumn(String, ArrayList<String>) - Method in class org.snpeff.stats.plot.GoogleLineChart
 
addEffect(EffectType) - Method in class org.snpeff.snpEffect.VariantEffect
 
addEffectImpact(VariantEffect.EffectImpact) - Method in class org.snpeff.snpEffect.VariantEffect
 
addEffectType(Variant, Marker, EffectType) - Method in class org.snpeff.snpEffect.VariantEffects
Add: If possible, only add an effect type (otherwise add the full effect)
addEffectType(EffectType) - Method in class org.snpeff.snpEffect.VariantEffect
 
addEffectType(EffectType) - Method in class org.snpeff.vcf.VcfEffect
 
addErrorMessage(ErrorWarningType) - Method in class org.snpeff.snpEffect.VariantEffect
 
addErrorWarning(Variant, ErrorWarningType) - Method in class org.snpeff.snpEffect.VariantEffects
 
addErrorWarningInfo(ErrorWarningType) - Method in class org.snpeff.snpEffect.VariantEffect
Add an error or warning
addExon(Transcript, GffMarker, String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Create a new exon
addExons(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Create and add a new exon
addFeatures(Features) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
Add all features
addFile(String) - Method in class org.snpeff.coverage.CountReadsOnMarkers
Add a SAM/BAM file to be processed
addFilter(String) - Method in class org.snpeff.vcf.VcfEntry
Add string to FILTER field
addFormat(String) - Method in class org.snpeff.vcf.VcfEntry
Add a 'FORMAT' field
addFormat(VcfHeaderFormat) - Method in class org.snpeff.vcf.VcfHeader
Add a 'FORMAT' meta info
addGene(String) - Method in class org.snpeff.geneSets.GeneSet
Add one gene to genesSet
addGene(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
 
addGene(GffMarker, boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Create and add a gene based on GffMarker
addGeneId(String) - Method in class org.snpeff.reactome.Entity
Add a geneId
addGeneSequences(String, String) - Method in class org.snpeff.binseq.GenomicSequences
Add sequences for each gene in the genome
addGeneSetCount(int) - Method in class org.snpeff.geneSets.Result
Add an item to the list of counts
addGenotype(String) - Method in class org.snpeff.vcf.VcfEntry
Add a genotype as a string
addHeader() - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
Add header
addHeaderRecord(String) - Method in class org.snpeff.sam.SamHeader
 
addHeaders(VcfFileIterator) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
addHeaders(VcfFileIterator) - Method in interface org.snpeff.snpEffect.VcfAnnotator
Add annotation headers to VCF file
addHeaders(VcfFileIterator) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
 
addInfo(String, String) - Method in class org.snpeff.vcf.VcfEntry
Add a "key=value" tuple the info field
addInfo(VcfEntry) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
Add effects to INFO field
addInfo(VcfHeaderInfo) - Method in class org.snpeff.vcf.VcfHeader
Add a VCF INFO header definition
addInfoMessage(ErrorWarningType) - Method in class org.snpeff.snpEffect.VariantEffect
 
addInput(Entity) - Method in class org.snpeff.reactome.events.Reaction
 
addInteresting(String) - Method in class org.snpeff.geneSets.GeneSets
Add a symbol as 'interesting' gene (to every corresponding GeneSet in this collection)
addInterestingSymbol(String, int, HashSet<String>) - Method in class org.snpeff.geneOntology.GoTerms
Add a symbol as 'interesting' symbol (to every corresponding GOTerm in this set)
addInterestingSymbolId(String) - Method in class org.snpeff.geneOntology.GoTerm
Add one gene to interestingGenesSet
addIntergenicConserved(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Add an intergenic conserved region
addInterval(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Add interval based on GffMarker data
addIntronConserved(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Add an intron conserved region
addIsoformSequence(String, String) - Method in class org.snpeff.nextProt.NextProtXmlEntry
Add an Isoform sequence
additionalEffect(String, String, int, int, String, String) - Method in class org.snpeff.interval.codonChange.CodonChange
Calculate additional effect due to codon changes E.g.
addLine(String) - Method in class org.snpeff.vcf.VcfHeader
Add line to header (can add many lines)
addMarker(Marker, boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Add a marker to the collection
addMarkers(NextProtMarkerFactory) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
Create all markers for this annotation
addMarkers(NextProtMarkerFactory) - Method in class org.snpeff.nextProt.NextProtXmlEntry
Create all Markers for this entry
addMarkers(NextProtXmlEntry, NextProtXmlIsoform, NextProtXmlAnnotation, Location, String) - Method in class org.snpeff.nextProt.NextProtMarkerFactory
Create markers and add them
addMarkerType(Marker, String) - Method in class org.snpeff.coverage.CountReads
 
addMarkerType(Marker, String) - Method in class org.snpeff.coverage.CountReadsOnMarkers
 
addOutput(Entity) - Method in class org.snpeff.reactome.events.Reaction
 
addPerGene(Marker) - Method in class org.snpeff.interval.Gene
Add a gene dependent marker
addProteinMapping(Attributes) - Method in class org.snpeff.nextProt.NextProtXmlIsoform
Add a transcript mapping
addRegulationTrack(String) - Method in class org.snpeff.SnpEff
 
addRegulator(Entity, String) - Method in class org.snpeff.reactome.events.Reaction
 
addRegulator(Entity, Reaction.RegulationType) - Method in class org.snpeff.reactome.events.Reaction
 
addResults(String) - Method in class org.snpeff.reactome.Monitor
 
addScore(String, double) - Method in class org.snpeff.stats.CountByType
Add score for a type
addSequences(String, String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Add genomic reference sequences
addSymbolId(String) - Method in class org.snpeff.geneOntology.GoTerm
Add one gene to genesSet
addSymbolId(GoTerm, String) - Method in class org.snpeff.geneOntology.GoTerms
Add a symbolId (as well as all needed mappings)
addSymbolsFromChilds() - Method in class org.snpeff.geneOntology.GoTerms
Use symbols for chids in DAG For every GOTerm, each child's symbols are added to the term so that root term contains every symbol and every interestingSymbol
addSymbolsFromChilds(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
Add all symbols from childs to goTerm
addTranscriptMapping(Attributes) - Method in class org.snpeff.nextProt.NextProtXmlIsoform
Add a protein mapping
addType(Marker, String) - Method in class org.snpeff.coverage.MarkerTypes
 
addUtr3(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Create new UTR3primes
addUtr5(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Create UTR5primes
addUtrs - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
addWarningMessge(ErrorWarningType) - Method in class org.snpeff.snpEffect.VariantEffect
 
adjust() - Method in class org.snpeff.interval.Gene
Adjust start, end and strand values
adjust() - Method in class org.snpeff.interval.Transcript
Adjust transcript coordinates
adjust(Marker) - Method in class org.snpeff.interval.Marker
Adjust [start,end] to include child
adjustChromosomes() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Adjust chromosome length using gene information This is used when the sequence is not available (which makes sense on test-cases and debugging only)
adjustedPvalue - Variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
 
adjustTranscripts() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Adjust transcripts: recalculate start, end, strand, etc.
after() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEmbl
 
after() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
after() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGtf22
 
after() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLof
 
after() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
align() - Method in class org.snpeff.align.NeedlemanWunsch
 
align() - Method in class org.snpeff.align.NeedlemanWunschOverlap
 
align() - Method in class org.snpeff.align.VcfRefAltAlign
 
ALL_ALLELES - Enum constant in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
 
ALLELE - Enum constant in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
 
ALLELE_FEQUENCY_COMMON - Static variable in class org.snpeff.vcf.VcfEntry
 
ALLELE_FEQUENCY_LOW - Static variable in class org.snpeff.vcf.VcfEntry
 
AlleleCountStats - Class in org.snpeff.stats
Count singletons and other allele counts per sample
AlleleCountStats() - Constructor for class org.snpeff.stats.AlleleCountStats
 
alleleFrequencyType() - Method in class org.snpeff.vcf.VcfEntry
Categorization by allele frequency
allSymbols() - Method in class org.snpeff.geneOntology.GoTerms
Create a set with all the symbols
alt - Variable in class org.snpeff.fileIterator.MatrixEntry
 
alt - Variable in class org.snpeff.interval.Variant
 
alt() - Method in class org.snpeff.snpEffect.HgvsDna
 
alts - Variable in class org.snpeff.vcf.VcfEntry
 
altStr - Variable in class org.snpeff.vcf.VcfEntry
 
ALTTENATIVE_3SS - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
 
ALTTENATIVE_5SS - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
 
ALTTENATIVE_POLY_A - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
 
ALTTENATIVE_PROMOMOTER - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
 
AMINO_ACIDS - Static variable in class org.snpeff.util.GprSeq
 
analyzeAndCreate() - Method in class org.snpeff.spliceSites.SpliceTypes
Analyze and create conserved splice sites donor-acceptor pairs.
and(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
 
andNot(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
 
andNotCount(OpenBitSet, OpenBitSet) - Static method in class org.snpeff.collections.OpenBitSet
Returns the popcount or cardinality of "a and not b" or "intersection(a, not(b))".
ANN_FIELD_NAMES - Static variable in class org.snpeff.vcf.VcfEffect
 
annotate(String, String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
Annotate: Calculate the effect of variants and show results
annotate(VcfEntry) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
Annotate a VCF entry
annotate(VcfEntry) - Method in interface org.snpeff.snpEffect.VcfAnnotator
Annotate a VCF file entry
annotate(VcfEntry) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
 
annotateFinish(VcfFileIterator) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
Finish annotations and create reports
annotateFinish(VcfFileIterator) - Method in interface org.snpeff.snpEffect.VcfAnnotator
This method is called after all annotations have been performed.
annotateFinish(VcfFileIterator) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
 
annotateInit(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
Calculate the effect of variants and show results
annotateInit(VcfFileIterator) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
annotateInit(VcfFileIterator) - Method in interface org.snpeff.snpEffect.VcfAnnotator
Initialize annotator: This method is called after vcfFile is opened, but before the header is output.
annotateInit(VcfFileIterator) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
 
antisense - Enum constant in enum class org.snpeff.interval.BioType
 
anyBackToRef(VcfEntry) - Method in class org.snpeff.vcf.Pedigree
Are there any "back to reference" cancer variant
anyDerived() - Method in class org.snpeff.vcf.Pedigree
Is there any derived sample?
anythingSet() - Method in interface org.snpeff.filter.Filter
Has any of the paremeters been set?
anythingSet() - Method in class org.snpeff.filter.VariantEffectFilter
Is any of the options set?
apply(Variant) - Method in class org.snpeff.interval.Exon
Apply variant to exon WARNING: There might be conditions which change the exon type (e.g.
apply(Variant) - Method in class org.snpeff.interval.IntervalAndSubIntervals
Apply a variant.
apply(Variant) - Method in class org.snpeff.interval.Intron
 
apply(Variant) - Method in class org.snpeff.interval.Marker
Apply a variant to a marker.
apply(Variant) - Method in class org.snpeff.interval.MarkerSeq
Apply variant
apply(Variant) - Method in class org.snpeff.interval.Transcript
Create a new transcript after applying changes in variant
applyDel(Variant) - Method in class org.snpeff.interval.Marker
Apply a Variant to a marker.
applyDel(Variant, MarkerSeq) - Method in class org.snpeff.interval.MarkerSeq
Apply a change type deletion (update sequence)
applyDup(Variant) - Method in class org.snpeff.interval.Marker
Apply a Variant to a marker.
applyDup(Variant, MarkerSeq) - Method in class org.snpeff.interval.MarkerSeq
Apply a change type duplication (update sequence)
applyIns(Variant) - Method in class org.snpeff.interval.Marker
Apply a Variant to a marker.
applyIns(Variant, MarkerSeq) - Method in class org.snpeff.interval.MarkerSeq
Apply a change type insertion (update sequence)
applyMixed(Variant) - Method in class org.snpeff.interval.Marker
Apply a mixed variant Note: MIXED variant is interpreted as "MNP + InDel"
applyMnp(Variant, MarkerSeq) - Method in class org.snpeff.interval.MarkerSeq
Apply a change type MNP (update sequence)
applySnp(Variant, MarkerSeq) - Method in class org.snpeff.interval.MarkerSeq
Apply a change type SNP (update sequence)
applyTranscript(String, String, String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Apply a variant to a transcript
args - Variable in class org.snpeff.SnpEff
 
ArrayUtil - Class in org.snpeff.collections
Methods for manipulating arrays.
ArrayUtil() - Constructor for class org.snpeff.collections.ArrayUtil
 
assign(String, int) - Method in class org.snpeff.fileIterator.TableFile
Assign values parse from 'line' into array elements indexed by 'idx'
autoClose - Variable in class org.snpeff.fileIterator.FileIterator
 
AutoHashMap<K,V> - Class in org.snpeff.collections
A Hash that creates new elements if they don't exists
AutoHashMap(V) - Constructor for class org.snpeff.collections.AutoHashMap
 
Average - Class in org.snpeff.stats
A simple class that calculates averages
Average() - Constructor for class org.snpeff.stats.Average
 
AverageInt - Class in org.snpeff.stats
A simple class that calculates average of integer numbers
AverageInt() - Constructor for class org.snpeff.stats.AverageInt
 
avg() - Method in class org.snpeff.gsa.ScoreList
Get average
avg() - Method in class org.snpeff.nmer.NmerCount
Average number of nmers
avg() - Method in class org.snpeff.stats.FloatStats
 
AVG - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
 
AVG_MAX_10 - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
 
AVG_MIN_10 - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
 
avgCoverage(int, int) - Method in class org.snpeff.coverage.CoverageChr
Calculate Coverage per base
avgCoverage(Marker) - Method in class org.snpeff.coverage.CountFragments
Calculate Fragments Per Kilobase of exon per Million fragments mapped (FPKM)
avgCoverage(Marker) - Method in class org.snpeff.coverage.Coverage
Calculate average coverage per base
avgLargestTop(int) - Method in class org.snpeff.gsa.ScoreList
Get average pvalue (largest N)
avgSmallestTop(int) - Method in class org.snpeff.gsa.ScoreList
Get average score (smallest N)

B

BAD - Static variable in class org.snpeff.probablility.RankSumPdf
 
BASE_DIR - Static variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
BASE_DIR - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
BASE2CODE - Static variable in class org.snpeff.binseq.DnaSequenceByte
 
base2index(char) - Static method in class org.snpeff.spliceSites.AcgtTree
 
baseAt(int) - Method in class org.snpeff.interval.Transcript
Find base at genomic coordinate 'pos'
baseName(String) - Static method in class org.snpeff.util.Gpr
Return file's name (without the path)
baseName(String, String) - Static method in class org.snpeff.util.Gpr
Return file's name (without the path)
baseNumber2MRnaPos(int) - Method in class org.snpeff.interval.Transcript
Calculate distance from transcript start to a position mRNA is roughly the same than cDNA.
baseNumberCds(int, boolean) - Method in class org.snpeff.interval.Transcript
Calculate base number in a CDS where 'pos' maps
baseNumberCds2Codon(int) - Method in class org.snpeff.interval.Transcript
Return a codon that includes 'cdsBaseNumber'
baseNumberCds2Pos() - Method in class org.snpeff.interval.Transcript
Calculate chromosome position as function of CDS number
baseNumberCds2Pos(int) - Method in class org.snpeff.interval.Transcript
 
BASES - Static variable in class org.snpeff.binseq.DnaSequenceByte
 
BASES - Static variable in class org.snpeff.motif.Pwm
 
BASES - Static variable in class org.snpeff.spliceSites.AcgtTree
 
BASES - Static variable in class org.snpeff.util.GprSeq
 
BASES_PER_BYTE - Static variable in class org.snpeff.binseq.DnaSequenceByte
 
BASES_PER_LONGWORD - Static variable in class org.snpeff.binseq.coder.DnaCoder
 
basesAt(int, int) - Method in class org.snpeff.interval.MarkerSeq
Base in this marker at position 'index' (relative to marker start)
basesAtPos(int, int) - Method in class org.snpeff.interval.MarkerSeq
Base at position 'pos' (genomic coordinates)
BasesChangeCounter - Class in org.snpeff.overlap
Counts how many bases changed, given an XOR between two longs
BasesChangeCounter(Coder) - Constructor for class org.snpeff.overlap.BasesChangeCounter
 
basesPerWord() - Method in class org.snpeff.binseq.coder.Coder
How many bases can we pack in a word
basesPerWord() - Method in class org.snpeff.binseq.coder.DnaCoder
 
basesPerWord() - Method in class org.snpeff.binseq.coder.DnaQualityCoder
 
baseToBits(char) - Method in class org.snpeff.binseq.coder.Coder
Encode a base using a binary representation
baseToBits(char) - Method in class org.snpeff.binseq.coder.DnaCoder
Encode a base using 2 bits
baseToBits(char, boolean) - Method in class org.snpeff.binseq.coder.DnaCoder
 
baseToBits(char, int) - Method in class org.snpeff.binseq.coder.DnaQualityCoder
 
BED - Enum constant in enum class org.snpeff.SnpEff.InputFormat
 
BED - Enum constant in enum class org.snpeff.SnpEff.OutputFormat
 
BED - Enum constant in enum class org.snpeff.snpEffect.commandLine.SnpEffCmdDump.DumpFormat
 
BED_OFFSET - Static variable in class org.snpeff.fileIterator.RegulationBedFileIterator
 
BEDANN - Enum constant in enum class org.snpeff.SnpEff.OutputFormat
 
BedAnnotationOutputFormatter - Class in org.snpeff.outputFormatter
Formats: Show all annotations that intersect the BED input file.
BedAnnotationOutputFormatter() - Constructor for class org.snpeff.outputFormatter.BedAnnotationOutputFormatter
 
BedFileIterator - Class in org.snpeff.fileIterator
Opens a sequence change file and iterates over all intervals in BED format.
BedFileIterator(String) - Constructor for class org.snpeff.fileIterator.BedFileIterator
 
BedFileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.BedFileIterator
 
BedOutputFormatter - Class in org.snpeff.outputFormatter
Formats output as BED file Referneces: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
BedOutputFormatter() - Constructor for class org.snpeff.outputFormatter.BedOutputFormatter
 
before() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
before() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEmbl
 
before() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
before() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGtf22
 
before() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
before() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
before() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose
 
beforeExonSequences() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Perform some actions before reading sequences
begin - Variable in class org.snpeff.nextProt.Location
 
bestId - Variable in class org.snpeff.binseq.indexer.OverlapRessult
 
bestReference - Variable in class org.snpeff.binseq.indexer.OverlapRessult
 
bestScore - Variable in class org.snpeff.binseq.indexer.OverlapRessult
 
bestSequence - Variable in class org.snpeff.binseq.indexer.OverlapRessult
 
bestU12Score(String) - Method in class org.snpeff.spliceSites.SpliceTypes
Find the best score for PWM matrix in U12 branch points
BETA - Static variable in class org.snpeff.reactome.Entity
 
BigBedFileIterator - Class in org.snpeff.fileIterator
FileIterator for BigBed features WARNING: Removed in 2022-01 due to dependency on IGV's code (which depends on Log4j, which has a major security issue) Note: I use Broad's IGV code to do all the work, this is just a wrapper
BigBedFileIterator(String) - Constructor for class org.snpeff.fileIterator.BigBedFileIterator
 
bin64(long) - Static method in class org.snpeff.util.Gpr
Show a long as a 64 bit binary number
BinarySequence - Class in org.snpeff.binseq
Base class for a binary 'read'.
BinarySequence() - Constructor for class org.snpeff.binseq.BinarySequence
 
Binomial - Class in org.snpeff.probablility
Calculate binomial distribution References http://en.wikipedia.org/wiki/Binomial_distribution
Binomial() - Constructor for class org.snpeff.probablility.Binomial
 
BinSeqFileIterator<T extends BinarySequence> - Class in org.snpeff.fileIterator
Reads all sequences from a file Warning: You should always call "close()" at the end of the iteration.
BinSeqFileIterator(String) - Constructor for class org.snpeff.fileIterator.BinSeqFileIterator
 
BIOMART - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
 
BioType - Enum Class in org.snpeff.interval
BioTypes: Gene or transcript bioType annotation References: http://www.ensembl.org/info/genome/genebuild/biotypes.html Biotypes classifies genes and transcripts into groups including: protein coding, pseudogene , processed pseudogene, miRNA, rRNA, scRNA, snoRNA, snRNA.
bits - Variable in class org.snpeff.collections.OpenBitSet
 
BITS_PER_BASE - Static variable in class org.snpeff.binseq.coder.DnaCoder
 
BITS_PER_BASE - Static variable in class org.snpeff.binseq.DnaSequenceByte
 
BITS_PER_LONGWORD - Static variable in class org.snpeff.binseq.coder.Coder
 
bits2words(long) - Static method in class org.snpeff.collections.OpenBitSet
returns the number of 64 bit words it would take to hold numBits
bitscore - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
bitsPerBase() - Method in class org.snpeff.binseq.coder.Coder
How many bits do we need for each base
bitsPerBase() - Method in class org.snpeff.binseq.coder.DnaCoder
 
BitUtil - Class in org.snpeff.collections
A variety of high efficiency bit twiddling routines.
BitUtil() - Constructor for class org.snpeff.collections.BitUtil
 
BlackBoxEvent - Class in org.snpeff.reactome.events
A black box event
BlackBoxEvent(int, String) - Constructor for class org.snpeff.reactome.events.BlackBoxEvent
 
BlastResultEntry - Class in org.snpeff.fileIterator
 
BlastResultEntry() - Constructor for class org.snpeff.fileIterator.BlastResultEntry
 
BlastResultFileIterator - Class in org.snpeff.fileIterator
Iterate on each line of a GWAS catalog (TXT format)
BlastResultFileIterator(String) - Constructor for class org.snpeff.fileIterator.BlastResultFileIterator
 
BND - Enum constant in enum class org.snpeff.interval.Variant.VariantType
 
BND_CURL_SIZE - Static variable in class org.snpeff.svg.SvgBnd
 
body - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
 
BONFERRONI - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
 
BooleanMutable - Class in org.snpeff.stats
A mutable boolean
BooleanMutable() - Constructor for class org.snpeff.stats.BooleanMutable
 
BooleanMutable(boolean) - Constructor for class org.snpeff.stats.BooleanMutable
 
branchU12Threshold(double) - Method in class org.snpeff.spliceSites.SpliceTypes
Calculate threshold of U12 PWM scores Pick the score that gives a 'thresholdU12Percentile'.
BUFFER_SIZE - Static variable in class org.snpeff.fastq.FastqSplit
 
BUFFER_SIZE - Static variable in class org.snpeff.osCmd.StreamGobbler
 
BUFFER_SIZE - Variable in class org.snpeff.snpEffect.testCases.integration.IntegrationTest
 
build() - Method in class org.snpeff.binseq.GenomicSequences
Build interval forest
build() - Method in class org.snpeff.interval.CytoBands
 
build() - Method in class org.snpeff.interval.tree.IntervalForest
Build all trees
build() - Method in class org.snpeff.interval.tree.IntervalTree
Build the interval tree to reflect the list of intervals, Will not run if this is currently in sync
build() - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
build() - Method in class org.snpeff.interval.tree.IntervalTreeOri
Build the interval tree to reflect the list of intervals, Will not run if this is currently in sync
build() - Method in interface org.snpeff.interval.tree.Itree
Build the interval tree to reflect the list of intervals.
build(String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Build a genome, return SnpEffectPredictor
build(Markers) - Method in class org.snpeff.interval.tree.IntervalNode
Build interval tree
build(Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
Index intervals from 'start' to 'end' (index in 'markers')
BUILD - Static variable in class org.snpeff.SnpEff
 
BUILD_DATE - Static variable in class org.snpeff.SnpEff
 
buildAndCompare(String, String, String, String, boolean) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Build a genome from a RefSeq file and compare results to 'expected' results
buildEmbl(String, String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Build a genome from a embl file and compare results to 'expected' results
buildForest() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Create interval trees (forest)
buildGeneBank(String, String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
buildGeneBank(String, String, boolean) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Build a genome from a genbank file and compare results to 'expected' results
buildGetBuildCmd(String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Build a genome and return the build command
buildGff3AndCompare(String, String, String, boolean, boolean) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Build a genome from a GFF3 file and compare results to 'expected' results
buildGtfAndCompare(String, String, String, String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Build a genome from a GTF file and compare results to 'expected' results
buildPerGene() - Method in class org.snpeff.interval.Gene
Build gene dependent interval tree
BY - Static variable in class org.snpeff.Pcingola
 
BYTES_PER_LONGWORD - Static variable in class org.snpeff.binseq.coder.Coder
 

C

CACHE_MAX_N - Static variable in class org.snpeff.probablility.RankSumNoReplacementPdf
Cache size roughly (N * NT)^2
CACHE_MAX_N - Static variable in class org.snpeff.probablility.RankSumPdf
Cache size roughly (N * NT)^2
CACHE_MAX_NT - Static variable in class org.snpeff.probablility.RankSumPdf
 
cacheSetPdf(int, int, long, double) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
 
calc() - Method in class org.snpeff.reactome.Entity
 
calc(HashSet<Entity>) - Method in class org.snpeff.reactome.Entity
Calculate entities.
calc(HashSet<Entity>) - Method in class org.snpeff.reactome.events.Reaction
Calculate entities.
calcAlignment() - Method in class org.snpeff.align.NeedlemanWunschOverlap
 
calcAlignmentScore() - Method in class org.snpeff.align.NeedlemanWunschOverlap
Calculate score matrix
calcHetero() - Method in class org.snpeff.vcf.VcfEntry
Is this entry heterozygous? Infer Hom/Her if there is only one sample in the file.
calcLogOddsWeight() - Method in class org.snpeff.motif.Pwm
Calculate log odds matrix from counts Reference: http://en.wikipedia.org/wiki/Position-specific_scoring_matrix
calcRor(int) - Method in class org.snpeff.overlap.SequenceRotator
 
calculateFromSam(String, boolean) - Static method in class org.snpeff.coverage.CountFragments
Calculate coverage from a SAM file
calculateFromSam(String, boolean) - Static method in class org.snpeff.coverage.Coverage
Calculate coverage from a SAM file
canBeCached(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Is the number in the cache
canBeCached(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
Is the number in the cache
canonical - Variable in class org.snpeff.SnpEff
 
canonical() - Method in class org.snpeff.interval.Gene
Get canonical transcript Canonical transcripts are defined as the longest CDS of amongst the protein coding transcripts.
canonical() - Method in class org.snpeff.SnpEff
Filter canonical transcripts
canonicalFile - Variable in class org.snpeff.SnpEff
 
canParseLine(String) - Static method in class org.snpeff.interval.GffMarker
Can this line (form a GFF file) be parsed? Note: Returns false for headers, empty lines and lines having less number of fields than expected
canRead(String) - Static method in class org.snpeff.util.Gpr
Can we read this file (either exact name or append a '.gz'
canUseChiSquareApproximation(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
Can ChiSquare approximation be used? A rule of the thumb says it can be used if every expected frequency is more than 10
capacity() - Method in class org.snpeff.collections.OpenBitSet
Returns the current capacity in bits (1 greater than the index of the last bit)
cardinality() - Method in class org.snpeff.collections.OpenBitSet
 
catalyst - Variable in class org.snpeff.reactome.events.Reaction
 
CatalystActivity - Class in org.snpeff.reactome.events
A catalyst activity event
CatalystActivity(int, String) - Constructor for class org.snpeff.reactome.events.CatalystActivity
 
cdf(double) - Method in class org.snpeff.gsa.ScoreList
Cumulative distribution function of p-values: P[ pValues <= p ] (i.e.
cdf(double, double, double) - Static method in class org.snpeff.probablility.NormalDistribution
DESCRIPTION The main computation evaluates near-minimax approximations derived from those in "Rational Chebyshev approximations for the error function" by W.
cdf(double, int, int) - Method in class org.snpeff.probablility.Binomial
Cumulative probability function P( K <= k )
cdf(int) - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
Cummulative distribution for this number
cdf(int, int, int) - Static method in class org.snpeff.probablility.RankSumPdf
Cumulative density function (cdf)
cdf(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Probability of getting a rank sum less or equal to 'r' when adding the ranks of 'nt' selected items.
cdfApfloat(double, double, double[], double[]) - Static method in class org.snpeff.probablility.NormalDistribution
CDF using apfloat
cdfExact(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Cumulative density function (cdf)
cdfNormal(int, int, int) - Static method in class org.snpeff.probablility.RankSumPdf
Normal approximation to rankSum CDF
cdfNormal(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Normal approximation to rankSum CDF
cdfTriangle(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Uniform 'approximation' to rank sum statistic
cdfUniform(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Uniform 'approximation' to rank sum statistic
cdfUp(double, int, int) - Method in class org.snpeff.probablility.Binomial
Cumulative probability function, upper tail P( K > k )
cdfUpEq(double, int, int) - Method in class org.snpeff.probablility.Binomial
Cumulative probability function, upper tail P( K >= k )
cdfUpper(double) - Method in class org.snpeff.gsa.ScoreList
Cumulative distribution function of p-values: P[ pValues > p ] (i.e.
cDnaPos - Variable in class org.snpeff.snpEffect.VariantEffect
 
cds() - Method in class org.snpeff.interval.Transcript
Retrieve coding sequence
Cds - Class in org.snpeff.interval
CDS: The coding region of a gene, also known as the coding sequence or CDS (from Coding DNA Sequence), is that portion of a gene's DNA or RNA, composed of exons, that codes for protein.
Cds() - Constructor for class org.snpeff.interval.Cds
 
Cds(Transcript, int, int, boolean, String) - Constructor for class org.snpeff.interval.Cds
 
CDS - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
CDS - Enum constant in enum class org.snpeff.interval.GffType
 
CDS - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
CDS_STAT_COMPLETE - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
 
CDS_STAT_COMPLETE - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRefSeq
 
cdsAlt - Variable in class org.snpeff.interval.codonChange.CodonChangeStructural
 
cdsBaseNumber(int) - Method in class org.snpeff.interval.codonChange.CodonChange
Calculate base number in a cds where 'pos' is
cdsDiff() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
Differences between two CDSs after removing equal codons from the beginning and from the end of both strings
cdsMarker() - Method in class org.snpeff.interval.Transcript
Create a marker of the coding region in this transcript
cdsRef - Variable in class org.snpeff.interval.codonChange.CodonChangeStructural
 
center - Variable in class org.snpeff.interval.tree.IntervalNode
 
CHANGE_SEPARATOR - Static variable in class org.snpeff.stats.VariantEffectStats
 
CHANGE_SEPARATOR - Static variable in class org.snpeff.stats.VariantStats
 
changeQuality(String, FastqVariant, FastqVariant) - Static method in class org.snpeff.util.GprSeq
Change a fastQ encoding in a quality sequence
Character - Enum constant in enum class org.snpeff.vcf.VcfInfoType
 
characterize() - Method in class org.snpeff.interval.ExonSpliceCharacterizer
Characterize all exons
characters(char[], int, int) - Method in class org.snpeff.nextProt.NextProtHandler
 
check() - Method in class org.snpeff.vcf.VcfEntry
Perform several simple checks and report problems (if any).
checkApply(Variant, Variant.VariantType, String, String, int, int, int) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
Apply a variant to a transcript and check resulting CDS sequence, protein sequence and exon coordinates
checkApplyDel(Variant, String, String, int, int, int) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
checkApplyIns(Variant, String, String, int, int, int) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
checkApplyMixed(Variant, String, String, int, int, int) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
checkApplyMnp(Variant, String, String, int, int, int) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
checkApplySnp(Variant, String, String, int, int, int) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
checkComapred() - Method in class org.snpeff.snpEffect.testCases.integration.CompareToVep
 
checkEffect(Variant, EffectType) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
checkEffect(Variant, EffectType, EffectType, VariantEffect.EffectImpact) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
checkEffect(Variant, EffectType, VariantEffect.EffectImpact, int) - Method in class org.snpeff.snpEffect.testCases.unity.TestGenome
Apply a predictor to a variant and check whether the expected number of matches are found
checkEffects(Variant, EffectType[], String[], String[], VariantEffect.EffectImpact, String[]) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
 
checkEffects(Variant, EffectType[], String[], String[], VariantEffect.EffectImpact, String[]) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
 
checkEffects(Variant, EffectType[], String[], VariantEffect.EffectImpact, String[]) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
 
checkEffects(Variant, EffectType[], String[], VariantEffect.EffectImpact, String[], Gene[]) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
 
checkEffects(Variant, EffectType[], EffectType[], String[], String[], VariantEffect.EffectImpact) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
 
checkHgvs(String, String, int) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Check HGVS annotations
checkHypergeometricParams(int, int, int, int) - Method in class org.snpeff.probablility.Hypergeometric
Check if hypergeometric paramters are correct
checkInterestingGenes(Set<String>) - Method in class org.snpeff.geneSets.GeneSets
Checks that every symboolID is in the set (as 'interesting' genes)
checkInterestingGenes(Set<String>) - Method in class org.snpeff.geneSets.GeneSetsRanked
Checks that every symboolID is in the set (as 'interesting' genes)
checkInterestingSymbolIds(Set<String>) - Method in class org.snpeff.geneOntology.GoTerms
Checks that every symboolID is in the set (as 'interesting' symbols)
checkNoChange(String[]) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
checkTranscriptError(String[], ErrorWarningType) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Run a predictor and check if the expected warnings appear
child - Variable in class org.snpeff.vcf.PedigreeEntry
 
childNum - Variable in class org.snpeff.vcf.PedigreeEntry
 
chiSquareApproximation(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
Chi-Square approximation for Fisher's exact test
chiSquareCDF(double, int) - Method in class org.snpeff.probablility.FisherExactTest
Chi-Square Cumulative Distribution Function probability that an observed chi-square value for a correct model should be less than chiSquare nu = the degrees of freedom
chiSquareCDFComplementary(double, int) - Static method in class org.snpeff.gsa.ScoreList
Upper tail 1 - ChiSquareCDF(p)
chiSquareCDFComplementary(double, int) - Method in class org.snpeff.probablility.FisherExactTest
Chi-Square Complementary of Cumulative Distribution Function: 1 - chiSquareCDF(x, nu) probability that an observed chi-square value for a correct model should be greater than chiSquare nu = the degrees of freedom
chr - Variable in class org.snpeff.fileIterator.MatrixEntry
 
chr - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
chr - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose
 
chr - Variable in class org.snpeff.snpEffect.testCases.unity.TestGenome
 
CHR_LEN_SEPARATE_FILE - Static variable in class org.snpeff.binseq.GenomicSequences
 
CHR_SIZE - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
chr1 - Variable in class org.snpeff.pdb.DistanceResult
 
chr2 - Variable in class org.snpeff.pdb.DistanceResult
 
CHROM_PREFIX - Static variable in class org.snpeff.vcf.VcfHeader
 
CHROMO_PREFIX - Static variable in class org.snpeff.interval.ChromosomeSimpleName
 
chromoBases - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
chromoBases - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
chromoSequence - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
chromoSequence - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
chromosome - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
chromosome - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
chromosome - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
Chromosome - Class in org.snpeff.interval
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
Chromosome() - Constructor for class org.snpeff.interval.Chromosome
 
Chromosome(Genome, int, int, String) - Constructor for class org.snpeff.interval.Chromosome
 
CHROMOSOME - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
CHROMOSOME_ELONGATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
CHROMOSOME_END - Static variable in class org.snpeff.interval.Intergenic
 
CHROMOSOME_LARGE_DELETION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
CHROMOSOME_LARGE_DUPLICATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
CHROMOSOME_LARGE_INVERSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
CHROMOSOME_START - Static variable in class org.snpeff.interval.Intergenic
 
chromosomeName - Variable in class org.snpeff.vcf.VcfEntry
 
chromosomeNameOri - Variable in class org.snpeff.interval.Interval
 
chromosomeNamesSorted() - Method in class org.snpeff.interval.Genome
Get a sorted list of chromosomes
ChromosomeSimpleName - Class in org.snpeff.interval
Convert chromosome names to simple names
ChrPosScoreList - Class in org.snpeff.gsa
A list of <chromosome, position, scores>
ChrPosScoreList() - Constructor for class org.snpeff.gsa.ChrPosScoreList
 
ChrPosStats - Class in org.snpeff.stats
How many changes per position do we have in a chromosome.
ChrPosStats(String, int) - Constructor for class org.snpeff.stats.ChrPosStats
 
CIRCULAR_GENE_ID - Static variable in class org.snpeff.interval.Gene
 
circularClone() - Method in class org.snpeff.interval.Gene
In a circular genome, a gene can have negative coordinates or crosses over chromosome end.
CircularCorrection - Class in org.snpeff.interval
Correct circular genomic coordinates Nomenclature: We use coordinates at the beginning of the chromosme and negative coordinates
CircularCorrection(Transcript) - Constructor for class org.snpeff.interval.CircularCorrection
 
CircularCorrection(Transcript, int) - Constructor for class org.snpeff.interval.CircularCorrection
 
clazz - Variable in class org.snpeff.fileIterator.LineClassFileIterator
 
cleanUnderscores(String) - Static method in class org.snpeff.vcf.VcfEntry
Return a string without leading, trailing and duplicated underscores
clear() - Method in class org.snpeff.binseq.GenomicSequences
 
clear() - Method in class org.snpeff.interval.Markers
 
clear(int, int) - Method in class org.snpeff.collections.OpenBitSet
Clears a range of bits.
clear(long) - Method in class org.snpeff.collections.OpenBitSet
clears a bit, allowing access beyond the current set size without changing the size.
clear(long, long) - Method in class org.snpeff.collections.OpenBitSet
Clears a range of bits.
clearStats() - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
Clear previous statistics
clone() - Method in class org.snpeff.binseq.BinarySequence
 
clone() - Method in class org.snpeff.binseq.DnaSequence
 
clone() - Method in class org.snpeff.collections.OpenBitSet
 
clone() - Method in class org.snpeff.interval.Interval
 
clone() - Method in class org.snpeff.interval.IntervalAndSubIntervals
 
clone() - Method in class org.snpeff.interval.Marker
 
clone() - Method in class org.snpeff.interval.Variant
 
clone() - Method in class org.snpeff.outputFormatter.OutputFormatter
 
clone() - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
 
clone() - Method in class org.snpeff.snpEffect.VariantEffect
 
cloneAndSet(String, int, int) - Method in class org.snpeff.pdb.IdMapperEntry
Clone the object and return a copy having a different chain ID
cloneShallow() - Method in class org.snpeff.interval.Cds
 
cloneShallow() - Method in class org.snpeff.interval.Chromosome
 
cloneShallow() - Method in class org.snpeff.interval.Custom
 
cloneShallow() - Method in class org.snpeff.interval.Exon
 
cloneShallow() - Method in class org.snpeff.interval.Gene
 
cloneShallow() - Method in class org.snpeff.interval.GenericMarker
 
cloneShallow() - Method in class org.snpeff.interval.Intergenic
 
cloneShallow() - Method in class org.snpeff.interval.IntervalAndSubIntervals
 
cloneShallow() - Method in class org.snpeff.interval.Intron
 
cloneShallow() - Method in class org.snpeff.interval.Marker
Perform a shallow clone
cloneShallow() - Method in class org.snpeff.interval.MarkerSeq
 
cloneShallow() - Method in class org.snpeff.interval.MicroRnaBindingSite
 
cloneShallow() - Method in class org.snpeff.interval.Motif
 
cloneShallow() - Method in class org.snpeff.interval.NextProt
 
cloneShallow() - Method in class org.snpeff.interval.ProteinInteractionLocus
 
cloneShallow() - Method in class org.snpeff.interval.ProteinProteinInteractionLocus
 
cloneShallow() - Method in class org.snpeff.interval.Regulation
 
cloneShallow() - Method in class org.snpeff.interval.Transcript
 
cloneShallow() - Method in class org.snpeff.interval.Variant
 
cloneShallow() - Method in class org.snpeff.interval.VariantWithScore
 
cloneShallow() - Method in class org.snpeff.vcf.VcfEntry
 
close() - Method in class org.snpeff.fileIterator.BinSeqFileIterator
Close file (if not already done)
close() - Method in class org.snpeff.fileIterator.FastqFileIterator
Close file
close() - Method in class org.snpeff.fileIterator.FileIterator
Close file
close() - Method in class org.snpeff.fileIterator.NullReader
 
close() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
close() - Method in class org.snpeff.osCmd.OsCmdRunner
Close (kill) command
close() - Method in class org.snpeff.outputFormatter.OutputFormatter
CLose output files, if any
close() - Method in class org.snpeff.svg.Svg
 
close() - Method in class org.snpeff.vcf.FileIndexChrPos
Close file
CLOSEST - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
 
cmd() - Method in class org.snpeff.SnpEff
Create an appropriate SnpEffCmd* object
CochranArmitageTest - Class in org.snpeff.probablility
Calculate a Cochran-Armitage test Reference: http://en.wikipedia.org/wiki/Cochran-Armitage_test_for_trend The trend test is applied when the data take the form of a 2 x k contingency table.
CODE_TO_AA - Static variable in class org.snpeff.util.GprSeq
 
CODE_TO_DNA - Static variable in class org.snpeff.util.GprSeq
 
code2aa(byte) - Static method in class org.snpeff.util.GprSeq
Convert from AA_code to AA letter
code2aa(byte[]) - Static method in class org.snpeff.util.GprSeq
Convert from AA_code to AA letter
code2aa(int[]) - Static method in class org.snpeff.util.GprSeq
Convert from AA_code to AA letter
code2aaPair(int) - Static method in class org.snpeff.util.GprSeq
 
code2dna(byte) - Static method in class org.snpeff.util.GprSeq
Convert from DNA_code to DNA letter
coder - Static variable in class org.snpeff.binseq.DnaSequencePe
 
Coder - Class in org.snpeff.binseq.coder
Class used to encode & decode sequences into binary and vice-versa They are usually stored in 'long' words
Coder() - Constructor for class org.snpeff.binseq.coder.Coder
 
coding - Variable in class org.snpeff.interval.codonChange.CodonChangeStructural
 
coding(boolean) - Static method in enum class org.snpeff.interval.BioType
Basic bioTypes for coding / non-coding genes
CODING - Enum constant in enum class org.snpeff.interval.Gene.GeneType
 
CODING - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.Coding
 
codingFromCds() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Only coding transcripts have CDS: Make sure that transcripts having CDS are protein coding It might not be always "precise" though: $ grep CDS genes.gtf | cut -f 2 | ~/snpEff/scripts/uniqCount.pl 113 IG_C_gene 64 IG_D_gene 24 IG_J_gene 366 IG_V_gene 21 TR_C_gene 3 TR_D_gene 82 TR_J_gene 296 TR_V_gene 461 non_stop_decay 63322 nonsense_mediated_decay 905 polymorphic_pseudogene 34 processed_transcript 1340112 protein_coding
codon(String) - Method in class org.snpeff.codons.CodonTable
Translate an amino acid into a codon
codon(String, Genome, String) - Method in class org.snpeff.codons.CodonTables
Translate an amino acid into a codon for a given genome+chromosome
CODON_CHANGE - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
CODON_CHANGE_PLUS_CODON_DELETION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
CODON_CHANGE_PLUS_CODON_INSERTION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
CODON_DELETION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
CODON_INSERTION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
CODON_SIZE - Static variable in class org.snpeff.interval.codonChange.CodonChange
 
codonChange() - Method in class org.snpeff.interval.codonChange.CodonChange
Calculate a list of codon changes
codonChange() - Method in class org.snpeff.interval.codonChange.CodonChangeInv
 
codonChange() - Method in class org.snpeff.interval.codonChange.CodonChangeMixed
 
codonChange() - Method in class org.snpeff.interval.codonChange.CodonChangeMnp
Calculate a list of codon changes
codonChange() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
 
codonChange(Exon) - Method in class org.snpeff.interval.codonChange.CodonChange
Calculate the effect on an exon
codonChange(Exon) - Method in class org.snpeff.interval.codonChange.CodonChangeDel
Analyze deletions in this transcript.
codonChange(Exon) - Method in class org.snpeff.interval.codonChange.CodonChangeIns
Analyze insertions in this transcript.
codonChange(Exon) - Method in class org.snpeff.interval.codonChange.CodonChangeInterval
Interval is not a variant, nothing to do
codonChange(Exon) - Method in class org.snpeff.interval.codonChange.CodonChangeSnp
Analyze SNPs in this transcript.
CodonChange - Class in org.snpeff.interval.codonChange
Analyze codon changes based on a variant and a Transcript
CodonChange(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChange
 
CodonChangeDel - Class in org.snpeff.interval.codonChange
Calculate codon changes produced by a deletion
CodonChangeDel(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeDel
 
CodonChangeDup - Class in org.snpeff.interval.codonChange
Calculate codon changes produced by a duplication
CodonChangeDup(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeDup
 
CodonChangeIns - Class in org.snpeff.interval.codonChange
Calculate codon changes produced by an insertion
CodonChangeIns(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeIns
 
CodonChangeInterval - Class in org.snpeff.interval.codonChange
Calculate codon changes produced by a Interval Note: An interval does not produce any effect.
CodonChangeInterval(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeInterval
 
CodonChangeInv - Class in org.snpeff.interval.codonChange
Calculate codon changes produced by an inversion
CodonChangeInv(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeInv
 
CodonChangeMixed - Class in org.snpeff.interval.codonChange
Calculate codon changes produced by a 'mixed' variant Essentially every 'mixed' variant can be represented as a concatenation of a SNP/MNP + an INS/DEL
CodonChangeMixed(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeMixed
 
CodonChangeMnp - Class in org.snpeff.interval.codonChange
Calculate codon changes produced by a MNP
CodonChangeMnp(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeMnp
 
CodonChangeSnp - Class in org.snpeff.interval.codonChange
Calculate codon changes produced by a SNP
CodonChangeSnp(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeSnp
 
CodonChangeStructural - Class in org.snpeff.interval.codonChange
Calculate codon changes produced by a duplication
CodonChangeStructural(Variant, Transcript, VariantEffects) - Constructor for class org.snpeff.interval.codonChange.CodonChangeStructural
 
codonChangeSuper() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
 
codonDegeneracy - Variable in class org.snpeff.snpEffect.VariantEffect
 
codonIndex - Variable in class org.snpeff.snpEffect.VariantEffect
 
codonNum - Variable in class org.snpeff.snpEffect.VariantEffect
 
codonNumber2Pos(int) - Method in class org.snpeff.interval.Transcript
Return an array of 3 genomic positions where amino acid number 'aaNum' maps
codonOldNew() - Method in class org.snpeff.interval.codonChange.CodonChangeMnp
Calculate codons old / codons new
CODONS_AROUND - Static variable in class org.snpeff.snpEffect.PurityChange
 
CODONS_SIZE - Static variable in class org.snpeff.snpEffect.PurityChange
 
codonsAlt - Variable in class org.snpeff.snpEffect.VariantEffect
 
codonsAlt() - Method in class org.snpeff.interval.codonChange.CodonChange
Calculate new codons
codonsAlt() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
Get alternative codons
codonsAlt() - Method in class org.snpeff.interval.codonChange.CodonChangeIns
Get new (modified) codons
codonsAlt() - Method in class org.snpeff.interval.codonChange.CodonChangeMnp
 
codonsAlt() - Method in class org.snpeff.interval.codonChange.CodonChangeSnp
Get new (modified) codons
codonsAroundNew - Variable in class org.snpeff.snpEffect.VariantEffect
 
codonsAroundOld - Variable in class org.snpeff.snpEffect.VariantEffect
 
codonsRef - Variable in class org.snpeff.snpEffect.VariantEffect
 
codonsRef() - Method in class org.snpeff.interval.codonChange.CodonChange
Calculate 'reference' codons
codonsRef() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
Get original codons in CDS
codonsRef() - Method in class org.snpeff.interval.codonChange.CodonChangeMnp
Calculate old codons
codonsRef() - Method in class org.snpeff.interval.codonChange.CodonChangeSnp
Get original codons in CDS
codonsRef(int) - Method in class org.snpeff.interval.codonChange.CodonChange
Calculate 'reference' codons
codonsRefAlt() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
Calculate codons by applying the variant and calculating the differences in CDS sequences This is a slow method, makes sense only for complex variants
codonTable - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
codonTable() - Method in class org.snpeff.interval.Marker
Get a suitable codon table
CodonTable - Class in org.snpeff.codons
A codon translation table
CodonTable(String, String) - Constructor for class org.snpeff.codons.CodonTable
 
CodonTables - Class in org.snpeff.codons
All codon tables are stored here.
collapseZeroGap() - Method in class org.snpeff.interval.Transcript
Collapses exons having gaps of zero (i.e.
collapseZeroGap(Markers) - Static method in class org.snpeff.interval.MarkerUtil
Collapse adjacent intervals (i.e.
collapseZeroLenIntrons() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Collapse exons having zero size introns between them
CombinatorialIterator - Class in org.snpeff.util
Generate all possible 'count' combinations
CombinatorialIterator(int) - Constructor for class org.snpeff.util.CombinatorialIterator
 
command - Variable in class org.snpeff.SnpEff
 
command(CommandLine) - Method in class org.snpeff.snpEffect.testCases.integration.IntegrationTest
Run a 'command' and return everything printed to stdout
command(CommandLine, String) - Method in class org.snpeff.snpEffect.testCases.integration.IntegrationTest
Run a command and compare to an expected output (form a file)
COMMAND_LINE_WIDTH - Static variable in class org.snpeff.SnpEff
 
CommandLine - Interface in org.snpeff.snpEffect.commandLine
Command line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }
commandLineStr(boolean) - Method in class org.snpeff.SnpEff
Command line argument list (try to fit it into COMMAND_LINE_WIDTH)
Common - Enum constant in enum class org.snpeff.vcf.VcfEntry.AlleleFrequencyType
 
compare(Long, Long) - Method in class org.snpeff.binseq.indexer.SequenceIndexer
Compare two references
compare(Object, Object) - Method in class org.snpeff.geneOntology.CompareByValue
 
compare(Object, Object) - Method in class org.snpeff.geneSets.CompareByValue
 
compare(String, String) - Static method in class org.snpeff.interval.Chromosome
Compare chromosome names
compare(DnaAndQualitySequence, int, DnaAndQualitySequence, int) - Method in class org.snpeff.binseq.comparator.DnaQualSubsequenceComparator
 
compare(DnaSequence, int, DnaSequence, int) - Method in class org.snpeff.binseq.comparator.DnaSubsequenceComparator
 
compare(Marker, Marker) - Method in class org.snpeff.interval.IntervalComparatorByEnd
 
compare(Marker, Marker) - Method in class org.snpeff.interval.IntervalComparatorByStart
 
compare(T, int, T, int) - Method in class org.snpeff.binseq.comparator.SubsequenceComparator
 
compareByPos(DistanceResult) - Method in class org.snpeff.pdb.DistanceResult
Compare by genomic position
CompareByValue - Class in org.snpeff.geneOntology
Compare two elements in a Map (e.g.
CompareByValue - Class in org.snpeff.geneSets
Compare two elements in a Map (e.g.
CompareByValue(Map) - Constructor for class org.snpeff.geneOntology.CompareByValue
 
CompareByValue(Map, boolean) - Constructor for class org.snpeff.geneSets.CompareByValue
 
compareCancerGenotypes(VcfEntry) - Method in class org.snpeff.vcf.Pedigree
Analyze which comparisons to make in cancer genomes
compareChromoName(Interval) - Method in class org.snpeff.interval.Chromosome
Compare only chromosome's name
CompareEffects - Class in org.snpeff.snpEffect.testCases.integration
Compare effects in tests cases
CompareEffects(String, long, boolean) - Constructor for class org.snpeff.snpEffect.testCases.integration.CompareEffects
 
CompareEffects(SnpEffectPredictor, long, boolean) - Constructor for class org.snpeff.snpEffect.testCases.integration.CompareEffects
 
compareEnsembl(String, String) - Method in class org.snpeff.snpEffect.testCases.integration.CompareToEnsembl
Compare our results to some ENSEMBL annotations
compareHgvs(String, String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
compareHgvs(String, String, boolean) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
compareNull(Comparable, Comparable) - Static method in class org.snpeff.util.Gpr
 
compareQuery(Marker, Itree) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
Perform a query using 'naive' lookup and interval forest.
compareTo(BinarySequence) - Method in class org.snpeff.binseq.DnaAndQualitySequence
 
compareTo(BinarySequence) - Method in class org.snpeff.binseq.DnaSequence
 
compareTo(BinarySequence) - Method in class org.snpeff.binseq.DnaSequencePe
 
compareTo(BlastResultEntry) - Method in class org.snpeff.fileIterator.BlastResultEntry
 
compareTo(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
 
compareTo(GeneSet) - Method in class org.snpeff.geneSets.GeneSet
Comparable interface (to order terms)
compareTo(Result) - Method in class org.snpeff.geneSets.Result
 
compareTo(Interval) - Method in class org.snpeff.interval.Interval
Compare by start and end
compareTo(Interval) - Method in class org.snpeff.interval.Marker
Compare by start and end
compareTo(Interval) - Method in class org.snpeff.interval.Variant
Compare by start and end
compareTo(IdMapperEntry) - Method in class org.snpeff.pdb.IdMapperEntry
 
compareTo(PedPedigree) - Method in class org.snpeff.ped.PedPedigree
 
compareTo(TfamEntry) - Method in class org.snpeff.ped.TfamEntry
 
compareTo(Entity) - Method in class org.snpeff.reactome.Entity
 
compareTo(VariantEffect) - Method in class org.snpeff.snpEffect.VariantEffect
 
compareTo(KeyValue<A, B>) - Method in class org.snpeff.util.KeyValue
 
compareTo(LineChrPos) - Method in class org.snpeff.vcf.LineChrPos
 
CompareToEnsembl - Class in org.snpeff.snpEffect.testCases.integration
Compare our results to ENSEML's Variant Effect predictor's output
CompareToEnsembl(String, boolean) - Constructor for class org.snpeff.snpEffect.testCases.integration.CompareToEnsembl
 
compareToFile(String, String) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Compare a string and a file.
compareToNumbers(double, double, String, String, boolean) - Method in class org.snpeff.geneSets.GeneSet
Compare 2 numbers and 2 'names' (if both numbers are equal) - NaN sorted in a way that they remain at the end of a sorted list - When two numbers are equal, the sort is done alphabetically by name
compareToPos(Interval) - Method in class org.snpeff.interval.Marker
Compare genomic coordinates
CompareToVep - Class in org.snpeff.snpEffect.testCases.integration
Compare our results to ENSEML's Variant Effect predictor's output
CompareToVep(String, boolean) - Constructor for class org.snpeff.snpEffect.testCases.integration.CompareToVep
 
CompareToVep(String, String[], boolean) - Constructor for class org.snpeff.snpEffect.testCases.integration.CompareToVep
 
compareVep(String) - Method in class org.snpeff.snpEffect.testCases.integration.CompareToVep
Compare all VCF entries
compareVep(String, String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
Compare with results from ENSEMBL's VEP to SnpEff Use VCF having VEP's results
compareVep(String, String, String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Compare with results from ENSEMBL's VEP on transcript ENST00000268124
compareVepSO(String, String, String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Benchmarking: Compare with results from ENSEMBL's VEP
compartment - Variable in class org.snpeff.reactome.Entity
 
Compartment - Class in org.snpeff.reactome
A Reactome compartment (a part of a cell)
Compartment(int, String) - Constructor for class org.snpeff.reactome.Compartment
 
COMPATIBLE_WITH_5_1 - Static variable in class org.snpeff.snpEffect.Config
 
compileDate(Class<?>) - Static method in class org.snpeff.util.Gpr
 
compileTimeStamp() - Static method in class org.snpeff.util.Gpr
 
compileTimeStamp(Class<?>) - Static method in class org.snpeff.util.Gpr
Return a time-stamp showing When was the JAR file created OR when was a class compiled
compileTimeStamp(Class<?>, SimpleDateFormat) - Static method in class org.snpeff.util.Gpr
Return a time-stamp showing When was the JAR file created OR when was a class compiled
complement - Variable in class org.snpeff.genBank.FeatureCoordinates
 
COMPLEMENT - Static variable in class org.snpeff.genBank.Features
 
COMPLEMENT_STRING - Static variable in class org.snpeff.genBank.Feature
 
completed() - Method in enum class org.snpeff.logStatsServer.LogStats.RequestResult
A request is "Completed" if the communication worked
Complex - Class in org.snpeff.reactome.events
A Reactome complex (a bunch of molecules or complexes
Complex(int, String) - Constructor for class org.snpeff.reactome.events.Complex
 
complexity(String) - Method in class org.snpeff.complexity.SequenceComplexity
Measure string's complexity
compressGenotypes() - Method in class org.snpeff.vcf.VcfEntry
Compress genotypes into "HO/HE/NA" INFO fields
config - Variable in class org.snpeff.SnpEff
 
config - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
config - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
config - Variable in class org.snpeff.snpEffect.testCases.unity.TestGenome
 
config() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
Read config file, load & build database
Config - Class in org.snpeff.snpEffect
 
Config(String) - Constructor for class org.snpeff.snpEffect.Config
Create a config (uses DEFAULT_CONFIG_FILE)
Config(String, String) - Constructor for class org.snpeff.snpEffect.Config
Create a configuration from 'configFileName'
Config(String, String, String, Map<String, String>) - Constructor for class org.snpeff.snpEffect.Config
Create a configuration from 'configFileName'
Config(String, String, String, Map<String, String>, boolean) - Constructor for class org.snpeff.snpEffect.Config
 
Config(Genome) - Constructor for class org.snpeff.snpEffect.Config
This constructor is used in test cases
configFile - Variable in class org.snpeff.SnpEff
 
configOverride - Variable in class org.snpeff.SnpEff
 
connect() - Method in class org.snpeff.logStatsServer.LogStats
Connect to server
consensus(Regulation) - Method in class org.snpeff.RegulationFileConsensus
Add to consensus
conservation() - Method in class org.snpeff.nextProt.NextProtMarkerFactory
Sequence conservations analysis.
CONSERVATION_THRESHOLD - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
 
considerOverlap(DnaSequenceId, DnaSequenceId) - Method in class org.snpeff.binseq.indexer.OverlapFilterCompareAllAll
Consider overlap between two sequences?
considerOverlap(DnaSequenceId, DnaSequenceId) - Method in class org.snpeff.binseq.indexer.OverlapFilterDnaId
Consider overlap between two sequences?
considerOverlap(T, T) - Method in interface org.snpeff.binseq.indexer.OverlapFilter
Consider overlap between two sequences?
contains(long, long) - Method in class org.snpeff.collections.HashLongLongArray
Return true if value is in the hash
contains(Object) - Method in class org.snpeff.interval.Markers
 
contains(Object) - Method in class org.snpeff.reactome.events.Complex
 
contains(Object) - Method in class org.snpeff.reactome.events.Pathway
 
contains(String) - Method in class org.snpeff.stats.CountByType
 
containsAll(Collection<?>) - Method in class org.snpeff.interval.Markers
 
containsId(String) - Method in class org.snpeff.interval.IntervalAndSubIntervals
Is 'id' in the subintervals?
convertFrame(int) - Method in enum class org.snpeff.interval.FrameType
 
copy(GeneSets) - Method in class org.snpeff.geneSets.GeneSets
Copy all data from geneSets
copyBases(long[], int, long[], int, int) - Method in class org.snpeff.binseq.coder.DnaCoder
Copy 'length' bases from 'src' (starting from 'srcStart') to 'dst' (starting from 'dstStart')
copyBases(long[], long[], int, int) - Method in class org.snpeff.binseq.coder.DnaCoder
Copy 'length' bases from 'src' to 'dst' (starting from 'start')
CORE_SPLICE_SITE_SIZE - Static variable in class org.snpeff.interval.SpliceSite
 
correct() - Method in class org.snpeff.interval.CircularCorrection
Return a circular corrected transcript or null if no correction is needed
count - Variable in class org.snpeff.stats.Counter
 
count - Variable in class org.snpeff.stats.CounterDouble
 
count() - Method in class org.snpeff.coverage.CountReads
Count markers from a file
count() - Method in class org.snpeff.coverage.CountReadsOnMarkers
Count markers from all files
count(Nmer) - Method in class org.snpeff.nmer.NmerCount
Count an instance of this Nmer
count(Nmer) - Method in class org.snpeff.nmer.NmerCountWc
 
COUNT_DIFFS - Variable in class org.snpeff.binseq.coder.DnaCoder
 
countAffectedExons() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
How many full / partial exons does the variant affect?
countBases() - Method in class org.snpeff.stats.ReadsOnMarkersModel
Count bases covered for each marker type
CountByKey<T> - Class in org.snpeff.stats
Counters indexed by key.
CountByKey() - Constructor for class org.snpeff.stats.CountByKey
 
CountByType - Class in org.snpeff.stats
Counters indexed by 'type' (type is a generic string that can mean anything)
CountByType() - Constructor for class org.snpeff.stats.CountByType
 
countColumns(String) - Static method in class org.snpeff.util.Gpr
Count number of column in a file
Counter - Class in org.snpeff.stats
A simple class that counts...
Counter() - Constructor for class org.snpeff.stats.Counter
 
CounterDouble - Class in org.snpeff.stats
A simple class that counts...
CounterDouble() - Constructor for class org.snpeff.stats.CounterDouble
 
CountFragments - Class in org.snpeff.coverage
Base by base coverage (one chromsome)
CountFragments() - Constructor for class org.snpeff.coverage.CountFragments
 
countGenes(List<Marker>) - Method in class org.snpeff.snpEffect.VariantEffectStructural
 
countGenotypes() - Method in class org.snpeff.ped.PedEntry
Number of phenotypes available
countIUB(String) - Static method in class org.snpeff.util.IubString
How many IUB bases are in this string?
countLessThan(int) - Method in class org.snpeff.nmer.NmerCount
Count how many nmers are below a given threshold
countLines(String) - Static method in class org.snpeff.util.Gpr
Count lines in a file (same as 'wc -l file' in unix)
countMissingCategory(String) - Method in class org.snpeff.nextProt.NextProtHandler
 
countNewLineChars - Variable in class org.snpeff.fileIterator.FileIterator
 
countNewLineChars() - Method in class org.snpeff.fileIterator.FileIterator
Guess number of newline characters used (e.g.
countOverlap(GeneSet) - Method in class org.snpeff.geneSets.GeneSet
COunt how many genes are in both GeneSets
CountReads - Class in org.snpeff.coverage
Count how many reads map (from many SAM/BAM files) onto markers
CountReads(String, SnpEffectPredictor) - Constructor for class org.snpeff.coverage.CountReads
 
CountReadsOnMarkers - Class in org.snpeff.coverage
Count how many reads map (from many SAM/BAM files) onto markers
CountReadsOnMarkers(SnpEffectPredictor) - Constructor for class org.snpeff.coverage.CountReadsOnMarkers
 
countTranscripts() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Count number of transcripts
coverage(int, int) - Method in class org.snpeff.coverage.CoverageChr
Calculate Coverage per base
coverage(Marker) - Method in class org.snpeff.coverage.Coverage
Calculate total coverage per base
Coverage - Class in org.snpeff.coverage
Base by base coverage (one chromsome)
Coverage() - Constructor for class org.snpeff.coverage.Coverage
 
coverageByType - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
 
CoverageByType - Class in org.snpeff.stats
 
CoverageByType() - Constructor for class org.snpeff.stats.CoverageByType
 
CoverageChr - Class in org.snpeff.coverage
Base by base coverage (one chromsome)
CoverageChr(int) - Constructor for class org.snpeff.coverage.CoverageChr
 
cpgExonBias() - Method in class org.snpeff.interval.Gene
Calculate CpG bias: number of CpG / expected[CpG]
cpgExonBias() - Method in class org.snpeff.interval.Transcript
Calculate CpG bias: number of CpG / expected[CpG]
cpgExons() - Method in class org.snpeff.interval.Transcript
Count total CpG in this transcript's exons
create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
 
create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenesFile
 
create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
 
create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
 
create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
 
create() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRefSeq
 
create1kgFile() - Static method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVcfs
Creates a test file
createCacheFile() - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Create a cache file
createChr(String, int) - Method in class org.snpeff.coverage.CountFragments
Create new chromosome coverage
createChr(String, int) - Method in class org.snpeff.coverage.Coverage
Create new chromosome coverage
createChromos - Variable in class org.snpeff.fileIterator.MarkerFileIterator
 
createCircularGenes() - Method in class org.snpeff.interval.Genes
In a circular genome, a gene can have negative coordinates or crosses over chromosome end.
createFromFaidx(String, String) - Static method in class org.snpeff.interval.Genome
Create a genome from a faidx file.
createGenomicRegions() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Create (and add) up-down stream, splice sites, intergenic, etc
createIntergenic() - Method in class org.snpeff.interval.Genes
Creates a list of Intergenic regions
createIntergenic(Gene, Gene) - Static method in class org.snpeff.interval.Intergenic
Creates an intergenic marker based on the "space" between two genes
createObject(String) - Method in class org.snpeff.fileIterator.LineClassFileIterator
Create an object using
createRandomLargeMarkers(Chromosome, int) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
createRandomMarkers() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
createRandomSmallMarkers(Chromosome, int) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
createRandSequences() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Create random sequences for exons Note: This is only used for test cases!
createSnpEffectPredictor() - Method in class org.snpeff.snpEffect.testCases.unity.TestGenome
Create a snpEff predictor and build the forest
createSpliceFasta(String) - Method in class org.snpeff.spliceSites.SpliceTypes
Create one fasta file for each donor-acceptor pair
createSpliceSiteAcceptor(int) - Method in class org.snpeff.interval.Intron
Create a splice site acceptor of 'size' length Acceptor site: 3' end of the intron
createSpliceSiteDonor(int) - Method in class org.snpeff.interval.Intron
Create a splice site donor of 'maxSize' length Donor site: 5' end of the intron
createSpliceSiteRegionEnd(int) - Method in class org.snpeff.interval.Exon
Create splice site regions
createSpliceSiteRegionEnd(int, int) - Method in class org.snpeff.interval.Intron
Create splice site region
createSpliceSiteRegionStart(int) - Method in class org.snpeff.interval.Exon
Create splice site regions
createSpliceSiteRegionStart(int, int) - Method in class org.snpeff.interval.Intron
Create splice site region
createSpliceSites(int, int, int, int) - Method in class org.snpeff.interval.Genes
Create splice sites.
createSpliceSites(int, int, int, int) - Method in class org.snpeff.interval.Transcript
Find all splice sites.
CreateSpliceSiteTestCase - Class in org.snpeff.snpEffect.testCases.integration
 
CreateSpliceSiteTestCase() - Constructor for class org.snpeff.snpEffect.testCases.integration.CreateSpliceSiteTestCase
 
createUpDownStream(int) - Method in class org.snpeff.interval.Genes
Creates a list of UP/DOWN stream regions (for each transcript) Upstream (downstream) stream is defined as upDownLength before (after) transcript Note: If upDownLength <=0 no interval is created
createUpDownStream(int) - Method in class org.snpeff.interval.Transcript
Creates a list of UP/DOWN stream regions (for each transcript) Upstream (downstream) stream is defined as upDownLength before (after) transcript
Custom - Class in org.snpeff.interval
This is a custom interval (i.e.
Custom() - Constructor for class org.snpeff.interval.Custom
 
Custom(Marker, int, int, boolean, String, String) - Constructor for class org.snpeff.interval.Custom
 
CUSTOM - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
customIntervalFiles - Variable in class org.snpeff.SnpEff
 
CvTerm - Class in org.snpeff.nextProt
A controlled vocabulary term
CvTerm(Attributes) - Constructor for class org.snpeff.nextProt.CvTerm
 
CytoBands - Class in org.snpeff.interval
Cytband definitions E.g.: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz
CytoBands(Genome) - Constructor for class org.snpeff.interval.CytoBands
 

D

DARK_ROW - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
 
DATABASE_COMPATIBLE_VERSIONS - Static variable in class org.snpeff.snpEffect.Config
 
dataDir - Variable in class org.snpeff.SnpEff
 
debug - Static variable in class org.snpeff.binseq.coder.DnaCoder
 
debug - Static variable in class org.snpeff.coverage.CountReadsOnMarkers
 
debug - Static variable in class org.snpeff.fastq.FastqTrimmer
 
debug - Static variable in class org.snpeff.fileIterator.FastqFileIterator
 
debug - Variable in class org.snpeff.fileIterator.FileIterator
 
debug - Static variable in class org.snpeff.fileIterator.GuessTableTypes
 
debug - Static variable in class org.snpeff.fileIterator.LineClassFileIterator
 
debug - Static variable in class org.snpeff.fileIterator.LineFileIterator
 
debug - Static variable in class org.snpeff.fileIterator.LineSeqFileIterator
 
debug - Static variable in class org.snpeff.fileIterator.SamFileIterator
 
debug - Static variable in class org.snpeff.genBank.Features
 
debug - Static variable in class org.snpeff.geneOntology.GoTerm
 
debug - Static variable in class org.snpeff.geneOntology.GoTerms
 
debug - Static variable in class org.snpeff.geneSets.GeneSet
 
debug - Static variable in class org.snpeff.geneSets.GeneSets
 
debug - Static variable in class org.snpeff.interval.codonChange.CodonChangeMixed
 
debug - Static variable in class org.snpeff.interval.codonChange.CodonChangeStructural
 
debug - Variable in class org.snpeff.interval.Genes
 
debug - Static variable in class org.snpeff.interval.Motif
 
debug - Static variable in class org.snpeff.interval.ProteinInteractionLocus
 
debug - Variable in class org.snpeff.interval.tree.IntervalTreeArray
 
debug - Static variable in class org.snpeff.logStatsServer.LogStats
 
debug - Static variable in class org.snpeff.logStatsServer.VersionCheck
 
debug - Static variable in class org.snpeff.nmer.NmerCount
 
debug - Static variable in class org.snpeff.osCmd.ExecuteOsCommand
 
debug - Static variable in class org.snpeff.osCmd.OsCmdQueue
 
debug - Static variable in class org.snpeff.outputFormatter.VcfOutputFormatter
 
debug - Static variable in class org.snpeff.overlap.OverlapDnaSeq
 
debug - Static variable in class org.snpeff.pdb.DistanceResult
 
debug - Static variable in class org.snpeff.ped.PlinkMap
 
debug - Static variable in class org.snpeff.reactome.Entity
 
debug - Variable in class org.snpeff.SnpEff
 
debug - Static variable in class org.snpeff.snpEffect.HgvsDna
 
debug - Static variable in class org.snpeff.snpEffect.HgvsProtein
 
debug - Static variable in class org.snpeff.snpEffect.PurityChange
 
debug - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
debug - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
debug - Static variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEmbl
 
debug - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
debug - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable
 
debug - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
debug - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIubString
 
debug - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesReactome
 
debug - Static variable in class org.snpeff.snpEffect.VariantEffects
 
debug - Static variable in class org.snpeff.stats.ChrPosStats
 
debug - Static variable in class org.snpeff.stats.GeneCountByTypeTable
 
debug - Static variable in class org.snpeff.svg.Svg
 
debug - Static variable in class org.snpeff.vcf.VcfEffect
 
debug(Object) - Static method in class org.snpeff.util.Log
Prints a debug message (prints class name, method and line number)
debug(Object, int) - Static method in class org.snpeff.util.Log
Prints a debug message (prints class name, method and line number)
debug(Object, int, boolean) - Static method in class org.snpeff.util.Log
Prints a debug message (prints class name, method and line number)
dec() - Method in class org.snpeff.stats.Counter
 
dec() - Method in class org.snpeff.stats.CounterDouble
 
decodeWord(long, int) - Method in class org.snpeff.binseq.coder.Coder
Decode bits from a given position in a word
decodeWord(long, int) - Method in class org.snpeff.binseq.coder.DnaCoder
Decode bits from a given position
decompose() - Method in class org.snpeff.interval.Variant
Decompose a variant into basic constituents At the moment this only makes sense for MIXED variants which are decomposed into two variants: MNP + InDel
DEFAULT_BASE_Y - Static variable in class org.snpeff.svg.Svg
 
DEFAULT_BINS - Static variable in class org.snpeff.stats.PosStats
 
DEFAULT_BUFFER_SIZE - Static variable in class org.snpeff.fileIterator.SeekableBufferedReader
 
DEFAULT_CACHE_FILE - Static variable in class org.snpeff.probablility.RankSumNoReplacementPdf
 
DEFAULT_COMMAND - Static variable in class org.snpeff.SnpEff
 
DEFAULT_CONFIG_FILE - Static variable in class org.snpeff.snpEffect.Config
 
DEFAULT_COORDINATES - Static variable in class org.snpeff.snpEffect.Config
 
DEFAULT_CYTOBAND_BED_FILE - Static variable in class org.snpeff.interval.CytoBands
 
DEFAULT_DATA_DIR - Static variable in class org.snpeff.snpEffect.Config
 
DEFAULT_DELETE_PROTEIN_CODING_BASES - Static variable in class org.snpeff.snpEffect.LossOfFunction
Larger deletions removing either the first exon or more than 50% of the protein-coding sequence of the affected transcript
DEFAULT_DISTANCE_THRESHOLD - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
DEFAULT_FORMAT_VERSION - Static variable in enum class org.snpeff.vcf.EffFormatVersion
 
DEFAULT_ID_MAP_FILE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
DEFAULT_IGNORE_PROTEIN_CODING_AFTER - Static variable in class org.snpeff.snpEffect.LossOfFunction
It is assumed that even with a protein coding change at the last 5% of the protein, the protein could still be functional.
DEFAULT_IGNORE_PROTEIN_CODING_BEFORE - Static variable in class org.snpeff.snpEffect.LossOfFunction
It is assumed that even with a protein coding change at the first 5% of the protein: "..suggesting some disrupted transcripts are rescued by transcriptional reinitiation at an alternative start codon."
DEFAULT_INTERACT_FILE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
DEFAULT_MAX_MISMATCH_RATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
DEFAULT_MAX_PVALUE - Static variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
 
DEFAULT_PDB_DIR - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
DEFAULT_PDB_MIN_AA_SEPARATION - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
DEFAULT_PDB_ORGANISM_COMMON - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
DEFAULT_PDB_ORGANISM_SCIENTIFIC - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
DEFAULT_PDB_RESOLUTION - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
DEFAULT_PROXY_PORT - Static variable in class org.snpeff.util.Download
 
DEFAULT_REPORT_HTML_FILE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
 
DEFAULT_SIZE_X - Static variable in class org.snpeff.svg.Svg
 
DEFAULT_SIZE_Y - Static variable in class org.snpeff.svg.Svg
 
DEFAULT_START_CODON - Static variable in class org.snpeff.codons.CodonTable
All start codons are translated as "M".
DEFAULT_SUMMARY_CSV_FILE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
DEFAULT_SUMMARY_GENES_FILE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
DEFAULT_SUMMARY_HTML_FILE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
DEFAULT_TYPES - Static variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
 
DEFAULT_UP_DOWN_LENGTH - Static variable in class org.snpeff.snpEffect.SnpEffectPredictor
 
defaultConfigFile() - Static method in class org.snpeff.snpEffect.Config
If Debian-preferred config file is available, give it.
degenerate(String, int) - Method in class org.snpeff.codons.CodonTable
Degree of "degenerate site" What is a "degenerate site"? Here is an explanation form Stephen Wright (Univ.
del() - Method in class org.snpeff.snpEffect.HgvsProtein
Deletions remove one or more amino acid residues from the protein and are described using "del" after an indication of the first and last amino acid(s) deleted separated by a "_" (underscore).
DEL - Enum constant in enum class org.snpeff.interval.Variant.VariantType
 
deleteProteinCodingBases - Variable in class org.snpeff.snpEffect.LossOfFunction
 
deleteRedundant() - Method in class org.snpeff.interval.Transcript
Deletes redundant exons (i.e.
deleteRedundant() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Consolidate transcripts: If two exons are one right next to the other, join them E.g.
delFilter(String) - Method in class org.snpeff.vcf.VcfEntry
Remove a string from FILTER field
delins() - Method in class org.snpeff.snpEffect.HgvsProtein
Mixed variants Deletion/insertions (indels) replace one or more amino acid residues with one or more other amino acid residues.
Depolymerisation - Class in org.snpeff.reactome.events
A depolymerization event
Depolymerisation(int, String) - Constructor for class org.snpeff.reactome.events.Depolymerisation
 
depth() - Method in class org.snpeff.vcf.VcfGenotype
Depth of coverage
derived() - Method in class org.snpeff.vcf.Pedigree
A list of all derived pedigree entries
description - Variable in class org.snpeff.nextProt.CvTerm
 
description - Variable in class org.snpeff.vcf.VcfHeaderInfo
 
description() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
detectCircular() - Method in class org.snpeff.interval.Chromosome
Is this a circular chromosome? See if any exon has evidence of 'circular coordinates'
Diff - Class in org.snpeff.util
 
Diff(String, String) - Constructor for class org.snpeff.util.Diff
 
diffCount(String, String) - Static method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
Count number of differences between strings
diffStr(String, String) - Static method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
Show difference between two strings
dirName(String) - Static method in class org.snpeff.util.Gpr
Return file's dir
disjointSet(List<GoTerm>, int) - Method in class org.snpeff.geneOntology.GoTerms
Produce a GOTerm based on a list of GOTerms and a 'mask'
disjointSet(List<GeneSet>, int) - Method in class org.snpeff.geneSets.GeneSets
Produce a GeneSet based on a list of GeneSets and a 'mask'
distance - Variable in class org.snpeff.pdb.DistanceResult
 
distance - Variable in class org.snpeff.snpEffect.VariantEffect
 
distance(Marker) - Method in class org.snpeff.interval.Marker
How far apart are these intervals?
distanceBases(List<? extends Marker>, boolean) - Method in class org.snpeff.interval.Marker
Distance from the beginning/end of a list of intervals, until this SNP It count the number of bases in 'markers'
DistanceResult - Class in org.snpeff.pdb
 
DistanceResult() - Constructor for class org.snpeff.pdb.DistanceResult
 
DistanceResult(String) - Constructor for class org.snpeff.pdb.DistanceResult
 
DistanceResult(AminoAcid, AminoAcid, Transcript, Transcript, double) - Constructor for class org.snpeff.pdb.DistanceResult
 
distanceToTr(Variant) - Method in class org.snpeff.interval.Downstream
Distance to transcript
distanceToTr(Variant) - Method in class org.snpeff.interval.Upstream
Distance to transcript
DNA_TO_CODE - Static variable in class org.snpeff.util.GprSeq
 
dna2Code(char) - Static method in class org.snpeff.util.GprSeq
Convert from DNA letter to code
DnaAndQualitySequence - Class in org.snpeff.binseq
Binary packed DNA sequence and base calling quality Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 8 bits: - Six bits for the base quality [0 , ..
DnaAndQualitySequence(String) - Constructor for class org.snpeff.binseq.DnaAndQualitySequence
 
DnaAndQualitySequence(String, String, FastqVariant) - Constructor for class org.snpeff.binseq.DnaAndQualitySequence
 
DnaAndQualitySequence(Fastq) - Constructor for class org.snpeff.binseq.DnaAndQualitySequence
 
DnaAndQualitySequenceWithId - Class in org.snpeff.binseq
DnaAndQualitySequence with an ID
DnaAndQualitySequenceWithId(String) - Constructor for class org.snpeff.binseq.DnaAndQualitySequenceWithId
 
DnaAndQualitySequenceWithId(String, String, FastqVariant) - Constructor for class org.snpeff.binseq.DnaAndQualitySequenceWithId
 
dnaBaseChange() - Method in class org.snpeff.snpEffect.HgvsDna
DNA level base changes
DnaCoder - Class in org.snpeff.binseq.coder
Class used to encode & decode sequences into binary and vice-versa Note:This is a singleton class.
DnaNSequence - Class in org.snpeff.binseq
Binary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}
DnaNSequence(int, long[]) - Constructor for class org.snpeff.binseq.DnaNSequence
 
DnaNSequence(String) - Constructor for class org.snpeff.binseq.DnaNSequence
 
DnaQualityCoder - Class in org.snpeff.binseq.coder
Class used to encode & decode sequences into binary and vice-versa - Every base is encoded in 8 bits: - Six bits for the base quality [0 , ..
DnaQualSubsequenceComparator - Class in org.snpeff.binseq.comparator
Compares two subsequences of DNA (DnaAndQualitySequence)
DnaQualSubsequenceComparator(boolean) - Constructor for class org.snpeff.binseq.comparator.DnaQualSubsequenceComparator
 
DnaQualSubsequenceComparator(boolean, int) - Constructor for class org.snpeff.binseq.comparator.DnaQualSubsequenceComparator
 
DnaSeqFileIterator - Class in org.snpeff.fileIterator
 
DnaSeqFileIterator(String) - Constructor for class org.snpeff.fileIterator.DnaSeqFileIterator
 
DnaSeqIdFileIterator - Class in org.snpeff.fileIterator
 
DnaSeqIdFileIterator(String) - Constructor for class org.snpeff.fileIterator.DnaSeqIdFileIterator
 
DnaSeqPeFileIterator - Class in org.snpeff.fileIterator
 
DnaSeqPeFileIterator(String) - Constructor for class org.snpeff.fileIterator.DnaSeqPeFileIterator
 
DnaSequence - Class in org.snpeff.binseq
Binary packed DNA sequence Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 2 bits {a, c, g, t} <=> {0, 1, 2, 3} - All bits are stored in an array of 'words' (integers) - Most significant bits are the first bases in the sequence (makes comparison easier)
DnaSequence(int, long[]) - Constructor for class org.snpeff.binseq.DnaSequence
 
DnaSequence(String) - Constructor for class org.snpeff.binseq.DnaSequence
 
DnaSequence(String, boolean) - Constructor for class org.snpeff.binseq.DnaSequence
 
DnaSequenceBaseAt(int) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Tests 'baseAt' method in DnaSequence
DnaSequenceByte - Class in org.snpeff.binseq
Binary packed DNA sequence.
DnaSequenceByte(int, byte[]) - Constructor for class org.snpeff.binseq.DnaSequenceByte
 
DnaSequenceByte(String) - Constructor for class org.snpeff.binseq.DnaSequenceByte
 
DnaSequenceId - Class in org.snpeff.binseq
Binary packed DNA sequence with an ID (long)
DnaSequenceId(long, int, long[]) - Constructor for class org.snpeff.binseq.DnaSequenceId
 
DnaSequenceId(long, String) - Constructor for class org.snpeff.binseq.DnaSequenceId
 
DnaSequenceId(String) - Constructor for class org.snpeff.binseq.DnaSequenceId
 
DnaSequencePe - Class in org.snpeff.binseq
Pair end DNA sequence (binary packed) It consists of 2 DNA sequences separated by a gap.
DnaSequencePe(String) - Constructor for class org.snpeff.binseq.DnaSequencePe
 
DnaSequencePe(String, String, int) - Constructor for class org.snpeff.binseq.DnaSequencePe
 
DnaSubsequenceComparator<T extends DnaSequence> - Class in org.snpeff.binseq.comparator
Compares two subsequences of DNA (DnaSequence)
DnaSubsequenceComparator(boolean) - Constructor for class org.snpeff.binseq.comparator.DnaSubsequenceComparator
 
DnaSubsequenceComparator(boolean, int) - Constructor for class org.snpeff.binseq.comparator.DnaSubsequenceComparator
 
doNotSave(Marker) - Method in class org.snpeff.serializer.MarkerSerializer
 
download - Variable in class org.snpeff.SnpEff
 
download(String, String) - Method in class org.snpeff.util.Download
 
download(URL, String) - Method in class org.snpeff.util.Download
Download a file
Download - Class in org.snpeff.util
Command line program: Build database
Download() - Constructor for class org.snpeff.util.Download
 
downloadUrl(String) - Method in class org.snpeff.snpEffect.Config
Get a list of URLs that can be used to download a database Use compatible versions from 'getDatabaseCompatibilityVersions()'
downloadUrl(String, String) - Method in class org.snpeff.snpEffect.Config
Build the URL for downloading a database file
Downstream - Class in org.snpeff.interval
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
Downstream() - Constructor for class org.snpeff.interval.Downstream
 
Downstream(Transcript, int, int, boolean, String) - Constructor for class org.snpeff.interval.Downstream
 
DOWNSTREAM - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
dump(String, int, int, boolean) - Method in class org.snpeff.vcf.FileIndexChrPos
Dump all lines in the interval chr:posStart-posEnd
DUMP - Enum constant in enum class org.snpeff.snpEffect.commandLine.SnpEffCmdDump.DumpFormat
 
dup() - Method in class org.snpeff.snpEffect.HgvsProtein
Duplications
DUP - Enum constant in enum class org.snpeff.interval.Variant.VariantType
 
duplication - Variable in class org.snpeff.snpEffect.Hgvs
 

E

EFF_FIELD_NAMES - Static variable in class org.snpeff.vcf.VcfEffect
 
effect() - Method in class org.snpeff.snpEffect.VariantEffectStructural
 
effect(boolean, boolean, boolean, boolean, boolean) - Method in class org.snpeff.snpEffect.VariantEffect
Show a string with overall effect
effect(Marker, EffectType, boolean) - Method in class org.snpeff.interval.codonChange.CodonChange
Calculate variant effect
EFFECT_TYPE_SEPARATOR - Static variable in enum class org.snpeff.vcf.EffFormatVersion
 
EFFECT_TYPE_SEPARATOR_OLD - Static variable in enum class org.snpeff.vcf.EffFormatVersion
 
effectImpact - Variable in class org.snpeff.snpEffect.VariantEffect
 
effectImpact() - Method in enum class org.snpeff.snpEffect.EffectType
Return effect impact
effectImpacts - Variable in class org.snpeff.snpEffect.VariantEffect
 
effectNoCodon(Marker, EffectType) - Method in class org.snpeff.interval.codonChange.CodonChange
 
effectNoCodon(Marker, EffectType, VariantEffect.EffectImpact) - Method in class org.snpeff.interval.codonChange.CodonChange
 
effectTranscript() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
 
effectTranscript() - Method in class org.snpeff.interval.codonChange.CodonChangeDup
 
effectTranscript() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
 
effectType - Variable in class org.snpeff.snpEffect.VariantEffect
 
EffectType - Enum Class in org.snpeff.snpEffect
Effect type: Note that effects are sorted (declared) by impact (highest to lowest putative impact).
effectTypes - Variable in class org.snpeff.snpEffect.VariantEffect
 
EffFormatVersion - Enum Class in org.snpeff.vcf
VcfFields in SnpEff version 2.X have a different format than 3.X As of version 4.1 we switch to a standard annotation format
elapsed() - Method in class org.snpeff.util.Timer
Elapsed time in milliseconds
EMAIL - Static variable in class org.snpeff.Pcingola
 
Embl - Class in org.snpeff.genBank
A class representing the same data as an EMBL file References: http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
Embl(String) - Constructor for class org.snpeff.genBank.Embl
Create a Genbank record from a 'GB' file
Embl(LineFileIterator) - Constructor for class org.snpeff.genBank.Embl
Create a Genbank record from a 'GB' file
EMBL - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
 
EmblFile - Class in org.snpeff.genBank
A file containing one or more set of features (e.g.
EmblFile(String) - Constructor for class org.snpeff.genBank.EmblFile
 
empty() - Static method in class org.snpeff.binseq.DnaAndQualitySequence
 
empty() - Static method in class org.snpeff.binseq.DnaAndQualitySequenceWithId
 
empty() - Static method in class org.snpeff.binseq.DnaNSequence
Empty sequence singleton
empty() - Static method in class org.snpeff.binseq.DnaSequence
Empty sequence singleton
empty() - Static method in class org.snpeff.binseq.DnaSequenceId
Empty sequence singleton
EMPTY_DISTANCES - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
EMPTY_MARKER_ARRAY - Static variable in class org.snpeff.interval.tree.IntervalTreeArray
 
EMPTY_STRING_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
 
EMPTY_VALUE - Static variable in class org.snpeff.collections.HashLongLongArray
 
encodeWord(char, int) - Method in class org.snpeff.binseq.coder.DnaCoder
Encode a base to a given position in a word
end - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
end - Variable in class org.snpeff.genBank.FeatureCoordinates
 
end - Variable in class org.snpeff.interval.Interval
 
end - Variable in class org.snpeff.nextProt.Location
 
end() - Method in class org.snpeff.util.Timer
 
endElement(String, String, String) - Method in class org.snpeff.nextProt.NextProtHandler
Parse XML's element end
endSection(Marker) - Method in class org.snpeff.outputFormatter.BedOutputFormatter
Finish up section
endSection(Marker) - Method in class org.snpeff.outputFormatter.OutputFormatter
Finish up section
endSection(Marker) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
Finish up section
EnrichmentAlgorithm - Class in org.snpeff.geneSets.algorithm
A generic enrichment algorithm for selecting gene-sets from a collection of gene-sets
EnrichmentAlgorithm(GeneSets, int) - Constructor for class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
EnrichmentAlgorithm.EnrichmentAlgorithmType - Enum Class in org.snpeff.geneSets.algorithm
 
EnrichmentAlgorithmGreedy - Class in org.snpeff.geneSets.algorithm
A generic greedy enrichment algorithm for selecting gene-sets
EnrichmentAlgorithmGreedy(GeneSets, int) - Constructor for class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
 
EnrichmentAlgorithmGreedyVariableSize - Class in org.snpeff.geneSets.algorithm
A greedy enrichment algorithm for selecting gene-sets using a variable geneSet-size strategy: i) Select only from geneSets in low-sizes e.g.
EnrichmentAlgorithmGreedyVariableSize(GeneSets, int) - Constructor for class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
 
ensureCapacity(long) - Method in class org.snpeff.collections.OpenBitSet
Ensure that the long[] is big enough to hold numBits, expanding it if necessary.
ensureCapacityWords(int) - Method in class org.snpeff.collections.OpenBitSet
Expand the long[] with the size given as a number of words (64 bit longs).
Entity - Class in org.snpeff.reactome
A reactome basic entity (e.g.
Entity(int, String) - Constructor for class org.snpeff.reactome.Entity
 
Entity.TransferFunction - Enum Class in org.snpeff.reactome
 
entropy() - Method in class org.snpeff.spliceSites.AcgtTree
Calculate the entropy
entropyAll(int) - Method in class org.snpeff.spliceSites.AcgtTree
 
EPSILON - Static variable in class org.snpeff.probablility.Binomial
A small number
EPSILON - Static variable in class org.snpeff.probablility.CochranArmitageTest
A small number
EPSILON - Static variable in class org.snpeff.probablility.Hypergeometric
A small number
EPSILON - Static variable in class org.snpeff.reactome.Reactome
 
EPSILON - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
 
EPSILON - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntStats
 
equalPos(DistanceResult) - Method in class org.snpeff.pdb.DistanceResult
Same genomic positions
equals() - Method in class org.snpeff.util.Diff
 
equals(Object) - Method in class org.snpeff.collections.OpenBitSet
returns true if both sets have the same bits set
equals(Object) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
equals(Object) - Method in class org.snpeff.util.KeyValue
 
equals(Object) - Method in class org.snpeff.util.Tuple
 
equals(Interval) - Method in class org.snpeff.interval.Interval
 
equals(Markers) - Method in class org.snpeff.interval.Markers
Are all intervals equal?
error - Variable in class org.snpeff.snpEffect.VariantEffect
 
error(String) - Static method in class org.snpeff.util.Log
Show a warning message (up to MAX_ERRORS times)
error(Throwable, String) - Static method in class org.snpeff.util.Log
 
ERROR - Enum constant in enum class org.snpeff.logStatsServer.LogStats.RequestResult
 
ERROR_CHROMOSOME_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
ERROR_FILE_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
ERROR_MISSING_CDS_SEQUENCE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
ERROR_OUT_OF_CHROMOSOME_RANGE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
ERROR_OUT_OF_EXON - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
ErrorWarningType - Enum Class in org.snpeff.snpEffect
Errors and warnings
ETC_CONFIG_FILE - Static variable in class org.snpeff.snpEffect.Config
 
evaluate() - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
Random sample and evaluate
evalue - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
Event - Class in org.snpeff.reactome.events
A reactome event (any generic event, from pathways to polymerizations)
Event(int, String) - Constructor for class org.snpeff.reactome.events.Event
 
EXCEPTION - Enum constant in enum class org.snpeff.util.Log.FatalErrorBehabiour
 
EXCEPTION_QUIET - Enum constant in enum class org.snpeff.util.Log.FatalErrorBehabiour
 
exec() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
ExecuteOsCommand - Class in org.snpeff.osCmd
Launches an 'OS command' (e.g.
ExecuteOsCommand(String) - Constructor for class org.snpeff.osCmd.ExecuteOsCommand
 
ExecuteOsCommand(String[]) - Constructor for class org.snpeff.osCmd.ExecuteOsCommand
 
exists(String) - Static method in class org.snpeff.util.Gpr
Does 'file' exist?
EXIT - Enum constant in enum class org.snpeff.util.Log.FatalErrorBehabiour
 
Exon - Class in org.snpeff.interval
Interval for an exon
Exon() - Constructor for class org.snpeff.interval.Exon
 
Exon(Transcript, int, int, boolean, String, int) - Constructor for class org.snpeff.interval.Exon
 
EXON - Enum constant in enum class org.snpeff.interval.GffType
 
EXON - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
EXON_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
EXON_DELETED_PARTIAL - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
EXON_DUPLICATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
EXON_DUPLICATION_PARTIAL - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
EXON_INVERSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
EXON_INVERSION_PARTIAL - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
Exon.ExonSpliceType - Enum Class in org.snpeff.interval
Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)
exonBase(char[], int, int) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
Count how many bases are there until the exon
exonFull - Variable in class org.snpeff.interval.codonChange.CodonChangeStructural
 
exonPartial - Variable in class org.snpeff.interval.codonChange.CodonChangeStructural
 
exons() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
Deletion analysis using full transcript information.
exons() - Method in class org.snpeff.interval.codonChange.CodonChangeDup
 
exons() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
Variant affect one or more exons
exonsCoding() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
 
exonsCoding() - Method in class org.snpeff.interval.codonChange.CodonChangeDup
One or more exons fully included (no partial overlap)
exonsCoding() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
Variant affect one or more coding exons
exonsFromCds() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Create exons from CDS info
exonsFromCds(Transcript) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Create exons from CDS info WARNING: We might end up with redundant exons if some exons existed before this process
exonsNoncoding() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
 
exonsNoncoding() - Method in class org.snpeff.interval.codonChange.CodonChangeDup
Effects for non-coding transcripts
exonsNoncoding() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
Variant affect one or more non-coding exons
ExonSpliceCharacterizer - Class in org.snpeff.interval
Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)
ExonSpliceCharacterizer(String) - Constructor for class org.snpeff.interval.ExonSpliceCharacterizer
 
ExonSpliceCharacterizer(Genome) - Constructor for class org.snpeff.interval.ExonSpliceCharacterizer
 
expand(String) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIubString
 
expandingWordNum(long) - Method in class org.snpeff.collections.OpenBitSet
 
expandIub - Variable in class org.snpeff.SnpEff
 
expected(String) - Method in class org.snpeff.stats.ObservedOverExpected
 
expected(String) - Method in class org.snpeff.stats.ObservedOverExpectedCHG
 
expected(String) - Method in class org.snpeff.stats.ObservedOverExpectedCHH
 
expected(String) - Method in class org.snpeff.stats.ObservedOverExpectedCpG
 
expected(Exon) - Method in class org.snpeff.stats.ObservedOverExpected
Expected number of sequences (average between plus and minus strand)
expected(Gene) - Method in class org.snpeff.stats.ObservedOverExpected
Expected number of sequences (average between plus and minus strand)
expected(Transcript) - Method in class org.snpeff.stats.ObservedOverExpected
Expected number of sequences (average between plus and minus strand)
EXTENSION_EMBL - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryEmbl
 
EXTENSION_GENBANK - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenBank
 
externalName - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
extName(String) - Static method in class org.snpeff.util.Gpr
Get a file's extension (all letters after the last '.'

F

factory() - Method in class org.snpeff.binseq.DnaNSequence
Create sequences
factory() - Method in class org.snpeff.binseq.DnaSequence
Create a new sequence
factory() - Method in class org.snpeff.binseq.DnaSequenceId
Create sequences
factory(String) - Static method in class org.snpeff.vcf.VcfHeaderEntry
 
factory(GoTerms) - Static method in class org.snpeff.geneSets.GeneSets
Create gene sets form GoTerms
factory(Chromosome, int, String, String, String, boolean) - Static method in class org.snpeff.interval.Variant
Create variants from ALT (which can be multiple values)
factory(Marker, Svg) - Static method in class org.snpeff.svg.Svg
 
factory(Transcript, int, Transcript, String) - Static method in class org.snpeff.interval.ProteinInteractionLocus
Create interaction.
factory(Variant, Transcript, VariantEffects) - Static method in class org.snpeff.interval.codonChange.CodonChange
Create a specific codon change for a variant
factory(VcfEntry) - Static method in class org.snpeff.vcf.VariantVcfEntry
Create a collection of all <Variant, VcfEntry>
FAKE_COUNTS - Static variable in class org.snpeff.spliceSites.AcgtTree
 
families() - Method in class org.snpeff.ped.PedPedigree
Split data into families
FASTA_DELIMITER - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
 
FastaFileIterator - Class in org.snpeff.fileIterator
Opens a fasta file and iterates over all fasta sequences in the file
FastaFileIterator(String) - Constructor for class org.snpeff.fileIterator.FastaFileIterator
 
fastaHeader2Ids() - Method in class org.snpeff.fileIterator.FastaFileIterator
Try to parse IDs from a fasta header
fastaSimpleRead(String) - Static method in class org.snpeff.util.GprSeq
Read a fasta file containing one (and only one) sequence
fastClear(int) - Method in class org.snpeff.collections.OpenBitSet
clears a bit.
fastClear(long) - Method in class org.snpeff.collections.OpenBitSet
clears a bit.
fastFlip(int) - Method in class org.snpeff.collections.OpenBitSet
flips a bit.
fastFlip(long) - Method in class org.snpeff.collections.OpenBitSet
flips a bit.
fastGet(int) - Method in class org.snpeff.collections.OpenBitSet
Returns true or false for the specified bit index.
fastGet(long) - Method in class org.snpeff.collections.OpenBitSet
Returns true or false for the specified bit index.
FASTQ_SANGER_ZERO - Static variable in class org.snpeff.util.GprSeq
 
Fastq2Fastq - Class in org.snpeff
Convert FASTQ (phred64) file to FASTQ (phred33)
Fastq2Fastq() - Constructor for class org.snpeff.Fastq2Fastq
 
FastqFileIterator - Class in org.snpeff.fileIterator
Opens a fastq file and iterates over all fastq sequences in the file Unlike BioJava's version, this one does NOT load all sequences in memory.
FastqFileIterator(InputStream, FastqVariant) - Constructor for class org.snpeff.fileIterator.FastqFileIterator
 
FastqFileIterator(String) - Constructor for class org.snpeff.fileIterator.FastqFileIterator
 
FastqFileIterator(String, FastqVariant) - Constructor for class org.snpeff.fileIterator.FastqFileIterator
 
fastqId(Fastq) - Static method in class org.snpeff.util.GprSeq
Get an ID from a fastq
FastqSplit - Class in org.snpeff.fastq
Split a fastq into N files
FastqSplit() - Constructor for class org.snpeff.fastq.FastqSplit
 
FastqTools - Class in org.snpeff.fastq
Simple maipulation of fastq sequences
FastqTools() - Constructor for class org.snpeff.fastq.FastqTools
 
FastqTrimmer - Class in org.snpeff.fastq
Trim fastq sequence when quality drops below a threshold The resulting sequence has to ba at least 'minBases'
FastqTrimmer(int, int) - Constructor for class org.snpeff.fastq.FastqTrimmer
 
FastqTrimmerAdrian - Class in org.snpeff.fastq
Trim fastq sequence when: - Median quality drops below a threshold (mean is calculated every 2 bases instead of every base) - Sequence length is at least 'minBases' From Adrian Platts ...Also the sliding window was not every base.
FastqTrimmerAdrian(int, int, int) - Constructor for class org.snpeff.fastq.FastqTrimmerAdrian
 
FastqTrimmerMedian - Class in org.snpeff.fastq
Trim fastq sequence when median quality drops below a threshold
FastqTrimmerMedian(int, int, int) - Constructor for class org.snpeff.fastq.FastqTrimmerMedian
 
fastSet(int) - Method in class org.snpeff.collections.OpenBitSet
Sets the bit at the specified index.
fastSet(long) - Method in class org.snpeff.collections.OpenBitSet
Sets the bit at the specified index.
fatalError(String) - Static method in class org.snpeff.util.Log
Show an error message and exit
fatalError(Throwable, String) - Static method in class org.snpeff.util.Log
 
father - Variable in class org.snpeff.vcf.PedigreeEntry
 
fatherNum - Variable in class org.snpeff.vcf.PedigreeEntry
 
FDR - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
 
feature - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
Feature - Class in org.snpeff.genBank
A feature in a GenBank or EMBL file
Feature(Feature.Type, String) - Constructor for class org.snpeff.genBank.Feature
 
Feature(Feature.Type, String, int, int, boolean, int) - Constructor for class org.snpeff.genBank.Feature
 
FEATURE_FUSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
FEATURE_KEY_LEN - Static variable in class org.snpeff.genBank.Embl
 
FEATURE_NAME_FIELD_LEN - Static variable in class org.snpeff.genBank.GenBank
 
FEATURE_NAME_LEN - Static variable in class org.snpeff.genBank.Embl
 
Feature.Type - Enum Class in org.snpeff.genBank
 
FeatureCoordinates - Class in org.snpeff.genBank
A feature in a GenBank or EMBL file
FeatureCoordinates(int, int, boolean) - Constructor for class org.snpeff.genBank.FeatureCoordinates
 
Features - Class in org.snpeff.genBank
A class representing a set of features References: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
Features(String) - Constructor for class org.snpeff.genBank.Features
Create features from a file
Features(LineFileIterator) - Constructor for class org.snpeff.genBank.Features
Create features from a file
FeaturesFile - Class in org.snpeff.genBank
A file containing one or more set of features (e.g.
FeaturesFile(String) - Constructor for class org.snpeff.genBank.FeaturesFile
 
Female - Enum constant in enum class org.snpeff.ped.Sex
 
FIELD_NAME_SEPARATOR - Static variable in class org.snpeff.fileIterator.LineClassFileIterator
 
FIELD_NAME_SEPARATOR - Static variable in class org.snpeff.fileIterator.TableFile
 
fieldByName - Variable in class org.snpeff.fileIterator.LineClassFileIterator
 
fieldByName - Variable in class org.snpeff.fileIterator.TableFile
 
fieldMap() - Method in class org.snpeff.fileIterator.LineClassFileIterator
Map field names to Field objects
fieldNames - Variable in class org.snpeff.fileIterator.LineClassFileIterator
 
fieldNames - Variable in class org.snpeff.fileIterator.TableFile
 
fieldNum(String) - Static method in class org.snpeff.vcf.VcfLof
Convert from field name to field number
fieldNum(String) - Static method in class org.snpeff.vcf.VcfNmd
Convert from field name to field number
fieldStr - Variable in class org.snpeff.fileIterator.LineClassFileIterator
 
fieldStr - Variable in class org.snpeff.fileIterator.TableFile
 
fileExists(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
Does either 'path' or 'path'+'.gz' exist?
FileIndexChrPos - Class in org.snpeff.vcf
Index a file that has "chr \t pos" as the beginning of a line (e.g.
FileIndexChrPos(String) - Constructor for class org.snpeff.vcf.FileIndexChrPos
 
FileIndexChrPos.FileRegion - Class in org.snpeff.vcf
A part of a file
FileIndexChrPos.LineAndPos - Class in org.snpeff.vcf
A line and the position on the file where it begins
FileIterator<T> - Class in org.snpeff.fileIterator
Opens a file and iterates over all objects in the file Note: The file is not loaded in memory, thus allows to iterate over very large files
FileIterator(BufferedReader) - Constructor for class org.snpeff.fileIterator.FileIterator
 
FileIterator(String) - Constructor for class org.snpeff.fileIterator.FileIterator
 
fileName - Variable in class org.snpeff.fileIterator.FileIterator
 
fileName - Variable in class org.snpeff.fileIterator.TableFile
 
FileRegion() - Constructor for class org.snpeff.vcf.FileIndexChrPos.FileRegion
 
fileSize - Variable in class org.snpeff.fileIterator.FileIterator
 
filter - Variable in class org.snpeff.vcf.VcfEntry
 
filter() - Method in class org.snpeff.spliceSites.TranscriptSet
Filter out "bad transcripts"
filter(String) - Method in interface org.snpeff.osCmd.LineFilter
Filter and prossible change a line
filter(VariantEffect) - Method in class org.snpeff.filter.VariantEffectFilter
Filter a sequence change
filter(T) - Method in interface org.snpeff.filter.Filter
Does 'objectToTest' satisfy the filter?
Filter<T> - Interface in org.snpeff.filter
A Generic filter interface
FILTER_PASS - Static variable in class org.snpeff.vcf.VcfEntry
 
filterIntervalFiles - Variable in class org.snpeff.SnpEff
 
filterTranscriptSupportLevel(TranscriptSupportLevel) - Method in class org.snpeff.interval.Gene
Filter transcripts by TSL
filterTranscriptSupportLevel(TranscriptSupportLevel) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Filter transcripts by TSL
find(String, int, boolean) - Method in class org.snpeff.vcf.FileIndexChrPos
Find the position in the file for the first character of the first line equal or less than a specific chr:pos
findBestOverlap(T) - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
Find best overlap for 'sequence'
findCds(Exon) - Method in class org.snpeff.interval.Transcript
Find a CDS that matches exactly the exon
findExon(int) - Method in class org.snpeff.interval.Transcript
Return the an exon that intersects 'pos'
findExon(Marker) - Method in class org.snpeff.interval.Transcript
Return an exon intersecting 'marker' (first exon found)
findGene(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
findGene(String, String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
findIntron(int) - Method in class org.snpeff.interval.Transcript
Return an intron overlapping position 'pos'
findMarker(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
findNodeNames(double, double, int) - Method in class org.snpeff.spliceSites.AcgtTree
Find node names that are within the thresholds
findOrCreateExon(String, GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Find an exon for a given parentId
findOrCreateGene(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Find or create a gene based on GffMarker
findOrCreateTranscript(GffMarker) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Create and add a transcript based on GffMarker
findParent(Class) - Method in class org.snpeff.interval.Interval
Go up (parent) until we find an instance of 'clazz'
findRareAa(String) - Method in class org.snpeff.codons.FindRareAaIntervals
Find all sites having rare amino acids
FindRareAaIntervals - Class in org.snpeff.codons
Find intervals where rare amino acids occur
FindRareAaIntervals(Genome) - Constructor for class org.snpeff.codons.FindRareAaIntervals
 
findTag(String) - Method in class org.snpeff.sam.SamEntry
Does this entry have a tag?
findTranscript(String) - Method in class org.snpeff.interval.Genes
Find a transcript by ID
findTranscript(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
findTranscript(String, String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
findUtr(int) - Method in class org.snpeff.interval.Transcript
Return the UTR that hits position 'pos'
findUtrs(Marker) - Method in class org.snpeff.interval.Transcript
Return the UTR that intersects 'marker' (null if not found)
finish() - Method in class org.snpeff.osCmd.OsCmdRunner
Stop execution of this thread
first - Variable in class org.snpeff.util.Tuple
 
FISHER - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
 
FISHER_CHI_SQUARE - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
 
FISHER_GREEDY - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
 
FisherExactTest - Class in org.snpeff.probablility
Calculate Fisher's exact test (based on hypergeometric distribution)
fisherExactTestDown(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
Fisher's exact test for 'k' or less (lower tail)
fisherExactTestDown(int, int, int, int, double) - Method in class org.snpeff.probablility.FisherExactTest
Fisher's exact test for less than 'k' (lower tail) It also compares to a 'threshold' value to speedup the process.
fisherExactTestUp(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
Fisher's exact test for 'k' or more (upper tail)
fisherExactTestUp(int, int, int, int, double) - Method in class org.snpeff.probablility.FisherExactTest
Fisher's exact test for 'k' or more It also compares to a 'threshold' value to speedup the process.
FisherPValueAlgorithm - Class in org.snpeff.geneSets.algorithm
 
FisherPValueAlgorithm(GeneSets, int) - Constructor for class org.snpeff.geneSets.algorithm.FisherPValueAlgorithm
 
FisherPValueGreedyAlgorithm - Class in org.snpeff.geneSets.algorithm
 
FisherPValueGreedyAlgorithm(GeneSets, int) - Constructor for class org.snpeff.geneSets.algorithm.FisherPValueGreedyAlgorithm
 
fixedOutput - Variable in class org.snpeff.reactome.Entity
 
fixStartEnd() - Method in class org.snpeff.fileIterator.BlastResultEntry
Swap start- end positions if they are not in order
Flag - Enum constant in enum class org.snpeff.vcf.VcfInfoType
 
flip(long) - Method in class org.snpeff.collections.OpenBitSet
flips a bit, expanding the set size if necessary
flip(long, long) - Method in class org.snpeff.collections.OpenBitSet
Flips a range of bits, expanding the set size if necessary
flipAndGet(int) - Method in class org.snpeff.collections.OpenBitSet
flips a bit and returns the resulting bit value.
flipAndGet(long) - Method in class org.snpeff.collections.OpenBitSet
flips a bit and returns the resulting bit value.
Float - Enum constant in enum class org.snpeff.vcf.VcfInfoType
 
FloatStats - Class in org.snpeff.stats
A simple class that does some basic statistics on double numbers
FloatStats() - Constructor for class org.snpeff.stats.FloatStats
 
format - Variable in class org.snpeff.vcf.VcfEntry
 
FORMAT_ANN - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
 
FORMAT_ANN_1 - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
 
FORMAT_EFF - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
 
FORMAT_EFF_2 - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
 
FORMAT_EFF_3 - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
 
FORMAT_EFF_4 - Enum constant in enum class org.snpeff.vcf.EffFormatVersion
 
FORMAT_PREFIX - Static variable in class org.snpeff.vcf.VcfHeader
 
formatFields - Variable in class org.snpeff.vcf.VcfEntry
 
formatVersion() - Method in class org.snpeff.vcf.VcfEffect
Guess effect format version
formatVersion(String) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
Get file's format version
formatVersion(String) - Method in class org.snpeff.vcf.VcfEffect
Guess format 'main' version (either 'ANN' of 'EFF') without trying to guess sub-version
foundAllTypes() - Method in class org.snpeff.fileIterator.GuessTableTypes
 
FRAME - Enum constant in enum class org.snpeff.interval.FrameType
 
FRAME_SHIFT - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
FRAME_SHIFT_AFTER_CDS_END - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
FRAME_SHIFT_BEFORE_CDS_START - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
frameCorrection() - Method in class org.snpeff.interval.Transcript
Correct exons based on frame information.
frameCorrection(int) - Method in class org.snpeff.interval.Cds
Correct coordinates according to frame differences
frameCorrection(int) - Method in class org.snpeff.interval.Exon
Correct exons according to frame information Shift the start position one base
frameFromLength(int) - Method in enum class org.snpeff.interval.FrameType
Calculate frame from cds length
FrameType - Enum Class in org.snpeff.interval
Type of frame calculations Internally, we use GFF style frame calculation for Exon / Transcript Technically, these are 'frame' and 'phase' which are calculated in different ways UCSC type: Indicated the coding base number modulo 3.
fs() - Method in class org.snpeff.snpEffect.HgvsProtein
Frame shifts are a special type of amino acid deletion/insertion affecting an amino acid between the first (initiation, ATG) and last codon (termination, stop), replacing the normal C-terminal sequence with one encoded by another reading frame (specified 2013-10-11).
FTP_PROTOCOL - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
 
fusions() - Method in class org.snpeff.snpEffect.VariantEffectStructural
Is there another 'fusion' effect?

G

G - Static variable in class org.snpeff.fastq.FastqSplit
 
GAP_CODE - Static variable in class org.snpeff.util.GprSeq
 
gapopen - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
GATK - Enum constant in enum class org.snpeff.SnpEff.OutputFormat
 
GB - Static variable in class org.snpeff.util.Gpr
 
GenBank - Class in org.snpeff.genBank
A class representing the same data as a GenBank file (a 'GB' file) References: http://www.insdc.org/documents/feature-table http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord
GenBank(String) - Constructor for class org.snpeff.genBank.GenBank
Create a Genbank record from a 'GB' file
GenBank(LineFileIterator) - Constructor for class org.snpeff.genBank.GenBank
 
GENBANK - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
 
GenBankFile - Class in org.snpeff.genBank
A file containing one or more set of features (e.g.
GenBankFile(String) - Constructor for class org.snpeff.genBank.GenBankFile
 
gene - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
gene - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
gene - Variable in class org.snpeff.snpEffect.testCases.unity.TestGenome
 
Gene - Class in org.snpeff.interval
Interval for a gene, as well as transcripts
Gene() - Constructor for class org.snpeff.interval.Gene
 
Gene(Marker, int, int, boolean, String, String, BioType) - Constructor for class org.snpeff.interval.Gene
 
GENE - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
GENE - Enum constant in enum class org.snpeff.interval.GffType
 
GENE - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
GENE_CPG_NUM_BINS - Static variable in class org.snpeff.stats.GeneCountByTypeTable
 
GENE_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
GENE_DUPLICATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
GENE_FUSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
GENE_FUSION_HALF - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
GENE_FUSION_REVERESE - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
GENE_INVERSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
GENE_REARRANGEMENT - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
Gene.GeneType - Enum Class in org.snpeff.interval
 
GeneCountByTypeTable - Class in org.snpeff.stats
Count for each 'type' and 'gene'.
GeneCountByTypeTable() - Constructor for class org.snpeff.stats.GeneCountByTypeTable
 
geneId(Feature, int, int) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
Try to get geneIDs
geneIds - Variable in class org.snpeff.reactome.Entity
 
GeneIds - Class in org.snpeff.reactome
Maps different Gene IDs: - ENSEMBL Gene ID to transcript ID - ENSEMBL Gene ID to Gene Name - ENSEMBL Gene ID to Refseq Gene ID - ENSEMBL Gene ID to Refseq Protein ID
GeneIds(String) - Constructor for class org.snpeff.reactome.GeneIds
 
geneName(Feature, int, int) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
Get gene name from feature
generate_test() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBinomial
Create new tests
generate_test() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest
Create commands in R to run and get test results
generate_test() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric
Create commands in R to run and get test results
GenericMarker - Class in org.snpeff.interval
An interval intended as a mark
GenericMarker() - Constructor for class org.snpeff.interval.GenericMarker
 
GenericMarker(Marker, int, int, String) - Constructor for class org.snpeff.interval.GenericMarker
 
GenericMarkerFileIterator - Class in org.snpeff.fileIterator
Opens a file and creates generic markers (one per line)
GenericMarkerFileIterator(String, int, int, int, int) - Constructor for class org.snpeff.fileIterator.GenericMarkerFileIterator
 
Genes - Class in org.snpeff.interval
A collection of genes (marker intervals) Note: It is assumed that all genes belong to the same genome
Genes(Genome) - Constructor for class org.snpeff.interval.Genes
 
GeneSet - Class in org.snpeff.geneSets
An set of genes (that belongs to a collection of gene-sets)
GeneSet(String, String, GeneSets) - Constructor for class org.snpeff.geneSets.GeneSet
Create an empty gene set (that belongs to a collection of gene sets 'geneSets')
GeneSet(List<GeneSet>, GeneSets) - Constructor for class org.snpeff.geneSets.GeneSet
Create a new GeneSet by joining all GeneSets in the list
GeneSets - Class in org.snpeff.geneSets
A collection of GeneSets Genes have associated "experimental values"
GeneSets() - Constructor for class org.snpeff.geneSets.GeneSets
Default constructor
GeneSets(String) - Constructor for class org.snpeff.geneSets.GeneSets
 
GeneSets(GeneSets) - Constructor for class org.snpeff.geneSets.GeneSets
 
GeneSetsRanked - Class in org.snpeff.geneSets
A collection of GeneSets Genes are ranked (usually by 'value')
GeneSetsRanked() - Constructor for class org.snpeff.geneSets.GeneSetsRanked
Default constructor
GeneSetsRanked(String) - Constructor for class org.snpeff.geneSets.GeneSetsRanked
 
GeneSetsRanked(GeneSets) - Constructor for class org.snpeff.geneSets.GeneSetsRanked
 
geneSetsSorted() - Method in class org.snpeff.geneSets.GeneSets
Iterate through each GeneSet in this GeneSets
geneSetsSortedSize(boolean) - Method in class org.snpeff.geneSets.GeneSets
Gene sets sorted by size (if same size, sort by name).
genesSorted() - Method in class org.snpeff.geneSets.GeneSet
Return a sorted list of genes
GeneStats - Class in org.snpeff.geneSets
Some statistics about a gene
GeneStats() - Constructor for class org.snpeff.geneSets.GeneStats
 
geneType() - Method in class org.snpeff.interval.Gene
 
genome - Variable in class org.snpeff.fileIterator.MarkerFileIterator
 
genome - Variable in class org.snpeff.fileIterator.VcfHapMapFileIterator
 
genome - Variable in class org.snpeff.SnpEff
 
genome - Variable in class org.snpeff.snpEffect.Hgvs
 
genome - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
genome - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
genome - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
genome - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose
 
genome - Variable in class org.snpeff.snpEffect.testCases.unity.TestGenome
 
Genome - Class in org.snpeff.interval
This is just used for the Interval class.
Genome() - Constructor for class org.snpeff.interval.Genome
 
Genome(String) - Constructor for class org.snpeff.interval.Genome
 
Genome(String, Properties) - Constructor for class org.snpeff.interval.Genome
 
GENOME - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
genomeName - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
genomeName - Variable in class org.snpeff.snpEffect.testCases.unity.TestGenome
 
GENOMES_DIR - Static variable in class org.snpeff.snpEffect.Config
 
genomeVer - Variable in class org.snpeff.SnpEff
 
GenomicSequences - Class in org.snpeff.binseq
This class stores all "relevant" sequences in a genome This class is able to: i) Add all regions of interest ii) Store genomic sequences for those regions of interest iii) Retrieve genomic sequences by interval
GenomicSequences(Genome) - Constructor for class org.snpeff.binseq.GenomicSequences
 
genotype - Variable in class org.snpeff.interval.Variant
 
GENOTYPE - Enum constant in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
 
genotypeFields - Variable in class org.snpeff.vcf.VcfEntry
 
genotypeFieldsStr - Variable in class org.snpeff.vcf.VcfEntry
 
Genotypes - Class in org.snpeff.genotypes
Simple test program
Genotypes() - Constructor for class org.snpeff.genotypes.Genotypes
 
genotypeScores - Variable in class org.snpeff.vcf.VcfEntry
 
GenotypeStats - Class in org.snpeff.stats
Calculate statistics on genotype
GenotypeStats() - Constructor for class org.snpeff.stats.GenotypeStats
 
GenotypeVector - Class in org.snpeff.genotypes
A vector of genotypes in a 'compact' structure Note: Genotypes 0/0, 0/1, 1/0, 1/1 are stored in 2 bits.
GenotypeVector(int) - Constructor for class org.snpeff.genotypes.GenotypeVector
 
get() - Static method in class org.snpeff.binseq.coder.DnaCoder
 
get() - Static method in class org.snpeff.binseq.coder.DnaQualityCoder
 
get() - Static method in class org.snpeff.probablility.Binomial
 
get() - Static method in class org.snpeff.probablility.CochranArmitageTest
 
get() - Static method in class org.snpeff.probablility.FisherExactTest
 
get() - Static method in class org.snpeff.probablility.Hypergeometric
 
get() - Static method in class org.snpeff.probablility.RankSumNoReplacementPdf
 
get() - Static method in class org.snpeff.snpEffect.Config
 
get() - Method in class org.snpeff.snpEffect.VariantEffects
Get (or create) the latest ChangeEffect
get() - Method in class org.snpeff.stats.Counter
 
get() - Method in class org.snpeff.stats.CounterDouble
 
get(char) - Method in class org.snpeff.spliceSites.AcgtTree
Get a node
get(int) - Method in class org.snpeff.binseq.indexer.SequenceIndexer
Get sequence in entry number 'idx'
get(int) - Method in class org.snpeff.collections.OpenBitSet
Returns true or false for the specified bit index.
get(int) - Method in class org.snpeff.genotypes.GenotypeVector
 
get(int) - Method in class org.snpeff.interval.Markers
 
get(int) - Method in class org.snpeff.ped.PedGenotype
 
get(int) - Method in class org.snpeff.snpEffect.VariantEffects
 
get(long) - Method in class org.snpeff.collections.OpenBitSet
Returns true or false for the specified bit index
get(long) - Method in class org.snpeff.nmer.NmerCount
 
get(long) - Method in class org.snpeff.vcf.FileIndexChrPos
Get a byte from a file
get(long, int) - Method in class org.snpeff.vcf.FileIndexChrPos
Read 'len' bytes after 'bytePosition' or until a '\n' is reached.
get(String) - Method in class org.snpeff.coverage.CountFragments
 
get(String) - Method in class org.snpeff.coverage.Coverage
 
get(String) - Method in class org.snpeff.genBank.Feature
Get a qualifier by name
get(String) - Static method in class org.snpeff.interval.ChromosomeSimpleName
Get a simple name for the chromosome
get(String) - Method in class org.snpeff.interval.Genes
Obtain a gene interval
get(String) - Method in class org.snpeff.interval.IntervalAndSubIntervals
Obtain a subinterval
get(String) - Method in class org.snpeff.ped.PedPedigree
 
get(String) - Method in class org.snpeff.spliceSites.AcgtTree
Get node indexed by this string
get(String) - Method in class org.snpeff.stats.CountByType
How many counts of this type?
get(String) - Method in class org.snpeff.vcf.VcfConsequence
 
get(String) - Method in class org.snpeff.vcf.VcfGenotype
Get a genotype field
get(Nmer) - Method in class org.snpeff.nmer.NmerCount
Get kmer count
get(T) - Method in class org.snpeff.stats.CountByKey
How many counts of this type?
get3primeUtrs() - Method in class org.snpeff.interval.Transcript
Create a list of 3 prime UTRs
get3primeUtrsSorted() - Method in class org.snpeff.interval.Transcript
 
get5primeUtrs() - Method in class org.snpeff.interval.Transcript
Create a list of 5 prime UTRs
get5primeUtrsSorted() - Method in class org.snpeff.interval.Transcript
 
getAa() - Method in class org.snpeff.vcf.VcfEffect
 
getAaAlt() - Method in class org.snpeff.snpEffect.VariantEffect
 
getAaChange() - Method in class org.snpeff.snpEffect.VariantEffect
Amino acid change string (HGVS style)
getAaChangeColor(String, String) - Method in class org.snpeff.stats.VariantEffectStats
Background color used for AA change table
getAaChangeCount(String, String) - Method in class org.snpeff.stats.VariantEffectStats
How many changes from oldAa to newAa do we have?
getAaChangeOld() - Method in class org.snpeff.snpEffect.VariantEffect
Amino acid change string (old style)
getAaIdxEnd() - Method in class org.snpeff.interval.Exon
 
getAaIdxStart() - Method in class org.snpeff.interval.Exon
 
getAaLen() - Method in class org.snpeff.vcf.VcfEffect
 
getAaLength() - Method in class org.snpeff.snpEffect.VariantEffect
Amino acid length (negative if there is none)
getAaList() - Method in class org.snpeff.stats.VariantEffectStats
Get list of all amino acisd involved
getAaNetChange() - Method in class org.snpeff.snpEffect.VariantEffect
Net AA change (InDels)
getAaNumLeftEnd() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
getAaNumLeftStart() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
getAaNumRightEnd() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
getAaNumRightStart() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
getAaPos() - Method in class org.snpeff.vcf.VcfEffect
 
getAaRef() - Method in class org.snpeff.snpEffect.VariantEffect
 
getAasequence() - Method in class org.snpeff.genBank.Feature
Get translated amino acid sequence
getAcc() - Method in class org.snpeff.geneOntology.GoTerm
 
getAcceptor(int) - Method in class org.snpeff.spliceSites.SpliceTypes
 
getAcceptorsByIntron(String) - Method in class org.snpeff.spliceSites.SpliceTypes
 
getAccession() - Method in class org.snpeff.genBank.Features
 
getAccession() - Method in class org.snpeff.nextProt.NextProtXmlNode
 
getAintersectB() - Method in class org.snpeff.stats.MineTwoMarkerIntervals
 
getAlert() - Method in class org.snpeff.osCmd.StreamGobbler
 
getAlertNotify() - Method in class org.snpeff.osCmd.StreamGobbler
 
getAligmentScore() - Method in class org.snpeff.align.NeedlemanWunschOverlap
 
getAlignment() - Method in class org.snpeff.align.NeedlemanWunsch
 
getAlignment() - Method in class org.snpeff.align.NeedlemanWunschOverlap
 
getAlignmentByTrId() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
getAlignmentScore() - Method in class org.snpeff.align.NeedlemanWunsch
 
getAllele() - Method in class org.snpeff.vcf.VcfEffect
 
getAlleleCount() - Method in class org.snpeff.stats.GenotypeStats
 
getAlleleCountHistoUrl() - Method in class org.snpeff.stats.GenotypeStats
 
getAlleleFrequency() - Method in class org.snpeff.stats.GenotypeStats
 
getAlleleFrequencyHistoUrl() - Method in class org.snpeff.stats.GenotypeStats
 
getAllLines() - Method in class org.snpeff.osCmd.StreamGobbler
 
getAlt() - Method in class org.snpeff.interval.Variant
 
getAltIndex(String) - Method in class org.snpeff.vcf.VcfEntry
Get index of matching ALT entry
getAltRealign() - Method in class org.snpeff.align.VariantRealign
 
getAlts() - Method in class org.snpeff.vcf.VcfEntry
 
getAltsStr() - Method in class org.snpeff.vcf.VcfEntry
Create a comma separated ALTS string
getAndSet(int) - Method in class org.snpeff.collections.OpenBitSet
Sets a bit and returns the previous value.
getAndSet(long) - Method in class org.snpeff.collections.OpenBitSet
Sets a bit and returns the previous value.
getAnnotations() - Method in class org.snpeff.nextProt.NextProtXmlEntry
 
getArgs() - Method in class org.snpeff.fastq.FastqSplit
 
getArgs() - Method in class org.snpeff.SnpEff
 
getArgs() - Method in interface org.snpeff.snpEffect.commandLine.CommandLine
 
getArgs() - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
 
getAssembly() - Method in class org.snpeff.sam.SamHeaderRecordSq
 
getAttr(String) - Method in class org.snpeff.interval.GffMarker
 
getAvg() - Method in class org.snpeff.stats.Average
 
getAvg() - Method in class org.snpeff.stats.AverageInt
 
getBarSpace() - Method in class org.snpeff.stats.plot.GooglePlotInt
 
getBarWidth() - Method in class org.snpeff.stats.plot.GooglePlotInt
 
getBase(int) - Method in class org.snpeff.binseq.BinarySequence
Return the base at position 'index'
getBase(int) - Method in class org.snpeff.binseq.DnaAndQualitySequence
 
getBase(int) - Method in class org.snpeff.binseq.DnaNSequence
 
getBase(int) - Method in class org.snpeff.binseq.DnaSequence
 
getBase(int) - Method in class org.snpeff.binseq.DnaSequenceByte
 
getBaseFileNameGenes() - Method in class org.snpeff.snpEffect.Config
Genes file path (no extension)
getBaseFileNameMotif() - Method in class org.snpeff.snpEffect.Config
 
getBaseFileNameRegulation() - Method in class org.snpeff.snpEffect.Config
Regulation file (GFF format)
getBaseFileNameSequence() - Method in class org.snpeff.snpEffect.Config
 
getBases() - Method in class org.snpeff.stats.VariantStats
 
getBases(int, int) - Method in class org.snpeff.binseq.DnaNSequence
Get a few bases from this sequence
getBases(int, int) - Method in class org.snpeff.binseq.DnaSequence
Get a few bases from this sequence
getBasesChangesColor(String, String) - Method in class org.snpeff.stats.VariantStats
Background color used for base change table
getBasesChangesCount(String, String) - Method in class org.snpeff.stats.VariantStats
 
getBestOffset() - Method in class org.snpeff.overlap.Overlap
 
getBestScore() - Method in class org.snpeff.overlap.Overlap
 
getBestSequence() - Method in class org.snpeff.motif.Pwm
Get best matching sequence (highest score)
getBestSequenceStr() - Method in class org.snpeff.motif.Pwm
 
getBiotype() - Method in class org.snpeff.interval.GffMarker
 
getBiotype() - Method in class org.snpeff.snpEffect.VariantEffect
Get biotype
getBioType() - Method in class org.snpeff.interval.Gene
 
getBioType() - Method in class org.snpeff.interval.GffMarker
 
getBioType() - Method in class org.snpeff.interval.Transcript
 
getBioType() - Method in class org.snpeff.vcf.VcfEffect
 
getBioType(String) - Method in class org.snpeff.stats.GeneCountByTypeTable
 
getBiotypeGeneric() - Method in class org.snpeff.interval.GffMarker
 
getBit(int) - Method in class org.snpeff.collections.OpenBitSet
returns 1 if the bit is set, 0 if not.
getBits() - Method in class org.snpeff.collections.OpenBitSet
Expert: returns the long[] storing the bits
getBranchByIntron(String) - Method in class org.snpeff.spliceSites.SpliceTypes
 
getBranchU12(String) - Method in class org.snpeff.spliceSites.SpliceTypes
Add a SpliceSiteBranchU12 for this donor-Acceptor pair
getBucket(long) - Method in class org.snpeff.collections.HashLongLongArray
Return all values for a given key WARNING: Not all elements in a bucket are used.
getBucketLength(long) - Method in class org.snpeff.collections.HashLongLongArray
Return used length of a bucket
getBundleName(String) - Method in class org.snpeff.snpEffect.Config
Is this genome packed in a bundle?
getByChromo(String) - Method in class org.snpeff.spliceSites.TranscriptSet
 
getById(int) - Method in class org.snpeff.serializer.MarkerSerializer
 
getByPdbId(String) - Method in class org.snpeff.pdb.IdMapper
 
getByPdbId(String, String) - Method in class org.snpeff.pdb.IdMapper
 
getByTrId(String) - Method in class org.snpeff.pdb.IdMapper
 
getCacheFile() - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
 
getCatalyst() - Method in class org.snpeff.reactome.events.Reaction
 
getCategory() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
getcDnaLen() - Method in class org.snpeff.vcf.VcfEffect
 
getcDnaPos() - Method in class org.snpeff.snpEffect.VariantEffect
 
getcDnaPos() - Method in class org.snpeff.vcf.VcfEffect
 
getCds() - Method in class org.snpeff.interval.Transcript
Get all CDSs
getCdsEnd() - Method in class org.snpeff.interval.Transcript
 
getCdsLen() - Method in class org.snpeff.vcf.VcfEffect
 
getCdsLength() - Method in class org.snpeff.snpEffect.VariantEffect
CDS length (negative if there is none)
getCdsPos() - Method in class org.snpeff.vcf.VcfEffect
 
getCdsStart() - Method in class org.snpeff.interval.Transcript
 
getCenter() - Method in class org.snpeff.interval.tree.IntervalNode
 
getCenter() - Method in class org.snpeff.interval.tree.IntervalNodeOri
 
getChangeEffectResutStats() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
getChangeType() - Method in class org.snpeff.stats.VariantStats
 
getChangeTypeLength() - Method in class org.snpeff.stats.VariantStats
 
getChilds() - Method in class org.snpeff.geneOntology.GoTerm
 
getChr1() - Method in class org.snpeff.stats.TranslocationReport
 
getChr2() - Method in class org.snpeff.stats.TranslocationReport
 
getChrName(int) - Method in class org.snpeff.ped.PlinkMap
 
getChromo() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
 
getChromoFastaFiles() - Method in class org.snpeff.interval.Genome
 
getChromos() - Method in class org.snpeff.vcf.FileIndexChrPos
Available chromosomes
getChromoSequence() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
 
getChromosome() - Method in class org.snpeff.interval.Interval
 
getChromosome(int) - Method in class org.snpeff.gsa.ChrPosScoreList
 
getChromosome(String) - Method in class org.snpeff.fileIterator.MarkerFileIterator
Find chromosome 'chromoName'.
getChromosome(String) - Method in class org.snpeff.interval.Genome
Find chromosome 'chromoName'
getChromosomeCount() - Method in class org.snpeff.interval.Genome
 
getChromosomeLength(String) - Method in class org.snpeff.stats.VariantStats
Choromosome length
getChromosomeName() - Method in class org.snpeff.interval.Interval
Find chromosome name
getChromosomeName(int) - Method in class org.snpeff.gsa.ChrPosScoreList
 
getChromosomeNameOri() - Method in class org.snpeff.interval.Interval
 
getChromosomeNameOri() - Method in class org.snpeff.vcf.VcfEntry
Original chromosome name (as it appeared in the VCF file)
getChromosomeNamesEffective() - Method in class org.snpeff.stats.VariantStats
A list of chromosomes that had at least one change Note: Chromosome names are sorted.
getChromosomeNum() - Method in class org.snpeff.interval.Interval
Find chromosome and return it's number
getChromosomes() - Method in class org.snpeff.interval.Genome
 
getChromosomesSortedSize() - Method in class org.snpeff.interval.Genome
Return chromosomes sorted by size (largest chromosomes first)
getChrPosStats(String) - Method in class org.snpeff.stats.VariantStats
 
getChrPosStatsChartUrl(String) - Method in class org.snpeff.stats.VariantStats
 
getCigar() - Method in class org.snpeff.sam.SamEntry
 
getCode(int) - Method in class org.snpeff.binseq.BinarySequence
Return the code at position 'index'
getCode(int) - Method in class org.snpeff.binseq.DnaAndQualitySequence
 
getCode(int) - Method in class org.snpeff.binseq.DnaSequence
Return the base at position 'index'
getCode(int) - Method in class org.snpeff.binseq.DnaSequencePe
 
getCoder() - Method in class org.snpeff.binseq.BinarySequence
Get sequence encoder & decoder
getCoder() - Method in class org.snpeff.binseq.DnaAndQualitySequence
 
getCoder() - Method in class org.snpeff.binseq.DnaSequence
 
getCoder() - Method in class org.snpeff.binseq.DnaSequencePe
 
getCodes() - Method in class org.snpeff.binseq.DnaAndQualitySequence
 
getCodes() - Method in class org.snpeff.binseq.DnaSequence
 
getCodes() - Method in class org.snpeff.binseq.DnaSequenceByte
 
getCoding() - Method in class org.snpeff.vcf.VcfEffect
 
getCodon() - Method in class org.snpeff.vcf.VcfEffect
 
getCodonChange() - Method in class org.snpeff.snpEffect.VariantEffect
Codon change string
getCodonChangeColor(String, String) - Method in class org.snpeff.stats.VariantEffectStats
 
getCodonChangeCount(String, String) - Method in class org.snpeff.stats.VariantEffectStats
How many changes from oldCodo to newCodon do we have?
getCodonChangeMax() - Method in class org.snpeff.snpEffect.VariantEffect
Codon change string (if it's not too long)
getCodonIndex() - Method in class org.snpeff.snpEffect.VariantEffect
 
getCodonList() - Method in class org.snpeff.stats.VariantEffectStats
Get a list of all codons involved
getCodonNum() - Method in class org.snpeff.snpEffect.VariantEffect
 
getCodonsAlt() - Method in class org.snpeff.snpEffect.VariantEffect
 
getCodonsRef() - Method in class org.snpeff.snpEffect.VariantEffect
 
getCodonTable() - Method in class org.snpeff.interval.Chromosome
 
getColorHtml(String) - Method in class org.snpeff.stats.CountByType
Background color used for table (heatmap)
getCommandArgs() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
getCompartment() - Method in class org.snpeff.reactome.Entity
 
getConfig() - Method in class org.snpeff.SnpEff
 
getConfig() - Method in class org.snpeff.snpEffect.testCases.integration.CompareEffects
 
getConfigFile() - Method in class org.snpeff.SnpEff
 
getConfigFileName() - Method in class org.snpeff.snpEffect.Config
 
getConsequence() - Method in class org.snpeff.vcf.VcfConsequence
 
getCoordinates() - Method in class org.snpeff.snpEffect.Config
 
getCount() - Method in class org.snpeff.coverage.CoverageChr
 
getCount() - Method in class org.snpeff.stats.Average
 
getCount() - Method in class org.snpeff.stats.AverageInt
 
getCount() - Method in class org.snpeff.stats.Counter
 
getCount() - Method in class org.snpeff.stats.CounterDouble
 
getCount() - Method in class org.snpeff.stats.FloatStats
 
getCount() - Method in class org.snpeff.stats.IntStats
 
getCount() - Method in class org.snpeff.stats.VariantStats
Total number of variants
getCount(char, int) - Method in class org.snpeff.motif.Pwm
Get counts for a given position
getCount(int) - Method in class org.snpeff.stats.ChrPosStats
 
getCount(int) - Method in class org.snpeff.stats.IntStats
 
getCount(String) - Method in class org.snpeff.stats.CountByType
Count for this type
getCountBases() - Method in class org.snpeff.coverage.CountReads
 
getCountBases() - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
getCountByChangeType() - Method in class org.snpeff.stats.VariantStats
Number of variants by type
getCountByChromosome(String) - Method in class org.snpeff.stats.VariantStats
Number of changes by chromosome
getCountByEffect() - Method in class org.snpeff.stats.VariantEffectStats
 
getCountByFunctionalClass() - Method in class org.snpeff.stats.VariantEffectStats
 
getCountByGeneRegion() - Method in class org.snpeff.stats.VariantEffectStats
 
getCountByImpact() - Method in class org.snpeff.stats.VariantEffectStats
 
getCounter(String) - Method in class org.snpeff.stats.GeneCountByTypeTable
Get counter for this type
getCountErrors() - Method in class org.snpeff.stats.VariantEffectStats
 
getCounterSize(String) - Method in class org.snpeff.stats.GeneCountByTypeTable
Get size counter for this type
getCountExceptions() - Method in class org.snpeff.coverage.CountReads
 
getCountMarkers() - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
getCountMultiallelic() - Method in class org.snpeff.stats.VcfStats
 
getCountNonEmptyId() - Method in class org.snpeff.stats.VariantStats
 
getCountNonVariants() - Method in class org.snpeff.stats.VariantStats
 
getCountReads() - Method in class org.snpeff.coverage.CountReads
 
getCountTotalReads() - Method in class org.snpeff.coverage.CountReads
 
getCountTypes() - Method in class org.snpeff.coverage.CountReads
 
getCountWarnings() - Method in class org.snpeff.stats.VariantEffectStats
 
getCoverageByExons() - Method in class org.snpeff.coverage.CountReads
 
getCoverageByType() - Method in class org.snpeff.coverage.CountReads
 
getCvTerm() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
getCytoBands() - Method in class org.snpeff.interval.Genome
 
getData() - Method in class org.snpeff.logStatsServer.VersionCheck
Get page as string
getDatabaseCompatibilityVersions() - Method in class org.snpeff.snpEffect.Config
Return a list of databases that are compatible with this SnpEff version number
getDatabaseLocal(String) - Method in class org.snpeff.snpEffect.Config
Database local file for a specific database, such as 'dbSnp', 'ClinVar', etc.
getDatabaseLocalKey(String) - Method in class org.snpeff.snpEffect.Config
 
getDatabaseRepository() - Method in class org.snpeff.snpEffect.Config
 
getDatabaseRepository(String) - Method in class org.snpeff.snpEffect.Config
Database repository for a specific database, such as 'dbSnp', 'ClinVar', etc.
getDatabaseRepositoryUrl(String) - Method in class org.snpeff.snpEffect.Config
 
getDate() - Method in class org.snpeff.genBank.Features
 
getDbNsfpFields() - Method in class org.snpeff.snpEffect.Config
 
getDefaultValue() - Method in class org.snpeff.gsa.PvaluesList
 
getDefaultValue() - Method in class org.snpeff.gsa.ScoreList
 
getDefaultWaitTime() - Method in class org.snpeff.osCmd.OsCmdRunner
 
getDefinition() - Method in class org.snpeff.genBank.Features
 
getDerived() - Method in class org.snpeff.vcf.PedigreeEntry
 
getDerivedNum() - Method in class org.snpeff.vcf.PedigreeEntry
 
getDescription() - Method in class org.snpeff.geneOntology.GoTerm
 
getDescription() - Method in class org.snpeff.geneSets.GeneSet
 
getDescription() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
getDescription() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
getDirData() - Method in class org.snpeff.snpEffect.Config
Main data directory
getDirDataGenomeVersion() - Method in class org.snpeff.snpEffect.Config
Data dir for a specific genome version (i.e.
getDirMain() - Method in class org.snpeff.snpEffect.Config
Main dir
getDirRegulationBed() - Method in class org.snpeff.snpEffect.Config
Directory where regulation 'BED' files are
getDistance() - Method in class org.snpeff.snpEffect.VariantEffect
 
getDistance() - Method in class org.snpeff.vcf.VcfEffect
 
getDistanceResults() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
getDistanceStats() - Method in class org.snpeff.stats.MineMarkerIntervals
 
getDivision() - Method in class org.snpeff.genBank.Features
 
getDnaSequence() - Method in class org.snpeff.interval.Chromosome
 
getDoesAintersectB() - Method in class org.snpeff.stats.MineTwoMarkerIntervals
 
getDoesBintersectA() - Method in class org.snpeff.stats.MineTwoMarkerIntervals
 
getDonor(int) - Method in class org.snpeff.spliceSites.SpliceTypes
 
getDonorAccPairSize() - Method in class org.snpeff.spliceSites.SpliceTypes
 
getDonorByIntron(String) - Method in class org.snpeff.spliceSites.SpliceTypes
 
getDouble(String, double) - Method in class org.snpeff.snpEffect.Config
Get a property as a double
getDownstream() - Method in class org.snpeff.interval.Transcript
 
getEffectDetails() - Method in class org.snpeff.vcf.VcfEffect
 
getEffectImpact() - Method in class org.snpeff.snpEffect.VariantEffect
Return impact of this effect
getEffectsStr() - Method in class org.snpeff.vcf.VcfEffect
 
getEffectsStrSo() - Method in class org.snpeff.vcf.VcfEffect
 
getEffectType() - Method in class org.snpeff.snpEffect.VariantEffect
Highest effect type
getEffectType() - Method in class org.snpeff.vcf.VcfEffect
 
getEffectTypes() - Method in class org.snpeff.snpEffect.VariantEffect
Highest effect type
getEffectTypes() - Method in class org.snpeff.vcf.VcfEffect
 
getEffectTypesStr() - Method in class org.snpeff.vcf.VcfEffect
 
getEffectTypeString(boolean) - Method in class org.snpeff.snpEffect.VariantEffect
 
getEffectTypeString(boolean, boolean) - Method in class org.snpeff.snpEffect.VariantEffect
 
getEffectTypeString(boolean, boolean, EffFormatVersion) - Method in class org.snpeff.snpEffect.VariantEffect
Get Effect Type as a string
getEffString() - Method in class org.snpeff.vcf.VcfEffect
 
getEnd() - Method in class org.snpeff.genBank.Feature
 
getEnd() - Method in class org.snpeff.interval.Interval
 
getEnd(int) - Method in class org.snpeff.gsa.ChrPosScoreList
 
getEnd(String) - Method in class org.snpeff.vcf.FileIndexChrPos
Get position where 'chr' ends
getEndPoint() - Method in class org.snpeff.interval.VariantBnd
 
getEntries() - Method in class org.snpeff.pdb.IdMapper
 
getError() - Method in class org.snpeff.osCmd.OsCmdRunner
 
getError() - Method in class org.snpeff.snpEffect.VariantEffect
 
getErrorsWarning() - Method in class org.snpeff.vcf.VcfEffect
 
getExitValue() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
getExitValue() - Method in class org.snpeff.osCmd.OsCmdRunner
 
getExon() - Method in class org.snpeff.snpEffect.VariantEffect
Get exon (if any)
getExonAfter() - Method in class org.snpeff.interval.Intron
 
getExonBefore() - Method in class org.snpeff.interval.Intron
 
getExonId() - Method in class org.snpeff.vcf.VcfEffect
 
getExons() - Method in class org.snpeff.interval.Transcript
A more intuitive name for 'subintervals'
getFamilyId() - Method in class org.snpeff.ped.PedPedigree
 
getFamilyId() - Method in class org.snpeff.ped.TfamEntry
 
getFatherId() - Method in class org.snpeff.ped.TfamEntry
 
getFeature() - Method in class org.snpeff.vcf.VcfConsequence
 
getFeatureId() - Method in class org.snpeff.vcf.VcfEffect
 
getFeatures() - Method in class org.snpeff.genBank.Features
 
getFeatureType() - Method in class org.snpeff.vcf.VcfEffect
 
getFieldByName(String) - Method in class org.snpeff.vcf.VcfEffect
Get a subfield by name
getFieldNames() - Method in class org.snpeff.fileIterator.GuessTableTypes
 
getFieldNames() - Method in class org.snpeff.vcf.VcfConsequenceHeader
 
getFieldNum(String) - Method in class org.snpeff.vcf.VcfConsequenceHeader
 
getFileListGenomeFasta() - Method in class org.snpeff.snpEffect.Config
Filenames for reference sequence (fasta files)
getFileName() - Method in class org.snpeff.fileIterator.GuessTableTypes
 
getFileNameCds() - Method in class org.snpeff.snpEffect.Config
 
getFileNameGenomeFasta() - Method in class org.snpeff.snpEffect.Config
Filename for reference sequence (fasta file) Scans the list of files 'getFileListGenomeFasta()' and finds the first file that exists
getFileNameProteins() - Method in class org.snpeff.snpEffect.Config
 
getFileNameSequence() - Method in class org.snpeff.snpEffect.Config
 
getFileNameSequence(String) - Method in class org.snpeff.snpEffect.Config
 
getFilePointer() - Method in class org.snpeff.fileIterator.FileIterator
Get position within file
getFilePointer() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
getFileSnpEffectPredictor() - Method in class org.snpeff.snpEffect.Config
 
getFilter() - Method in class org.snpeff.vcf.VcfEntry
 
getFirst() - Method in class org.snpeff.util.Tuple
 
getFirstChild() - Method in class org.snpeff.geneOntology.GoTerm
Return first child in the list
getFirstCodingExon() - Method in class org.snpeff.interval.Transcript
Get first coding exon
getFirstParent() - Method in class org.snpeff.geneOntology.GoTerm
Return first parent in the list
getFlag() - Method in class org.snpeff.sam.SamEntry
 
getFormat() - Method in class org.snpeff.vcf.VcfEntry
 
getFormatFields() - Method in class org.snpeff.vcf.VcfEntry
 
getFormatVersion() - Method in class org.snpeff.vcf.VcfEffect
 
getFrame() - Method in class org.snpeff.interval.Cds
 
getFrame() - Method in class org.snpeff.interval.Exon
 
getFrame() - Method in class org.snpeff.interval.GffMarker
 
getFrame() - Method in interface org.snpeff.interval.MarkerWithFrame
 
getFunClass() - Method in class org.snpeff.vcf.VcfEffect
 
getFunctionalClass() - Method in class org.snpeff.snpEffect.VariantEffect
Return functional class of this effect (i.e.
getGap() - Method in class org.snpeff.binseq.DnaSequencePe
 
getGene() - Method in class org.snpeff.interval.Transcript
 
getGene() - Method in class org.snpeff.snpEffect.VariantEffect
 
getGene() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
getGene() - Method in class org.snpeff.snpEffect.VariantEffectStructural
 
getGene(String) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Obtain a gene by geneId
getGeneBiotype() - Method in class org.snpeff.interval.GffMarker
 
getGeneByName(String) - Method in class org.snpeff.interval.Genes
Obtain a gene by GeneName WARNING: The first match is returned.
getGeneCount() - Method in class org.snpeff.geneSets.GeneSet
Number of symbols in this node (total = interesting + not-interesting)
getGeneCount() - Method in class org.snpeff.geneSets.GeneSets
How many genes do we have?
getGeneCountByEffectTable() - Method in class org.snpeff.stats.VariantEffectStats
 
getGeneCountByImpactTable() - Method in class org.snpeff.stats.VariantEffectStats
 
getGeneCountByRegionTable() - Method in class org.snpeff.stats.VariantEffectStats
 
getGeneId() - Method in class org.snpeff.genBank.Feature
 
getGeneId() - Method in class org.snpeff.gsa.ScoreList
 
getGeneId() - Method in class org.snpeff.interval.GffMarker
 
getGeneId() - Method in class org.snpeff.vcf.VcfEffect
 
getGeneId() - Method in class org.snpeff.vcf.VcfLof
 
getGeneIds() - Method in class org.snpeff.gtex.Gtex
 
getGeneIds() - Method in class org.snpeff.reactome.Entity
 
getGeneLeft() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
getGeneName() - Method in class org.snpeff.genBank.Feature
Get gene name from feature
getGeneName() - Method in class org.snpeff.interval.Gene
 
getGeneName() - Method in class org.snpeff.interval.GffMarker
 
getGeneName() - Method in class org.snpeff.vcf.VcfEffect
 
getGeneName() - Method in class org.snpeff.vcf.VcfLof
 
getGeneName1() - Method in class org.snpeff.stats.TranslocationReport
 
getGeneName2() - Method in class org.snpeff.stats.TranslocationReport
 
getGeneRegion() - Method in enum class org.snpeff.snpEffect.EffectType
 
getGeneRegion() - Method in class org.snpeff.snpEffect.VariantEffect
 
getGeneRight() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
getGenes() - Method in class org.snpeff.geneSets.GeneSet
 
getGenes() - Method in class org.snpeff.geneSets.GeneSets
Get all genes in this set
getGenes() - Method in class org.snpeff.interval.Genome
 
getGenes() - Method in class org.snpeff.snpEffect.VariantEffect
 
getGenes() - Method in class org.snpeff.snpEffect.VariantEffectStructural
 
getGeneSet(String) - Method in class org.snpeff.geneSets.GeneSets
Get a gene set named 'geneSetName'
getGeneSetCount() - Method in class org.snpeff.geneSets.GeneSets
Get number of gene sets
getGeneSetCount() - Method in class org.snpeff.geneSets.Result
 
getGeneSetCountLast() - Method in class org.snpeff.geneSets.Result
 
getGeneSets() - Method in class org.snpeff.geneSets.GeneSet
 
getGeneSets() - Method in class org.snpeff.geneSets.Result
 
getGeneSetsByGene(String) - Method in class org.snpeff.geneSets.GeneSets
All gene sets that this gene belongs to
getGeneSetsByName() - Method in class org.snpeff.geneSets.GeneSets
 
getGenesSorted() - Method in class org.snpeff.interval.Genome
Create a sorted list of genes (sorted by gene Id)
getGenesSortedPos() - Method in class org.snpeff.interval.Genome
Create a sorted list of genes (sorted by genomic position)
getGenome() - Method in class org.snpeff.fileIterator.MarkerFileIterator
 
getGenome() - Method in class org.snpeff.interval.Interval
Find genome
getGenome() - Method in class org.snpeff.snpEffect.Config
 
getGenome() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
getGenome(String) - Method in class org.snpeff.snpEffect.Config
 
getGenomeId() - Method in class org.snpeff.interval.Genome
 
getGenomeLen() - Method in class org.snpeff.stats.VariantStats
Genome length
getGenomeLenEffective() - Method in class org.snpeff.stats.VariantStats
Genome effective length: The sum of length of every chromosome that had a change (e.g.
getGenomeName() - Method in class org.snpeff.interval.Interval
Find genome name
getGenomeVersion() - Method in class org.snpeff.snpEffect.Config
 
getGenomicSequences() - Method in class org.snpeff.interval.Genome
 
getGenotype() - Method in class org.snpeff.interval.Variant
 
getGenotype() - Method in class org.snpeff.interval.VariantNonRef
 
getGenotype() - Method in class org.snpeff.snpEffect.VariantEffect
Get genotype string
getGenotype() - Method in class org.snpeff.vcf.VcfEffect
 
getGenotype() - Method in class org.snpeff.vcf.VcfGenotype
Get genotype numbers as an array E.g.
getGenotype(int) - Method in class org.snpeff.ped.PedEntry
Get genotype WARNING: Empty string means that no genotpye is available
getGenotype(int) - Method in class org.snpeff.vcf.VcfGenotype
Get genotype string by index WARNING: If the genotype is missing, it returns an empty string.
getGenotype(String) - Method in class org.snpeff.ped.PedEntry
Get phenotype by String ID
getGenotypeCode() - Method in class org.snpeff.vcf.VcfGenotype
Return as a genotype SNP code: -1: if missing data of more than one ALT 0: if aa (0/0) 1: if Aa (0/1 or 1/0) 2: if AA (1/1) WARNING: In multi-allelic case, any non-ref is treated as ALT
getGenotypeCodeIgnoreMissing() - Method in class org.snpeff.vcf.VcfGenotype
Return as a genotype SNP code: 0: if aa (0/0) or any missing value 1: if Aa (0/1 or 1/0) 2: if AA (1/1)
getGenotypeNames() - Method in class org.snpeff.ped.PedEntry
Get all genotype names WARNING: the returned string collection is unsorted!
getGenotypeNames() - Method in class org.snpeff.ped.PlinkMap
 
getGenotypeNames(String) - Method in class org.snpeff.ped.PlinkMap
 
getGenotypes() - Method in class org.snpeff.ped.PedEntry
 
getGenotypes() - Method in class org.snpeff.ped.PedGenotype
 
getGenotypesScores() - Method in class org.snpeff.vcf.VcfEntry
Return genotypes parsed as an array of codes
getGenotypeStats() - Method in class org.snpeff.stats.VcfStats
 
getGenotypeStr() - Method in class org.snpeff.vcf.VcfGenotype
Return genotypes as string (e.g.
getGffParentId(boolean) - Method in class org.snpeff.interval.GffMarker
 
getGffParentIds() - Method in class org.snpeff.interval.GffMarker
Parent can have multiple, comma separated entries
getGffType() - Method in class org.snpeff.interval.GffMarker
 
getGoTerm(String) - Method in class org.snpeff.geneOntology.GoTerms
 
getGoTerms() - Method in class org.snpeff.geneOntology.GoTerm
 
getGoTermsByGoTermAcc() - Method in class org.snpeff.geneOntology.GoTerms
 
getGoTermsBySymbolId() - Method in class org.snpeff.geneOntology.GoTerms
 
getGoTermsBySymbolId(String) - Method in class org.snpeff.geneOntology.GoTerms
 
getGtex() - Method in class org.snpeff.gtex.GtexExperiment
 
getHandler() - Method in class org.snpeff.nextProt.NextProtXmlEntry
 
getHead() - Method in class org.snpeff.osCmd.ExecuteOsCommand
First lines of stdout
getHead() - Method in class org.snpeff.osCmd.OsCmdRunner
 
getHead() - Method in class org.snpeff.osCmd.StreamGobbler
Head: First HEAD_SIZE lines of this output
getHeader() - Method in class org.snpeff.fileIterator.FastaFileIterator
Current sequence header
getHeaders() - Method in class org.snpeff.fileIterator.SamFileIterator
 
getHeadStderr() - Method in class org.snpeff.osCmd.ExecuteOsCommand
First lines of stderr
getHeadStderr() - Method in class org.snpeff.osCmd.OsCmdRunner
 
getHetBySampleUrl() - Method in class org.snpeff.stats.GenotypeStats
 
getHgvs() - Method in class org.snpeff.snpEffect.VariantEffect
Change in HGVS notation
getHgvsC() - Method in class org.snpeff.stats.TranslocationReport
 
getHgvsC() - Method in class org.snpeff.vcf.VcfEffect
 
getHgvsDna() - Method in class org.snpeff.snpEffect.VariantEffect
Change in HGVS (Dna) notation
getHgvsDna() - Method in class org.snpeff.vcf.VcfConsequence
 
getHgvsDna() - Method in class org.snpeff.vcf.VcfEffect
 
getHgvsP() - Method in class org.snpeff.stats.TranslocationReport
 
getHgvsP() - Method in class org.snpeff.vcf.VcfEffect
 
getHgvsProt() - Method in class org.snpeff.snpEffect.VariantEffect
Change in HGVS (Protein) notation
getHgvsProt() - Method in class org.snpeff.vcf.VcfConsequence
 
getHgvsProt() - Method in class org.snpeff.vcf.VcfEffect
 
getHomBySampleUrl() - Method in class org.snpeff.stats.GenotypeStats
 
getHomHetTable() - Method in class org.snpeff.stats.GenotypeStats
 
getId() - Method in class org.snpeff.binseq.DnaAndQualitySequenceWithId
 
getId() - Method in class org.snpeff.binseq.DnaSequenceId
 
getId() - Method in class org.snpeff.gtex.GtexExperiment
 
getId() - Method in class org.snpeff.interval.Interval
 
getId() - Method in class org.snpeff.motif.Pwm
 
getId() - Method in class org.snpeff.pdb.DistanceResult
 
getId() - Method in class org.snpeff.ped.TfamEntry
 
getId() - Method in class org.snpeff.reactome.Entity
 
getId() - Method in class org.snpeff.sam.SamEntry
 
getId() - Method in class org.snpeff.vcf.VcfHeaderEntry
 
getId(int) - Method in class org.snpeff.ped.PlinkMap
 
getId2geneName() - Method in class org.snpeff.reactome.GeneIds
 
getId2refseqId() - Method in class org.snpeff.reactome.GeneIds
 
getId2refseqProtId() - Method in class org.snpeff.reactome.GeneIds
 
getId2tr() - Method in class org.snpeff.reactome.GeneIds
 
getIdByMarker(Marker) - Method in class org.snpeff.serializer.MarkerSerializer
 
getIdentifiers() - Method in class org.snpeff.nextProt.NextProtXmlEntry
 
getIds(String) - Method in class org.snpeff.gtex.IdMap
Get all IDs corresponding to this name
getImpact() - Method in class org.snpeff.stats.TranslocationReport
 
getImpact() - Method in class org.snpeff.vcf.VcfEffect
 
getIndelLen() - Method in class org.snpeff.stats.VariantStats
 
getIndelLenHistoUrl() - Method in class org.snpeff.stats.VariantStats
 
getIndex() - Method in class org.snpeff.stats.TranslocationReport
 
getIndex(String) - Method in class org.snpeff.gtex.Gtex
 
getInfo(String) - Method in class org.snpeff.vcf.VcfEntry
Get info string
getInfo(String, String) - Method in class org.snpeff.vcf.VcfEntry
Get info string for a specific allele
getInfo(String, Variant) - Method in class org.snpeff.vcf.VcfEntry
Get an INFO field matching a variant
getInfoFlag(String) - Method in class org.snpeff.vcf.VcfEntry
Does the entry exists?
getInfoFloat(String) - Method in class org.snpeff.vcf.VcfEntry
Get info field as a 'double' number The norm specifies data type as 'FLOAT', that is why the name of this method might be not intuitive
getInfoInt(String) - Method in class org.snpeff.vcf.VcfEntry
Get info field as an long number The norm specifies data type as 'INT', that is why the name of this method might be not intuitive
getInfoKeys() - Method in class org.snpeff.vcf.VcfEntry
Get all keys available in the info field
getInfoStr() - Method in class org.snpeff.vcf.VcfEntry
Get the full (unparsed) INFO field
getInputs() - Method in class org.snpeff.reactome.events.Reaction
 
getInstance() - Static method in class org.snpeff.codons.CodonTables
 
getInterestingGenes() - Method in class org.snpeff.geneSets.GeneSet
Get 'interesting' genes
getInterestingGenes() - Method in class org.snpeff.geneSets.GeneSets
 
getInterestingGenesCount() - Method in class org.snpeff.geneSets.GeneSet
Number of 'interesting' symbols
getInterestingGenesCount() - Method in class org.snpeff.geneSets.GeneSets
 
getInterestingSymbolIdSet() - Method in class org.snpeff.geneOntology.GoTerm
 
getInterestingSymbolIdsSet() - Method in class org.snpeff.geneOntology.GoTerms
 
getInterestingSymbolIdsSize() - Method in class org.snpeff.geneOntology.GoTerm
Number of 'interesting' symbols
getInterestingSymbolIdsSize() - Method in class org.snpeff.geneOntology.GoTerms
 
getIntervalForest() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
getIntervals() - Method in class org.snpeff.interval.tree.IntervalTree
 
getIntervals() - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
getIntervals() - Method in class org.snpeff.interval.tree.IntervalTreeOri
 
getIntervals() - Method in interface org.snpeff.interval.tree.Itree
 
getIntron() - Method in class org.snpeff.snpEffect.VariantEffect
Get intron (if any)
getIntronKeySet() - Method in class org.snpeff.spliceSites.SpliceTypes
 
getIsoform(String) - Method in class org.snpeff.nextProt.NextProtXmlEntry
Get or create an isoform
getIsoformsByAccession() - Method in class org.snpeff.nextProt.NextProtXmlEntry
 
getJobId() - Method in class org.snpeff.osCmd.OsCmdRunner
 
getKey() - Method in class org.snpeff.util.KeyValue
 
getKeyList() - Method in class org.snpeff.stats.GeneCountByTypeTable
Get a sorted list of keys
getKeywords() - Method in class org.snpeff.genBank.Features
 
getKnownRatio() - Method in class org.snpeff.stats.VariantStats
Ratio of known variants (the one with a non-empty ID) and total variants
getLabel() - Method in class org.snpeff.geneOntology.GoTerms
 
getLabel() - Method in class org.snpeff.geneSets.GeneSets
 
getLabel() - Method in class org.snpeff.interval.Custom
 
getLatestBucketLength() - Method in class org.snpeff.collections.HashLongLongArray
Get bucket length for latest bucket search WARNING: Obviously this is not a thread safe operation
getLatestGeneSet() - Method in class org.snpeff.geneSets.Result
 
getLatestReleaseDate() - Method in class org.snpeff.logStatsServer.VersionCheck
 
getLatestUrl() - Method in class org.snpeff.logStatsServer.VersionCheck
 
getLatestVersion() - Method in class org.snpeff.logStatsServer.VersionCheck
 
getLeft() - Method in class org.snpeff.interval.tree.IntervalNode
 
getLeft() - Method in class org.snpeff.interval.tree.IntervalNodeOri
 
getLength() - Method in class org.snpeff.binseq.DnaSequenceByte
 
getLength() - Method in class org.snpeff.sam.SamHeaderRecordSq
 
getLengthStats() - Method in class org.snpeff.stats.MineMarkerIntervals
 
getLevel() - Method in class org.snpeff.geneOntology.GoTerm
Calculate node's level
getLine() - Method in class org.snpeff.fileIterator.FileIterator
 
getLine() - Method in class org.snpeff.interval.GenericMarker
 
getLine() - Method in class org.snpeff.sam.SamEntry
 
getLine() - Method in class org.snpeff.vcf.LineChrPos
 
getLine() - Method in class org.snpeff.vcf.VcfEntry
Original VCF line (from file)
getLine(long) - Method in class org.snpeff.vcf.FileIndexChrPos
Get the line where 'pos' hits
getLineNum() - Method in class org.snpeff.fileIterator.FastqFileIterator
 
getLineNum() - Method in class org.snpeff.fileIterator.FileIterator
 
getLineNum() - Method in class org.snpeff.vcf.VcfEntry
 
getLines() - Method in class org.snpeff.vcf.VcfHeader
 
getLineSlow(long) - Method in class org.snpeff.vcf.FileIndexChrPos
A slow method for getLine
getLocations() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
getLocusName() - Method in class org.snpeff.genBank.Features
 
getLofDeleteProteinCodingBases() - Method in class org.snpeff.snpEffect.Config
 
getLofIgnoreProteinCodingAfter() - Method in class org.snpeff.snpEffect.Config
 
getLofIgnoreProteinCodingBefore() - Method in class org.snpeff.snpEffect.Config
 
getLogOdds(char, int) - Method in class org.snpeff.motif.Pwm
 
getLong(String, long) - Method in class org.snpeff.snpEffect.Config
Get a property as a long
getMapq() - Method in class org.snpeff.sam.SamEntry
 
getMarker() - Method in class org.snpeff.snpEffect.VariantEffect
 
getMarker() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
getMarker() - Method in class org.snpeff.snpEffect.VariantEffectStructural
 
getMarker(Genome) - Method in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
Create a MicroRnaBindingSite marker
getMarkerById(int) - Method in class org.snpeff.serializer.MarkerSerializer
 
getMarkers() - Method in class org.snpeff.interval.Markers
 
getMarkers() - Method in class org.snpeff.nextProt.NextProtMarkerFactory
 
getMarkers() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
getMarkerTypes() - Method in class org.snpeff.coverage.CountReads
 
getMarkerTypes() - Method in class org.snpeff.coverage.CountReadsOnMarkers
 
getMaturePeptideId() - Method in class org.snpeff.genBank.Feature
Create an ID based on a feature
getMax() - Method in class org.snpeff.stats.FloatStats
 
getMax() - Method in class org.snpeff.stats.IntStats
 
getMaxBins() - Method in class org.snpeff.stats.IntStats
 
getMaxBins() - Method in class org.snpeff.stats.plot.GoogleHistogram
 
getMaxCount() - Method in class org.snpeff.stats.IntStats
 
getMaxPvalueAdjusted() - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
getMaxRank() - Method in class org.snpeff.geneOntology.GoTerm
 
getMaxRank() - Method in class org.snpeff.geneOntology.GoTerms
 
getMaxRank() - Method in class org.snpeff.geneSets.GeneSet
 
getMaxRank() - Method in class org.snpeff.geneSets.GeneSetsRanked
Get maximum rank
getMd5() - Method in class org.snpeff.sam.SamHeaderRecordSq
 
getMean() - Method in class org.snpeff.stats.IntStats
 
getMedian() - Method in class org.snpeff.interval.Markers
Calculate the median point in this set of markers
getMedian() - Method in class org.snpeff.stats.IntStats
Calculate the median
getMin() - Method in class org.snpeff.stats.FloatStats
 
getMin() - Method in class org.snpeff.stats.IntStats
 
getMinCount() - Method in class org.snpeff.stats.IntStats
 
getMinOverlap() - Method in class org.snpeff.overlap.OverlapDnaSeq
 
getMissingBySampleUrl() - Method in class org.snpeff.stats.GenotypeStats
 
getMissingCategories() - Method in class org.snpeff.nextProt.NextProtHandler
 
getMoleculeType() - Method in class org.snpeff.genBank.Features
 
getMonitor() - Method in class org.snpeff.reactome.Reactome
 
getMonitorTrace() - Method in class org.snpeff.reactome.Reactome
 
getMotherId() - Method in class org.snpeff.ped.TfamEntry
 
getMultipleValues() - Method in class org.snpeff.fileIterator.GuessTableTypes
 
getN() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
getName() - Method in class org.snpeff.codons.CodonTable
 
getName() - Method in class org.snpeff.fileIterator.FastaFileIterator
Sequence name (first 'word') It extracts the characters after the leading '>' and before the first space, then removes leading 'chr', 'chr:', etc.
getName() - Method in class org.snpeff.geneSets.GeneSet
 
getName() - Method in class org.snpeff.interval.Intergenic
 
getName() - Method in class org.snpeff.interval.Markers
 
getName() - Method in class org.snpeff.interval.NextProt
 
getName() - Method in class org.snpeff.interval.Regulation
 
getName() - Method in class org.snpeff.interval.tree.IntervalForest
 
getName() - Method in class org.snpeff.motif.Pwm
 
getName() - Method in class org.snpeff.reactome.Entity
 
getName(String) - Method in class org.snpeff.snpEffect.Config
 
getNames(String) - Method in class org.snpeff.gtex.IdMap
Get all names corresponding to this Id
getNames2index() - Method in class org.snpeff.fileIterator.GuessTableTypes
 
getNameSpace() - Method in class org.snpeff.geneOntology.GoTerm
 
getNameSpace() - Method in class org.snpeff.geneOntology.GoTerms
 
getNewHeaderLines() - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
New lines to be added to header
getNextField() - Method in class org.snpeff.serializer.MarkerSerializer
 
getNextFieldBoolean() - Method in class org.snpeff.serializer.MarkerSerializer
 
getNextFieldInt() - Method in class org.snpeff.serializer.MarkerSerializer
 
getNextFieldMarker() - Method in class org.snpeff.serializer.MarkerSerializer
 
getNextFieldMarkers() - Method in class org.snpeff.serializer.MarkerSerializer
 
getNextId() - Method in class org.snpeff.serializer.MarkerSerializer
 
getNextSize(int) - Static method in class org.snpeff.collections.ArrayUtil
 
getNmer() - Method in class org.snpeff.nmer.Nmer
Set nmer (binary coded)
getNumber() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
getNumberLabelsXaxis() - Method in class org.snpeff.stats.plot.GooglePlotInt
 
getNumberOfSamples() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
getNumberOfSamples() - Method in class org.snpeff.vcf.VcfEntry
number of samples in this VCF file
getNumberOfSamples() - Method in class org.snpeff.vcf.VcfHeader
Number of samples
getNumTranscripts() - Method in class org.snpeff.vcf.VcfLof
 
getNumWords() - Method in class org.snpeff.collections.OpenBitSet
Expert: gets the number of longs in the array that are in use
getOffset() - Method in class org.snpeff.align.NeedlemanWunsch
 
getOrCreate(char) - Method in class org.snpeff.spliceSites.AcgtTree
Get a node (create it if it doesn't exist)
getOrCreate(K) - Method in class org.snpeff.collections.AutoHashMap
 
getOrCreate(K) - Method in class org.snpeff.collections.MultivalueHashMap
Get a list of values (or create it if not available)
getOrCreateChromosome(String) - Method in class org.snpeff.interval.Genome
Get or create a chromosome
getOrCreateChromosome(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Get a chromosome.
getOrCreateIsoform(String) - Method in class org.snpeff.nextProt.NextProtXmlEntry
 
getOrCreateTree(String) - Method in class org.snpeff.interval.tree.IntervalForest
Get (or create) an interval tree for ID
getOrCreateTreeChromo(String) - Method in class org.snpeff.interval.tree.IntervalForest
Get (or create) an interval tree based for "chromo" (chromosome name)
getOrganism() - Method in class org.snpeff.genBank.Features
 
getOriginal() - Method in class org.snpeff.vcf.PedigreeEntry
 
getOriginalNum() - Method in class org.snpeff.vcf.PedigreeEntry
 
getOsCmd() - Method in class org.snpeff.osCmd.OsCmdRunner
 
getOutput() - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
getOutput() - Method in class org.snpeff.reactome.Entity
 
getOutput() - Method in class org.snpeff.SnpEff
 
getOutputs() - Method in class org.snpeff.reactome.events.Reaction
 
getOverlapFilter() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
 
getParent() - Method in class org.snpeff.interval.Interval
 
getParent() - Method in class org.snpeff.interval.Marker
 
getParentId() - Method in class org.snpeff.interval.MarkerParentId
 
getParents() - Method in class org.snpeff.geneOntology.GoTerm
 
getPedigree() - Method in class org.snpeff.vcf.VcfHeader
Get pedigree (if any)
getPercentAffected() - Method in class org.snpeff.vcf.VcfLof
 
getPercentAffectedStr() - Method in class org.snpeff.vcf.VcfLof
 
getPhenotype() - Method in class org.snpeff.ped.TfamEntry
 
getPlinkMap() - Method in class org.snpeff.ped.PedFileIterator
 
getPlinkMap() - Method in class org.snpeff.ped.PedPedigree
 
getPlotGene() - Method in class org.snpeff.stats.VariantEffectStats
Barplot of different gene regions
getPlotMaxData() - Method in class org.snpeff.stats.plot.GooglePlotInt
 
getPlotSizeX() - Method in class org.snpeff.stats.plot.GooglePlotInt
 
getPlotSizeY() - Method in class org.snpeff.stats.plot.GooglePlotInt
 
getPnext() - Method in class org.snpeff.sam.SamEntry
 
getPos() - Method in class org.snpeff.sam.SamEntry
 
getPos1OneBased() - Method in class org.snpeff.stats.TranslocationReport
Get position (as one-based coordinates)
getPos2OneBased() - Method in class org.snpeff.stats.TranslocationReport
Get position (as one-based coordinates)
getPosition() - Method in class org.snpeff.ped.PedGenotype
 
getPosition(int) - Method in class org.snpeff.ped.PlinkMap
 
getProb() - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
getProgress() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
getProgress() - Method in class org.snpeff.osCmd.OsCmdRunner
 
getProgress() - Method in interface org.snpeff.osCmd.Progress
 
getProteinByTrId() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
getProteinByTrId() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
 
getProteinIds() - Method in class org.snpeff.nextProt.NextProtXmlIsoform
 
getPvalue() - Method in class org.snpeff.geneSets.Result
 
getPvalueAdjusted() - Method in class org.snpeff.geneSets.Result
P-Value adjusted using
getPvalueDouble() - Method in class org.snpeff.geneSets.Result
 
getPwd() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
getPwm() - Method in class org.snpeff.interval.Motif
 
getPwm(String) - Method in class org.snpeff.motif.Jaspar
 
getPwmId() - Method in class org.snpeff.interval.Motif
 
getPwmName() - Method in class org.snpeff.interval.Motif
 
getQname() - Method in class org.snpeff.sam.SamEntry
 
getQual() - Method in class org.snpeff.sam.SamEntry
 
getQuality() - Method in class org.snpeff.binseq.DnaAndQualitySequence
Get quality string (encoded FastQ-Sanger style)
getQuality() - Method in class org.snpeff.vcf.VcfEntry
 
getQuality(int) - Method in class org.snpeff.binseq.DnaAndQualitySequence
 
getQualityStats() - Method in class org.snpeff.stats.VcfStats
 
getQualityStatsHistoUrl() - Method in class org.snpeff.stats.VcfStats
 
getQuantile(double) - Method in class org.snpeff.stats.IntStats
Get value at a given quantile
getRank() - Method in class org.snpeff.interval.Exon
 
getRank() - Method in class org.snpeff.interval.Intron
 
getRank() - Method in class org.snpeff.vcf.VcfEffect
 
getRank(String) - Method in class org.snpeff.geneOntology.GoTerms
Get symbol's rank
getRank(String) - Method in class org.snpeff.geneSets.GeneSetsRanked
Get gene's rank
getRankByGene() - Method in class org.snpeff.geneSets.GeneSetsRanked
Get geneId <-> Rank mapping
getRankedGenesCount() - Method in class org.snpeff.geneSets.GeneSet
 
getRankedSetsCount() - Method in class org.snpeff.geneSets.GeneSetsRanked
How many gene sets have ranked genes (i.e.
getRankedSymbols() - Method in class org.snpeff.geneOntology.GoTerm
 
getRankMax() - Method in class org.snpeff.vcf.VcfEffect
 
getRankSum() - Method in class org.snpeff.geneSets.GeneSet
 
getRankSum() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
getRankSymbolId() - Method in class org.snpeff.geneOntology.GoTerms
 
getRareThreshold() - Method in class org.snpeff.codons.FindRareAaIntervals
 
getRateOfChange() - Method in class org.snpeff.stats.VariantStats
Rate of change
getRateOfChangeByChromosome(String) - Method in class org.snpeff.stats.VariantStats
Rate of change by chromosome
getRawCountBases() - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
getRawCountMarkers() - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
getReadLengthAvg() - Method in class org.snpeff.coverage.CountReads
Average read length
getReadLengthAvg() - Method in class org.snpeff.coverage.CountReadsOnMarkers
Average read length
getReadLengthCount() - Method in class org.snpeff.coverage.CountReads
 
getReadLengthSum() - Method in class org.snpeff.coverage.CountReads
 
getRecords(String) - Method in class org.snpeff.sam.SamHeader
Get a list of records for this 'recordType'
getRecordTypeCode() - Method in class org.snpeff.sam.SamHeaderRecord
 
getRedirectStderr() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
getRedirectStdout() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
getRedirectTo() - Method in class org.snpeff.osCmd.StreamGobbler
 
getRef() - Method in class org.snpeff.vcf.VcfEntry
 
getReference() - Method in class org.snpeff.interval.Variant
 
getReference(int, int) - Static method in class org.snpeff.binseq.comparator.SequenceReference
 
getReference(String) - Method in class org.snpeff.snpEffect.Config
 
getReferences() - Method in class org.snpeff.genBank.Features
 
getRefRealign() - Method in class org.snpeff.align.VariantRealign
 
getRegFileNames() - Method in class org.snpeff.RegulationFileSplitBytType
 
getRegTypes() - Method in class org.snpeff.RegulationFileConsensus
 
getRegTypes() - Method in class org.snpeff.RegulationFileSplitBytType
 
getRegulationList(String) - Method in class org.snpeff.RegulationFileConsensus
Get regulation list by type (or create a new list)
getRegulationType() - Method in class org.snpeff.interval.Regulation
 
getRegulator() - Method in class org.snpeff.reactome.events.Reaction
 
getRes() - Method in class org.snpeff.logStatsServer.LogStats
 
getRight() - Method in class org.snpeff.interval.tree.IntervalNode
 
getRight() - Method in class org.snpeff.interval.tree.IntervalNodeOri
 
getRname() - Method in class org.snpeff.sam.SamEntry
 
getRnext() - Method in class org.snpeff.sam.SamEntry
 
getSampleIds() - Method in class org.snpeff.ped.PedPedigree
Get a list of sample IDs
getSampleNames() - Method in class org.snpeff.fileIterator.VcfFileIterator
Get sample names
getSampleNames() - Method in class org.snpeff.vcf.VcfHeader
Get sample names
getSampleNum(String) - Method in class org.snpeff.vcf.VcfHeader
Sample number (position in "#CHROM" line)
getSamples() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
getScore() - Method in class org.snpeff.interval.Custom
 
getScore() - Method in class org.snpeff.interval.VariantWithScore
 
getScore(int) - Method in class org.snpeff.gsa.ChrPosScoreList
 
getScore(int) - Method in class org.snpeff.gsa.ScoreList
 
getScore(String) - Method in class org.snpeff.stats.CountByType
Score for this type
getSecond() - Method in class org.snpeff.util.Tuple
 
getSeq() - Method in class org.snpeff.sam.SamEntry
 
getSeq1() - Method in class org.snpeff.binseq.DnaSequencePe
 
getSeq2() - Method in class org.snpeff.binseq.DnaSequencePe
 
getSeqIdx(long) - Static method in class org.snpeff.binseq.comparator.SequenceReference
 
getSequence() - Method in class org.snpeff.binseq.BinarySequence
Get the sequence as a String
getSequence() - Method in class org.snpeff.binseq.DnaAndQualitySequence
 
getSequence() - Method in class org.snpeff.binseq.DnaSequence
 
getSequence() - Method in class org.snpeff.binseq.DnaSequencePe
 
getSequence() - Method in class org.snpeff.genBank.Features
 
getSequence() - Method in class org.snpeff.interval.Chromosome
 
getSequence() - Method in class org.snpeff.interval.MarkerSeq
Get sequence WARNING: Sequence is always according to coding strand.
getSequence() - Method in class org.snpeff.interval.Utr5prime
 
getSequence() - Method in class org.snpeff.nextProt.NextProtXmlIsoform
 
getSequence(Marker) - Method in class org.snpeff.interval.MarkerSeq
Get sequence intersecting 'marker' WARNING: Sequence is always according to coding strand.
getSequenceLength() - Method in class org.snpeff.genBank.Features
 
getSequenceName() - Method in class org.snpeff.sam.SamHeaderRecordSq
 
getSex() - Method in class org.snpeff.ped.TfamEntry
 
getShape() - Method in class org.snpeff.genBank.Features
 
getShrinkSize(int, int) - Static method in class org.snpeff.collections.ArrayUtil
 
getSilentRatio() - Method in class org.snpeff.stats.VariantEffectStats
 
getSizeByType(String, String) - Method in class org.snpeff.stats.GeneCountByTypeTable
 
getSnpEffCmdCds() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
 
getSnpEffCmdProtein() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
 
getSnpEffectPredictor() - Method in class org.snpeff.snpEffect.Config
 
getSource() - Method in class org.snpeff.genBank.Features
 
getSpecies() - Method in class org.snpeff.interval.Genome
 
getSpecies() - Method in class org.snpeff.sam.SamHeaderRecordSq
 
getSpliceRegionExonSize() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
getSpliceRegionIntronMax() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
getSpliceRegionIntronMin() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
getSpliceSites() - Method in class org.snpeff.interval.Exon
 
getSpliceSites() - Method in class org.snpeff.interval.Intron
 
getSpliceType() - Method in class org.snpeff.interval.Exon
 
getSpliceType() - Method in class org.snpeff.interval.Intron
 
getSplitFileNames() - Method in class org.snpeff.fastq.FastqSplit
 
getStart() - Method in class org.snpeff.genBank.Feature
 
getStart() - Method in class org.snpeff.interval.Interval
 
getStart(int) - Method in class org.snpeff.gsa.ChrPosScoreList
 
getStart(long) - Static method in class org.snpeff.binseq.comparator.SequenceReference
 
getStart(String) - Method in class org.snpeff.vcf.FileIndexChrPos
Get position where 'chr' starts
getStd() - Method in class org.snpeff.stats.IntStats
Calculate the standard deviation
getStderr() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
getStderr() - Method in class org.snpeff.osCmd.OsCmdRunner
 
getStdin() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
getStdout() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
getStdout() - Method in class org.snpeff.osCmd.OsCmdRunner
 
getStdOutFilter() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
getStr() - Method in class org.snpeff.vcf.VcfEntry
 
getStrand() - Method in class org.snpeff.interval.Interval
 
getString(String) - Method in class org.snpeff.snpEffect.Config
Get a property as a string
getString(String, String) - Method in class org.snpeff.snpEffect.Config
Get a property as a string
getStructure(String) - Method in class org.snpeff.pdb.PdbFile
Opens filename, parses it and returns aStructure object .
getSubType(Marker) - Method in class org.snpeff.coverage.MarkerTypes
Some markers have sub-types
getSum() - Method in class org.snpeff.stats.Average
 
getSum() - Method in class org.snpeff.stats.AverageInt
 
getSum() - Method in class org.snpeff.stats.FloatStats
 
getSum() - Method in class org.snpeff.stats.IntStats
 
getSvgPlot() - Method in class org.snpeff.stats.TranslocationReport
 
getSymbolIdSet() - Method in class org.snpeff.geneOntology.GoTerm
Number of symbols in this node (total = interesting + not-interesting)
getTable(String) - Method in class org.snpeff.codons.CodonTables
Get a codon table by name
getTable(Genome) - Method in class org.snpeff.codons.CodonTables
Get default genome-wide codon table
getTable(Genome, String) - Method in class org.snpeff.codons.CodonTables
Get a codon table WARNING: It will return the standard codon table if nothing if found
getTissueType() - Method in class org.snpeff.gtex.GtexExperiment
 
getTissueTypeDetail() - Method in class org.snpeff.gtex.GtexExperiment
 
getTitle() - Method in class org.snpeff.stats.plot.GooglePlotInt
 
getTlen() - Method in class org.snpeff.sam.SamEntry
 
getTotal() - Method in class org.snpeff.stats.ChrPosStats
 
getTotalCount() - Method in class org.snpeff.geneOntology.GoTerm
Number of symbols in this node (total = interesting + not-interesting)
getTotalCount() - Method in class org.snpeff.motif.Pwm
 
getTotalCount() - Method in class org.snpeff.spliceSites.AcgtTree
 
getTotalCount() - Method in class org.snpeff.stats.CountByType
 
getTotalErrors() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
getTotalErrs() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
getTotalNotFound() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
getTotalOk() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
getTotalWarnings() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
getTranscript() - Method in class org.snpeff.snpEffect.VariantEffect
 
getTranscript(String) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
getTranscriptBiotype() - Method in class org.snpeff.interval.GffMarker
 
getTranscriptId() - Method in class org.snpeff.fileIterator.FastaFileIterator
Get transcript name from FASTA header (ENSEMBL protein files) Format example: '>ENSP00000356130 pep:known chromosome:GRCh37:1:205111633:205180694:-1 gene:ENSG00000133059 transcript:ENST00000367162'
getTranscriptId() - Method in class org.snpeff.genBank.Feature
Create a transcript ID based on a feature
getTranscriptId() - Method in class org.snpeff.interval.GffMarker
 
getTranscriptId() - Method in class org.snpeff.interval.NextProt
 
getTranscriptId() - Method in class org.snpeff.vcf.VcfEffect
 
getTranscriptIds() - Method in class org.snpeff.nextProt.NextProtXmlIsoform
 
getTranscriptSupportLevel() - Method in class org.snpeff.interval.Transcript
 
getTranscriptVersion() - Method in class org.snpeff.interval.GffMarker
 
getTransitions() - Method in class org.snpeff.stats.TsTvStats
 
getTransversions() - Method in class org.snpeff.stats.TsTvStats
 
getTree(String) - Method in class org.snpeff.interval.tree.IntervalForest
Get an interval tree using an ID
getTreeChromo(String) - Method in class org.snpeff.interval.tree.IntervalForest
Get an interval tree using a chromosome name
getTrId1() - Method in class org.snpeff.stats.TranslocationReport
 
getTrId2() - Method in class org.snpeff.stats.TranslocationReport
 
getTrLeft() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
getTrRight() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
getTss() - Method in class org.snpeff.interval.Transcript
Create a TSS marker
getTsTvRatio() - Method in class org.snpeff.stats.TsTvStats
Transitions / transverions ratio WARNING: I removed the '2.0' factor because it mostly confused people.
getTsTvStats() - Method in class org.snpeff.stats.VcfStats
 
getTsTvStatsKnown() - Method in class org.snpeff.stats.VcfStats
 
getType() - Method in class org.snpeff.genBank.Feature
 
getType() - Method in class org.snpeff.interval.Marker
 
getType(String) - Method in class org.snpeff.fileIterator.GuessTableTypes
Get field type
getType(Marker) - Method in class org.snpeff.coverage.MarkerTypes
Get marker type
getTypeList() - Method in class org.snpeff.stats.CountByType
List all types (alphabetically sorted) We need it as a getter for summary page (freemarker)
getTypeList() - Method in class org.snpeff.stats.GeneCountByTypeTable
Get a sorted list of keys
getTypeRank(Marker) - Method in class org.snpeff.coverage.MarkerTypes
Get marker + rank (in case of exon or intron)
getTypes() - Method in class org.snpeff.fileIterator.GuessTableTypes
Get an array of types (ordered by column)
getUpDownStreamLength() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
getUpstream() - Method in class org.snpeff.interval.Transcript
 
getUri() - Method in class org.snpeff.sam.SamHeaderRecordSq
 
getUtrs() - Method in class org.snpeff.interval.Transcript
Get all UTRs
getValue() - Method in class org.snpeff.util.KeyValue
 
getValue(int) - Method in class org.snpeff.gtex.GtexExperiment
 
getValue(String) - Method in class org.snpeff.geneSets.GeneSets
Get experimental value
getValue(String) - Method in class org.snpeff.gtex.GtexExperiment
Get value by geneID
getValueByGene() - Method in class org.snpeff.geneSets.GeneSets
 
getValues() - Method in class org.snpeff.fileIterator.MatrixEntry
Get an array of values
getVariant() - Method in class org.snpeff.snpEffect.VariantEffect
 
getVariantEffect() - Method in class org.snpeff.stats.TranslocationReport
 
getVariantRealigned() - Method in class org.snpeff.align.VariantRealign
 
getVariantRef() - Method in class org.snpeff.interval.VariantNonRef
 
getvariantStats() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
getVariantType() - Method in class org.snpeff.align.VcfRefAltAlign
 
getVariantType() - Method in class org.snpeff.interval.Variant
 
getVcfEffect() - Method in class org.snpeff.stats.TranslocationReport
 
getVcfEffects() - Method in class org.snpeff.vcf.VcfEntry
 
getVcfEffects(EffFormatVersion) - Method in class org.snpeff.vcf.VcfEntry
Parse 'EFF' info field and get a list of effects
getVcfEntry() - Method in class org.snpeff.vcf.VariantVcfEntry
 
getVcfEntry() - Method in class org.snpeff.vcf.VcfGenotype
 
getVcfEntry() - Method in class org.snpeff.vcf.VcfLof
 
getVcfFieldString() - Method in class org.snpeff.vcf.VcfEffect
String from VCF file (original, unparsed, string)
getVcfFieldString(int) - Method in class org.snpeff.vcf.VcfEffect
Get a subfield as an index
getVcfFileIterator() - Method in class org.snpeff.vcf.VcfEntry
 
getVcfGenotype(int) - Method in class org.snpeff.vcf.VcfEntry
 
getVcfGenotypes() - Method in class org.snpeff.vcf.VcfEntry
 
getVcfHeader() - Method in class org.snpeff.fileIterator.VcfFileIterator
Get VcfHeader
getVcfHeaderFormat() - Method in class org.snpeff.vcf.VcfHeader
 
getVcfHeaderFormat(String) - Method in class org.snpeff.vcf.VcfHeader
 
getVcfHeaderInfo() - Method in class org.snpeff.vcf.VcfHeader
Get all VcfInfo entries
getVcfHeaderInfo(String) - Method in class org.snpeff.vcf.VcfHeader
Get Info type for a given ID
getVcfInfo(String) - Method in class org.snpeff.vcf.VcfEntry
Get VcfInfo type for a given ID
getVcfInfoNumber() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
getVcfInfoNumber(String) - Method in class org.snpeff.vcf.VcfEntry
Get Info number for a given ID
getVcfInfoType() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
getVersion() - Method in class org.snpeff.genBank.Features
 
getVersion() - Method in class org.snpeff.interval.Genome
 
getVersion() - Method in class org.snpeff.interval.Transcript
 
getVersionsUrl() - Method in class org.snpeff.snpEffect.Config
 
getWarnCount() - Static method in class org.snpeff.util.Log
 
getWarning() - Method in class org.snpeff.snpEffect.VariantEffect
 
getWeight() - Method in class org.snpeff.reactome.Entity
 
getxAxisLabel() - Method in class org.snpeff.stats.plot.GooglePlotInt
 
GFF - Enum constant in enum class org.snpeff.interval.FrameType
 
GFF_OFFSET - Static variable in class org.snpeff.fileIterator.MotifFileIterator
 
GFF_OFFSET - Static variable in class org.snpeff.fileIterator.RegulationGffFileIterator
 
GFF2 - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
 
GFF3 - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
 
Gff3FileIterator - Class in org.snpeff.fileIterator
Opens a sequence change file and iterates over all intervals in GFF3 format.
Gff3FileIterator(String) - Constructor for class org.snpeff.fileIterator.Gff3FileIterator
 
Gff3FileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.Gff3FileIterator
 
Gff3FileIterator(String, Genome, int) - Constructor for class org.snpeff.fileIterator.Gff3FileIterator
 
GffMarker - Class in org.snpeff.interval
An interval intended as a mark
GffMarker() - Constructor for class org.snpeff.interval.GffMarker
 
GffMarker(Genome, String) - Constructor for class org.snpeff.interval.GffMarker
 
GffMarker(Marker, int, int, boolean, String) - Constructor for class org.snpeff.interval.GffMarker
 
GffType - Enum Class in org.snpeff.interval
 
GoogleBarChart - Class in org.snpeff.stats.plot
 
GoogleBarChart(String) - Constructor for class org.snpeff.stats.plot.GoogleBarChart
 
GoogleBarChart(String, int, int) - Constructor for class org.snpeff.stats.plot.GoogleBarChart
 
GoogleChartVenn - Class in org.snpeff.stats.plot
A simple wrapper to goolge charts API (from charts4j) Plots integer data
GoogleChartVenn(String, String, String, int, int, int, int, int, int, int) - Constructor for class org.snpeff.stats.plot.GoogleChartVenn
 
GoogleGenePercentBar - Class in org.snpeff.stats.plot
A simple wrapper to goolge charts API (from charts4j)
GoogleGenePercentBar(String, String, String, double, double, double, double, double, double, double, double, double) - Constructor for class org.snpeff.stats.plot.GoogleGenePercentBar
 
GoogleGeneRegionChart - Class in org.snpeff.stats.plot
 
GoogleGeneRegionChart(CoverageByType, String) - Constructor for class org.snpeff.stats.plot.GoogleGeneRegionChart
 
GoogleGeneRegionNumExonsChart - Class in org.snpeff.stats.plot
 
GoogleGeneRegionNumExonsChart(CoverageByType, String, int) - Constructor for class org.snpeff.stats.plot.GoogleGeneRegionNumExonsChart
 
GoogleHistogram - Class in org.snpeff.stats.plot
A simple wrapper to goolge charts API (from charts4j)
GoogleHistogram(int[], int[], String, String, String) - Constructor for class org.snpeff.stats.plot.GoogleHistogram
 
GoogleLineChart - Class in org.snpeff.stats.plot
 
GoogleLineChart(String) - Constructor for class org.snpeff.stats.plot.GoogleLineChart
 
GoogleLineChart(String, int, int) - Constructor for class org.snpeff.stats.plot.GoogleLineChart
 
GooglePlot - Class in org.snpeff.stats.plot
A simple wrapper to goolge charts API (from charts4j)
GooglePlot(double[], double[], String, String, String) - Constructor for class org.snpeff.stats.plot.GooglePlot
 
GooglePlotInt - Class in org.snpeff.stats.plot
A simple wrapper to goolge charts API (from charts4j) Plots integer data
GooglePlotInt(int[], int[], String, String, String) - Constructor for class org.snpeff.stats.plot.GooglePlotInt
 
GoTerm - Class in org.snpeff.geneOntology
An instance of a GO term (a node in the DAG)
GoTerm(String, GoTerms, String, String) - Constructor for class org.snpeff.geneOntology.GoTerm
 
GoTerm(List<GoTerm>, GoTerms) - Constructor for class org.snpeff.geneOntology.GoTerm
Create a new GOTerm by joining all GOTerms in the list
GoTerms - Class in org.snpeff.geneOntology
A collection of GO terms
GoTerms() - Constructor for class org.snpeff.geneOntology.GoTerms
Default constructor
GoTerms(String, String, String, String, boolean, boolean) - Constructor for class org.snpeff.geneOntology.GoTerms
Constructor
Gpr - Class in org.snpeff.util
General pupose rutines
Gpr() - Constructor for class org.snpeff.util.Gpr
 
GprHtml - Class in org.snpeff.util
General stuff realted to HTML
GprHtml() - Constructor for class org.snpeff.util.GprHtml
 
GprSeq - Class in org.snpeff.util
 
GprSeq() - Constructor for class org.snpeff.util.GprSeq
 
greedyPvalue(Result) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum)
greedyPvalue(Result) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
Find best p-value using a greedy algorithm (smaller gene sets first)
greedyPvalue(Result, int, int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum) Only look for genesets within [minGeneSetSize, maxGeneSetSize] size range
group - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
grow(byte[]) - Static method in class org.snpeff.collections.ArrayUtil
 
grow(byte[], int) - Static method in class org.snpeff.collections.ArrayUtil
 
grow(int[]) - Static method in class org.snpeff.collections.ArrayUtil
 
grow(int[], int) - Static method in class org.snpeff.collections.ArrayUtil
 
grow(long[]) - Static method in class org.snpeff.collections.ArrayUtil
 
grow(long[], int) - Static method in class org.snpeff.collections.ArrayUtil
 
GT_FIELD_ALLELIC_DEPTH_OF_COVERAGE - Static variable in class org.snpeff.vcf.VcfGenotype
 
GT_FIELD_DEPTH_OF_COVERAGE - Static variable in class org.snpeff.vcf.VcfGenotype
 
Gtex - Class in org.snpeff.gtex
Load data from GTEx files.
Gtex() - Constructor for class org.snpeff.gtex.Gtex
 
GtexExperiment - Class in org.snpeff.gtex
A 'column' in a GTEx file (values from one experiment
GtexExperiment(Gtex, String) - Constructor for class org.snpeff.gtex.GtexExperiment
 
GtexExperiment(Gtex, String, String, String) - Constructor for class org.snpeff.gtex.GtexExperiment
 
GTF22 - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
 
Gtf2Marker - Class in org.snpeff.interval
An interval intended as a mark
Gtf2Marker() - Constructor for class org.snpeff.interval.Gtf2Marker
 
Gtf2Marker(Genome, String) - Constructor for class org.snpeff.interval.Gtf2Marker
 
Gtf2Marker(Marker, int, int, boolean, String) - Constructor for class org.snpeff.interval.Gtf2Marker
 
guessGenesFormat() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
Try to guess database format by checking which file type is present
guessNewLineChars() - Method in class org.snpeff.fileIterator.FileIterator
Guess number of newline characters used (e.g.
GuessTableTypes - Class in org.snpeff.fileIterator
Given a table in a TXT file, try to guess the value types for each column
GuessTableTypes(String) - Constructor for class org.snpeff.fileIterator.GuessTableTypes
 
guessType(String) - Method in class org.snpeff.fileIterator.GuessTableTypes
Guess data type for this value
guessTypes() - Method in class org.snpeff.fileIterator.GuessTableTypes
Find column names form header and guess data types from values
GZIP_EXTENTIONS - Static variable in class org.snpeff.util.Gpr
 

H

has(String) - Method in class org.snpeff.ped.PedGenotype
Is 'genotype' in this one?
hasAdditionalAnnotations() - Method in class org.snpeff.snpEffect.VariantEffect
Do we have an associated marker with additional annotations?
hasAnnotations() - Method in class org.snpeff.interval.Custom
Do we have additional annotations?
hasAnnotations() - Method in class org.snpeff.interval.GffMarker
When annotating a VCF file, add fields from this GFF
hasAttr(String) - Method in class org.snpeff.interval.GffMarker
 
hasCds() - Method in class org.snpeff.interval.Transcript
 
hasChromosome(String) - Method in class org.snpeff.binseq.GenomicSequences
Do we have sequence information for this chromosome?
hasChromosome(String) - Method in class org.snpeff.interval.Genome
Is this chromosome in this genome?
hasCodingInfo() - Method in class org.snpeff.interval.Genome
 
hasCount(String) - Method in class org.snpeff.stats.CountByType
 
hasCvTerm() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
hasData() - Method in class org.snpeff.stats.AlleleCountStats
 
hasData() - Method in class org.snpeff.stats.CountByType
 
hasData() - Method in class org.snpeff.stats.GenotypeStats
 
hasData() - Method in class org.snpeff.stats.HomHetStats
 
hasData() - Method in interface org.snpeff.stats.SamplingStats
Does this statistic have any data?
hasData() - Method in class org.snpeff.stats.TsTvStats
Does this stat have any data
hasData() - Method in class org.snpeff.stats.VariantEffectStats
 
hasData() - Method in class org.snpeff.stats.VariantStats
 
hasData() - Method in class org.snpeff.stats.VariantTypeStats
 
hasData() - Method in class org.snpeff.stats.VcfStats
 
hasEffect(String, String) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
Is effectExpected included in effStr (many effects delimited by '&'
hasEffectImpact(VariantEffect.EffectImpact) - Method in class org.snpeff.snpEffect.VariantEffect
 
hasEffectType(EffectType) - Method in class org.snpeff.snpEffect.VariantEffect
 
hasEffectType(EffectType) - Method in class org.snpeff.vcf.VcfEffect
Does it have 'effType' ?
hasError() - Method in class org.snpeff.interval.Transcript
Does this transcript have any errors?
hasError() - Method in class org.snpeff.snpEffect.VariantEffect
 
hasErrorOrWarning() - Method in class org.snpeff.interval.Transcript
Does this transcript have any errors?
hasField(String) - Method in class org.snpeff.vcf.VcfEntry
 
hasFormat(VcfHeaderFormat) - Method in class org.snpeff.vcf.VcfHeader
Do we already have this 'format' entry?
hasGene(String) - Method in class org.snpeff.geneSets.GeneSet
 
hasGene(String) - Method in class org.snpeff.geneSets.GeneSets
 
hasGenotypes() - Method in class org.snpeff.vcf.VcfEntry
 
hashCode() - Method in class org.snpeff.binseq.BinarySequence
 
hashCode() - Method in class org.snpeff.binseq.DnaAndQualitySequence
 
hashCode() - Method in class org.snpeff.binseq.DnaSequence
 
hashCode() - Method in class org.snpeff.binseq.DnaSequenceByte
 
hashCode() - Method in class org.snpeff.binseq.DnaSequencePe
 
hashCode() - Method in class org.snpeff.collections.OpenBitSet
 
hashCode() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
hashCode() - Method in class org.snpeff.interval.Interval
 
hashCode() - Method in class org.snpeff.interval.Variant
 
hashCode() - Method in class org.snpeff.nmer.Nmer
 
hashCode() - Method in class org.snpeff.util.KeyValue
 
hashCode() - Method in class org.snpeff.util.Tuple
 
hashCode(byte[], int, int) - Static method in class org.snpeff.collections.ArrayUtil
Returns hash of chars in range start (inclusive) to end (inclusive)
hashCode(char[], int, int) - Static method in class org.snpeff.collections.ArrayUtil
Returns hash of chars in range start (inclusive) to end (inclusive)
HashLongLongArray - Class in org.snpeff.collections
A Hash<long, long[]> using primitive types instead or warped object The idea is to be able to add many long values for each key This could be implemented by simply doing HashMap<Long, Set > (but it would consume much more memory) Note: We call each 'long[]' a bucket WARNING: This collection does NOT allow elements to be deleted! But you can replace values.
HashLongLongArray() - Constructor for class org.snpeff.collections.HashLongLongArray
 
hasInfo(String) - Method in class org.snpeff.vcf.VcfEntry
 
hasInfo(VcfHeaderInfo) - Method in class org.snpeff.vcf.VcfHeader
Do we already have this 'info' header?
hasIUB(String) - Static method in class org.snpeff.util.IubString
Does the string have ANY IUB base?
hasIUBMax(String) - Static method in class org.snpeff.util.IubString
Does the string have at most 'MAX_IUB_BASES' IUB bases?
hasMapq() - Method in class org.snpeff.sam.SamEntry
Some aligners just use '255' in the mapping quality field (bowtie)
hasMarker() - Method in class org.snpeff.snpEffect.VariantEffects
 
hasMultipleCoordinates() - Method in class org.snpeff.genBank.Feature
 
hasNext() - Method in class org.snpeff.fileIterator.BinSeqFileIterator
 
hasNext() - Method in class org.snpeff.fileIterator.FastqFileIterator
 
hasNext() - Method in class org.snpeff.fileIterator.FileIterator
 
hasNext() - Method in class org.snpeff.fileIterator.VariantTxtFileIterator
 
hasNext() - Method in class org.snpeff.genBank.FeaturesFile
 
hasNext() - Method in class org.snpeff.interval.IntervalSetIterator
 
hasNext() - Method in class org.snpeff.util.CombinatorialIterator
 
hasNext() - Method in class org.snpeff.util.IubString
 
hasOutput() - Method in class org.snpeff.reactome.Entity
 
hasQuality() - Method in class org.snpeff.vcf.VcfEntry
 
hasScore(String) - Method in class org.snpeff.stats.CountByType
 
hasSeek() - Method in class org.snpeff.fileIterator.FileIterator
Is 'seek' operation supported?
hasSequence() - Method in class org.snpeff.interval.MarkerSeq
Do we have a sequence for this exon?
hasTitle - Variable in class org.snpeff.fileIterator.TableFile
 
hasTranscriptSupportLevelInfo() - Method in class org.snpeff.interval.Genome
Do we have coding info from genes?
hasTranscriptSupportLevelInfo() - Method in class org.snpeff.interval.Transcript
 
hasTree(String) - Method in class org.snpeff.interval.tree.IntervalForest
Is the tree 'chromo' available?
hasValidCoords() - Method in class org.snpeff.pdb.DistanceResult
 
hasValue(String) - Method in class org.snpeff.geneSets.GeneSets
 
hasWarning() - Method in class org.snpeff.interval.Transcript
Does this transcript have any errors?
hasWarning() - Method in class org.snpeff.snpEffect.VariantEffect
 
head - Variable in class org.snpeff.interval.tree.IntervalTree
 
head - Variable in class org.snpeff.interval.tree.IntervalTreeOri
 
head(Object) - Static method in class org.snpeff.util.Gpr
 
HEAD_SIZE - Static variable in class org.snpeff.osCmd.StreamGobbler
 
header - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
 
heatMapColor(double, double, double, int, int) - Static method in class org.snpeff.util.GprHtml
Create a color (heat-map) based in a value and maximum possible value
heatMapColor(long, long, long, int, int) - Static method in class org.snpeff.util.GprHtml
Create a color (heat-map) based in a value and maximum possible value
help - Variable in class org.snpeff.SnpEff
 
hgvs - Variable in class org.snpeff.SnpEff
 
Hgvs - Class in org.snpeff.snpEffect
HGSV notation References: http://www.hgvs.org/
Hgvs(VariantEffect) - Constructor for class org.snpeff.snpEffect.Hgvs
 
HgvsDna - Class in org.snpeff.snpEffect
Coding DNA reference sequence References http://www.hgvs.org/mutnomen/recs.html Nucleotide numbering: - there is no nucleotide 0 - nucleotide 1 is the A of the ATG-translation initiation codon - the nucleotide 5' of the ATG-translation initiation codon is -1, the previous -2, etc.
HgvsDna(VariantEffect) - Constructor for class org.snpeff.snpEffect.HgvsDna
 
hgvsForce - Variable in class org.snpeff.SnpEff
 
hgvsOld - Variable in class org.snpeff.SnpEff
 
hgvsOneLetterAa - Variable in class org.snpeff.SnpEff
 
HgvsProtein - Class in org.snpeff.snpEffect
Coding change in HGVS notation (amino acid changes) References: http://www.hgvs.org/mutnomen/recs.html
HgvsProtein(VariantEffect) - Constructor for class org.snpeff.snpEffect.HgvsProtein
 
hgvsShift - Variable in class org.snpeff.SnpEff
 
hgvsTrId - Variable in class org.snpeff.SnpEff
 
hgvsTrId - Variable in class org.snpeff.snpEffect.Hgvs
 
HIGH - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
 
highestImpact(String) - Method in class org.snpeff.snpEffect.VariantEffects
Find the highest impact effect for transcript 'trId'
HIGHLY_CONSERVED_AA_COUNT - Static variable in class org.snpeff.nextProt.NextProtSequenceConservation
 
HIGHLY_CONSERVED_AA_PERCENT - Static variable in class org.snpeff.nextProt.NextProtSequenceConservation
 
hline(int) - Method in class org.snpeff.svg.Svg
 
HOME - Static variable in class org.snpeff.PromoterSequences
 
HOME - Static variable in class org.snpeff.util.Gpr
 
HomHetStats - Class in org.snpeff.stats
Count Hom/Het per sample From Pierre: For multiple ALT, I suggest to count the number of REF allele 0/1 => ALT1 0/2 => ALT1 1/1 => ALT2 2/2 => ALT2 1/2 => ALT2
HomHetStats() - Constructor for class org.snpeff.stats.HomHetStats
 
html() - Method in class org.snpeff.coverage.CountReadsOnMarkers
Show charts in html
HTML_BG_COLOR - Static variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
HTML_BG_COLOR_TITLE - Static variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
HTML_HEIGHT - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
HTML_TD_GENES_MAX_LEN - Static variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
HTML_WIDTH - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
HTTP_PROTOCOL - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
 
HUGE_DELETION_RATIO_THRESHOLD - Static variable in class org.snpeff.interval.Variant
 
HUGE_DELETION_SIZE_THRESHOLD - Static variable in class org.snpeff.interval.Variant
 
hypergeometric(int, int, int, int) - Method in class org.snpeff.probablility.Hypergeometric
See http://en.wikipedia.org/wiki/Hypergeometric_distribution
Hypergeometric - Class in org.snpeff.probablility
Calculate hypergeometric distribution using an optimized algorithm that avoids problems with big factorials.

I

id - Variable in class org.snpeff.fileIterator.MatrixEntry
 
id - Variable in class org.snpeff.interval.Interval
 
id - Variable in class org.snpeff.reactome.Entity
 
id - Variable in class org.snpeff.vcf.VcfHeaderEntry
 
id() - Static method in class org.snpeff.binseq.IdGenerator
 
id() - Method in class org.snpeff.svg.Svg
 
id() - Method in class org.snpeff.svg.SvgTranscript
 
ID - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
idChain() - Method in class org.snpeff.interval.Marker
 
idChain(String, String, boolean) - Method in class org.snpeff.interval.Marker
 
idChain(String, String, boolean, VariantEffect) - Method in class org.snpeff.interval.Marker
A list of all IDs and parent IDs until chromosome
IdGenerator - Class in org.snpeff.binseq
Generates Id
IdGenerator() - Constructor for class org.snpeff.binseq.IdGenerator
 
IdMap - Class in org.snpeff.gtex
Maps many IDs to many Names I.e.
IdMap() - Constructor for class org.snpeff.gtex.IdMap
 
IdMapper - Class in org.snpeff.pdb
Map IDs
IdMapper() - Constructor for class org.snpeff.pdb.IdMapper
 
IdMapperEntry - Class in org.snpeff.pdb
An entry in a ID mapping file
IdMapperEntry(String, String) - Constructor for class org.snpeff.pdb.IdMapperEntry
 
IG_C_gene - Enum constant in enum class org.snpeff.interval.BioType
 
IG_C_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
IG_D_gene - Enum constant in enum class org.snpeff.interval.BioType
 
IG_J_gene - Enum constant in enum class org.snpeff.interval.BioType
 
IG_J_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
IG_V_gene - Enum constant in enum class org.snpeff.interval.BioType
 
IG_V_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
ignoreChromosomeErrors - Variable in class org.snpeff.fileIterator.MarkerFileIterator
 
ignoreErrors - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
ignoreProteinCodingAfter - Variable in class org.snpeff.snpEffect.LossOfFunction
 
ignoreProteinCodingBefore - Variable in class org.snpeff.snpEffect.LossOfFunction
 
implicit - Variable in class org.snpeff.vcf.VcfHeaderInfo
 
imprecise - Variable in class org.snpeff.interval.Variant
 
inc() - Method in class org.snpeff.stats.Counter
 
inc() - Method in class org.snpeff.stats.CounterDouble
 
inc() - Method in class org.snpeff.util.CombinatorialIterator
 
inc(char) - Method in class org.snpeff.spliceSites.AcgtTree
Increment counter for a base
inc(int, int) - Method in class org.snpeff.coverage.CoverageChr
Increment a region
inc(String) - Method in class org.snpeff.stats.CountByType
 
inc(String, int) - Method in class org.snpeff.stats.CountByType
Increment counter for a given type
inc(String, int, int) - Method in class org.snpeff.coverage.CountFragments
Increment a region
inc(String, int, int) - Method in class org.snpeff.coverage.Coverage
Increment a region
inc(T) - Method in class org.snpeff.stats.CountByKey
Increment (by 1)
inc(T, int) - Method in class org.snpeff.stats.CountByKey
Increment counter for a given type
includes(Marker) - Method in class org.snpeff.interval.Marker
Is 'interval' completely included in 'this'?
index() - Method in class org.snpeff.vcf.FileIndexChrPos
Index chromosomes in the whole file
indexOf(String) - Method in class org.snpeff.binseq.DnaAndQualitySequence
Find the position of 'seq' in this sequence
info - Variable in class org.snpeff.vcf.VcfEntry
 
info(Object) - Static method in class org.snpeff.util.Log
Show absolute timer value and a message on STDERR
INFO_KEY_PATTERN - Static variable in class org.snpeff.vcf.VcfEntry
 
INFO_LINE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
 
INFO_PREFIX - Static variable in class org.snpeff.vcf.VcfHeader
 
INFO_REALIGN_3_PRIME - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
infoFieldName() - Method in enum class org.snpeff.vcf.EffFormatVersion
Get INF field name for corresponding format
infoFieldName(EffFormatVersion) - Static method in class org.snpeff.vcf.VcfEffect
Get info field name based on format version
infoln(Object) - Static method in class org.snpeff.util.Log
Show absolute timer value and a message on STDERR (prepend a newline)
infoStr - Variable in class org.snpeff.vcf.VcfEntry
 
init() - Method in class org.snpeff.fileIterator.VcfFileIterator
 
init() - Method in class org.snpeff.sam.SamHeaderRecord
Initialize records before parsing
init() - Method in class org.snpeff.sam.SamHeaderRecordSq
 
init() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
init() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCds
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDel
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDels
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIns
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesMnps
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSnps
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
 
init() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
 
init(boolean, boolean) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
 
init(String, int) - Method in class org.snpeff.fileIterator.FileIterator
Initialize
init(String, int) - Method in class org.snpeff.fileIterator.MarkerFileIterator
Initialize
initFields() - Method in class org.snpeff.fileIterator.TableFile
Map field names to Field objects
INITIAL_BASES_EXTRA - Static variable in class org.snpeff.align.VariantRealign
 
INITIAL_BASES_MULTIPLIER - Static variable in class org.snpeff.align.VariantRealign
 
INITIAL_CAPACITY - Static variable in class org.snpeff.interval.tree.IntervalTreeArray
 
initialize() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
Load all data
initRand() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
initRand() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMarkerSeq
 
initRand() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
initRand() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
 
initRand() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntStats
 
initSamples() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
Initialize samples (ranks: 1 to N)
initSnpEffPredictor() - Method in class org.snpeff.snpEffect.testCases.integration.CompareEffects
 
initSnpEffPredictor() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
initSnpEffPredictor() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBaseApply
 
initSnpEffPredictor(boolean, boolean) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
Create a predictor
initSnpEffPredictor(Gene[]) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
Create a predictor For the default parameters the first predictor created has only one transcript: 1:880-1001, strand: +, id:transcript_0, Protein Exons: 1:880-1001 'exon_0_0', rank: 1, frame: ., sequence: taaccccatatgattagtacggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgatgaccgatttatttgattccccacatttatttcatcggga CDS : taaccccatatgattagtacggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgatgaccgatttatttgattccccacatttatttcatcgggac Protein : *PHMISTVEEKHLTPIEQDLFRNTLYR*PIYLIPHIYFIG?
initStrand() - Method in class org.snpeff.snpEffect.Hgvs
 
inOffset - Variable in class org.snpeff.fileIterator.MarkerFileIterator
 
inputs - Variable in class org.snpeff.reactome.events.Reaction
 
inputStream2StringBuffer(InputStream) - Static method in class org.snpeff.util.Gpr
 
ins() - Method in class org.snpeff.snpEffect.HgvsProtein
Insertions Insertions add one or more amino acid residues between two existing amino acids and this insertion is not a copy of a sequence immediately 5'-flanking (see Duplication).
INS - Enum constant in enum class org.snpeff.interval.Variant.VariantType
 
inSync - Variable in class org.snpeff.interval.tree.IntervalTree
 
inSync - Variable in class org.snpeff.interval.tree.IntervalTreeArray
 
inSync - Variable in class org.snpeff.interval.tree.IntervalTreeOri
 
Integer - Enum constant in enum class org.snpeff.vcf.VcfInfoType
 
IntegrationTest - Class in org.snpeff.snpEffect.testCases.integration
Base class for integration tests
IntegrationTest() - Constructor for class org.snpeff.snpEffect.testCases.integration.IntegrationTest
 
interaction - Variable in class org.snpeff.SnpEff
 
Intergenic - Class in org.snpeff.interval
Interval for in intergenic region
Intergenic() - Constructor for class org.snpeff.interval.Intergenic
 
Intergenic(Chromosome, int, int, boolean, String, String) - Constructor for class org.snpeff.interval.Intergenic
 
INTERGENIC - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
INTERGENIC_CONSERVED - Enum constant in enum class org.snpeff.interval.GffType
 
INTERGENIC_CONSERVED - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
IntergenicConserved - Class in org.snpeff.interval
Interval for a conserved intergenic region
IntergenicConserved() - Constructor for class org.snpeff.interval.IntergenicConserved
 
IntergenicConserved(Chromosome, int, int, boolean, String) - Constructor for class org.snpeff.interval.IntergenicConserved
 
intersect() - Method in class org.snpeff.interval.Markers
Perform the intersection of all overlapping sub-intervals
intersect(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
this = this AND other
intersect(Marker) - Method in class org.snpeff.interval.Marker
Intersect of two markers
intersect(Marker) - Method in class org.snpeff.interval.Markers
Intersection between 'marker' and all sub-intervals
intersect(Markers) - Method in class org.snpeff.interval.tree.IntervalForest
Return the intersection of 'markers' and this IntervalForest For each marker 'm' in 'markers' - query the tree to get all markers intersecting 'm' - create a new interval which is the intersection of 'm' with all the resutls from the previous query.
intersection(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
Intersects this term with 'goTerm' (intersects 'symbolIdSet' and 'interestingSymbolIdSet').
intersection(GeneSet) - Method in class org.snpeff.geneSets.GeneSet
Intersects this term with 'geneSet' (intersects 'geneSet' and 'interestingGeneSet').
intersectionCount(OpenBitSet, OpenBitSet) - Static method in class org.snpeff.collections.OpenBitSet
Returns the popcount or cardinality of the intersection of the two sets.
intersectMarkers - Variable in class org.snpeff.interval.tree.IntervalTreeArray
 
intersects(int, int) - Method in class org.snpeff.interval.Interval
Return true if this intersects '[iStart, iEnd]'
intersects(long) - Method in class org.snpeff.interval.Interval
 
intersects(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
returns true if the sets have any elements in common
intersects(Interval) - Method in class org.snpeff.interval.Interval
Return true if this intersects 'interval'
intersects(Marker) - Method in class org.snpeff.interval.Interval
Do the intervals intersect?
intersects(Markers, Marker) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
 
intersectsCoreSpliceSite(Marker) - Method in class org.snpeff.interval.SpliceSite
Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins.
intersectsCoreSpliceSite(Marker) - Method in class org.snpeff.interval.SpliceSiteAcceptor
 
intersectsCoreSpliceSite(Marker) - Method in class org.snpeff.interval.SpliceSiteBranch
These are NOT core splice sites
intersectsCoreSpliceSite(Marker) - Method in class org.snpeff.interval.SpliceSiteDonor
 
intersectsCoreSpliceSite(Marker) - Method in class org.snpeff.interval.SpliceSiteRegion
 
intersectsExons() - Method in class org.snpeff.interval.codonChange.CodonChange
Does the variant intersect any exons?
intersectSize(Marker) - Method in class org.snpeff.interval.Interval
How much do intervals intersect?
Interval - Class in org.snpeff.interval
A genomic interval.
Interval() - Constructor for class org.snpeff.interval.Interval
 
Interval(Interval, int, int, boolean, String) - Constructor for class org.snpeff.interval.Interval
 
INTERVAL - Enum constant in enum class org.snpeff.interval.Variant.VariantType
 
IntervalAndSubIntervals<T extends Marker> - Class in org.snpeff.interval
Interval that contains sub intervals.
IntervalAndSubIntervals() - Constructor for class org.snpeff.interval.IntervalAndSubIntervals
 
IntervalAndSubIntervals(Marker, int, int, boolean, String) - Constructor for class org.snpeff.interval.IntervalAndSubIntervals
 
IntervalComparatorByEnd - Class in org.snpeff.interval
Compare intervals by end position
IntervalComparatorByEnd() - Constructor for class org.snpeff.interval.IntervalComparatorByEnd
 
IntervalComparatorByEnd(boolean) - Constructor for class org.snpeff.interval.IntervalComparatorByEnd
 
IntervalComparatorByStart - Class in org.snpeff.interval
Compare intervals by start position
IntervalComparatorByStart() - Constructor for class org.snpeff.interval.IntervalComparatorByStart
 
IntervalComparatorByStart(boolean) - Constructor for class org.snpeff.interval.IntervalComparatorByStart
 
IntervalForest - Class in org.snpeff.interval.tree
A set of interval trees (e.g.
IntervalForest() - Constructor for class org.snpeff.interval.tree.IntervalForest
 
IntervalForest(Markers) - Constructor for class org.snpeff.interval.tree.IntervalForest
 
IntervalNode - Class in org.snpeff.interval.tree
Node for interval tree structure
IntervalNode() - Constructor for class org.snpeff.interval.tree.IntervalNode
 
IntervalNode(Markers) - Constructor for class org.snpeff.interval.tree.IntervalNode
 
IntervalNodeOri - Class in org.snpeff.interval.tree
The Node class contains the interval tree information for one single node
IntervalNodeOri() - Constructor for class org.snpeff.interval.tree.IntervalNodeOri
 
IntervalNodeOri(Markers) - Constructor for class org.snpeff.interval.tree.IntervalNodeOri
 
intervals - Variable in class org.snpeff.interval.tree.IntervalTree
 
intervals - Variable in class org.snpeff.interval.tree.IntervalTreeOri
 
intervalsCenter - Variable in class org.snpeff.interval.tree.IntervalNode
 
IntervalSetIterator - Class in org.snpeff.interval
Iterate over intervals.
IntervalSetIterator(Markers) - Constructor for class org.snpeff.interval.IntervalSetIterator
 
IntervalTree - Class in org.snpeff.interval.tree
An Interval Tree is essentially a map from intervals to objects, which can be queried for all data associated with a particular interval of point
IntervalTree() - Constructor for class org.snpeff.interval.tree.IntervalTree
Instantiate a new interval tree with no intervals
IntervalTree(Markers) - Constructor for class org.snpeff.interval.tree.IntervalTree
Instantiate an interval tree with a list of intervals
IntervalTreeArray - Class in org.snpeff.interval.tree
Interval tree structure using arrays This is slightly faster than the new IntervalTree implementation
IntervalTreeArray() - Constructor for class org.snpeff.interval.tree.IntervalTreeArray
 
IntervalTreeArray(Markers) - Constructor for class org.snpeff.interval.tree.IntervalTreeArray
Instantiate an interval tree with a list of intervals
IntervalTreeOri - Class in org.snpeff.interval.tree
An Interval Tree is essentially a map from intervals to objects, which can be queried for all data associated with a particular interval of point
IntervalTreeOri() - Constructor for class org.snpeff.interval.tree.IntervalTreeOri
Instantiate a new interval tree with no intervals
IntervalTreeOri(Markers) - Constructor for class org.snpeff.interval.tree.IntervalTreeOri
Instantiate an interval tree with a list of intervals
IntHisto - Class in org.snpeff.snpEffect
Histogram of integer numbers
IntHisto() - Constructor for class org.snpeff.snpEffect.IntHisto
 
intLen(int) - Method in class org.snpeff.binseq.DnaSequencePe
Calculate the length of a sequence
INTRAGENIC - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
intron() - Method in class org.snpeff.interval.codonChange.CodonChangeDel
 
intron() - Method in class org.snpeff.interval.codonChange.CodonChangeDup
Inversion does not intersect any exon
intron() - Method in class org.snpeff.interval.codonChange.CodonChangeStructural
Variant affect one intron
Intron - Class in org.snpeff.interval
Intron
Intron() - Constructor for class org.snpeff.interval.Intron
 
Intron(Transcript, int, int, boolean, String, Exon, Exon) - Constructor for class org.snpeff.interval.Intron
 
INTRON - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
INTRON_CONSERVED - Enum constant in enum class org.snpeff.interval.GffType
 
INTRON_CONSERVED - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
IntronConserved - Class in org.snpeff.interval
Interval for a conserved non-coding region in an intron
IntronConserved() - Constructor for class org.snpeff.interval.IntronConserved
 
IntronConserved(Transcript, int, int, boolean, String) - Constructor for class org.snpeff.interval.IntronConserved
 
intronHgsv(char[], int, int, String, String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
Intronic HGS notation
introns() - Method in class org.snpeff.interval.Transcript
Get all introns (lazy init)
IntStats - Class in org.snpeff.stats
A simple class that does some basic statistics on integer numbers
IntStats() - Constructor for class org.snpeff.stats.IntStats
 
INV - Enum constant in enum class org.snpeff.interval.Variant.VariantType
 
invalidateSorted() - Method in class org.snpeff.interval.IntervalAndSubIntervals
Invalidate sorted collections
is() - Method in class org.snpeff.stats.BooleanMutable
 
isAaCheck() - Method in class org.snpeff.interval.Transcript
 
isAdjustIfParentDoesNotInclude(Marker) - Method in class org.snpeff.interval.Exon
 
isAdjustIfParentDoesNotInclude(Marker) - Method in class org.snpeff.interval.Marker
Adjust parent if it does not include child?
isAdjustIfParentDoesNotInclude(Marker) - Method in class org.snpeff.interval.Transcript
 
isAlertDone() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
isAlertDone() - Method in class org.snpeff.osCmd.StreamGobbler
 
isAmbiguous(String) - Static method in class org.snpeff.util.GprSeq
Are there any ambiguous bases in this sequence?
isAnn() - Method in enum class org.snpeff.vcf.EffFormatVersion
Is this an 'ANN' format?
isBefore() - Method in class org.snpeff.interval.VariantBnd
 
isBiAllelic() - Method in class org.snpeff.vcf.VcfEntry
Is this bi-allelic (based ONLY on the number of ALTs) WARINIG: You should use 'calcHetero()' method for a more precise calculation.
isBinary() - Method in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
Is the algorithm base on "interesting / not-interesting" binary clasification?
isBinary() - Method in class org.snpeff.osCmd.StreamGobbler
 
isBinaryStderr() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
isBinaryStdout() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
isBnd() - Method in class org.snpeff.interval.Variant
 
isBnd() - Method in class org.snpeff.interval.VariantBnd
 
isCanonical() - Method in class org.snpeff.interval.Transcript
 
isCase() - Method in class org.snpeff.ped.TfamEntry
Is phenotype 'Case'?
isChecked() - Method in class org.snpeff.interval.Transcript
Has this transcript been checked against CDS/DNA/AA sequences?
isCircular() - Method in class org.snpeff.interval.Chromosome
 
isCircular() - Method in class org.snpeff.interval.Interval
Is this interval part of a circular chromosome and it spans the 'chromosome zero / chromosome end' line?
isComplement() - Method in class org.snpeff.genBank.Feature
 
isCompressedGenotypes() - Method in class org.snpeff.vcf.VcfEntry
Do we have compressed genotypes in "HO,HE,NA" INFO fields?
isConserved(int) - Method in class org.snpeff.motif.Pwm
Is position 'pos' conserved (only one base has non-zero counts)
isControl() - Method in class org.snpeff.ped.TfamEntry
Is phenotype 'Control'?
isCorrected() - Method in class org.snpeff.interval.CircularCorrection
 
isCorrected() - Method in class org.snpeff.interval.Transcript
 
isCustom() - Method in class org.snpeff.snpEffect.VariantEffect
 
isDebug() - Method in class org.snpeff.fileIterator.FileIterator
 
isDebug() - Method in class org.snpeff.interval.CircularCorrection
 
isDebug() - Method in class org.snpeff.snpEffect.Config
 
isDeferredAnalysis() - Method in class org.snpeff.interval.Marker
Deferred analysis markers must be analyzed after 'standard' ones because their impact depends on other results For instance, a NextProt marker's impact would be different if the variant is synonymous or non-synonymous
isDeferredAnalysis() - Method in class org.snpeff.interval.NextProt
Deferred analysis markers must be analyzed after 'standard' ones because their impact depends on other results For instance, a NextProt marker's impact would be different if the variant is synonymous or non-synonymous
isDel() - Method in class org.snpeff.interval.Variant
 
isDerived() - Method in class org.snpeff.vcf.PedigreeEntry
Is this an 'Original-Derived' entry type?
isDnaCheck() - Method in class org.snpeff.interval.Transcript
 
isDone() - Method in class org.snpeff.osCmd.OsCmdRunner
Has this runner finished?
isDownstream(int) - Method in class org.snpeff.interval.Transcript
 
isDup() - Method in class org.snpeff.interval.Variant
 
isDuplicate() - Method in class org.snpeff.sam.SamEntry
PCR or optical duplicate
isDuplication() - Method in class org.snpeff.snpEffect.HgvsDna
Is this a duplication?
isDuplication() - Method in class org.snpeff.snpEffect.HgvsProtein
Is this variant a duplication Reference: http://www.hgvs.org/mutnomen/disc.html#dupins ...the description "dup" (see Standards) may by definition only be used when the additional copy is directly 3'-flanking of the original copy (tandem duplication)
isEff() - Method in enum class org.snpeff.vcf.EffFormatVersion
Id this an 'EFF' format?
isEffectVcfInfoField(String) - Static method in enum class org.snpeff.vcf.EffFormatVersion
Is this one of the VCF INFO keys?
isElongation() - Method in class org.snpeff.interval.Variant
 
isEmpty() - Method in class org.snpeff.binseq.DnaSequence
Is this sequence empty?
isEmpty() - Method in class org.snpeff.binseq.GenomicSequences
 
isEmpty() - Method in class org.snpeff.collections.OpenBitSet
Returns true if there are no set bits
isEmpty() - Method in class org.snpeff.genBank.Features
 
isEmpty() - Method in class org.snpeff.geneSets.Result
 
isEmpty() - Method in class org.snpeff.interval.CytoBands
 
isEmpty() - Method in class org.snpeff.interval.Markers
 
isEmpty() - Method in class org.snpeff.interval.tree.IntervalTree
 
isEmpty() - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
isEmpty() - Method in class org.snpeff.interval.tree.IntervalTreeOri
 
isEmpty() - Method in interface org.snpeff.interval.tree.Itree
 
isEmpty() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
isEmpty() - Method in class org.snpeff.reactome.events.Complex
 
isEmpty() - Method in class org.snpeff.reactome.events.Pathway
 
isEmpty() - Method in class org.snpeff.snpEffect.VariantEffects
 
isEmpty() - Method in class org.snpeff.stats.CountByKey
 
isEmpty() - Method in class org.snpeff.stats.CountByType
Is this empty
isEmpty(String) - Static method in class org.snpeff.vcf.VcfEntry
Does 'value' represent an EMPTY / MISSING value in a VCF field? (or multiple MISSING comma-separated values)
isError() - Method in enum class org.snpeff.snpEffect.ErrorWarningType
 
isErrorChromoHit() - Method in class org.snpeff.snpEffect.Config
 
isErrorOnMissingChromo() - Method in class org.snpeff.snpEffect.Config
 
isErrorProteinLength() - Method in class org.snpeff.interval.Transcript
Check if coding length is multiple of 3 in protein coding transcripts
isErrorStartCodon() - Method in class org.snpeff.interval.Transcript
Is the first codon a START codon?
isErrorStopCodonsInCds() - Method in class org.snpeff.interval.Transcript
Check if protein sequence has STOP codons in the middle of the coding sequence
isExecuting() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
isExecuting() - Method in class org.snpeff.osCmd.OsCmdRunner
 
isExon() - Method in class org.snpeff.snpEffect.VariantEffect
 
isExonPart() - Method in class org.snpeff.interval.SpliceSiteRegion
 
isExpandIub() - Method in class org.snpeff.fileIterator.VcfFileIterator
 
isExpandIub() - Method in class org.snpeff.snpEffect.Config
 
isFilterPass() - Method in class org.snpeff.vcf.VcfEntry
 
isFirstFragment() - Method in class org.snpeff.sam.SamEntry
The first fragment in the template
isFixed() - Method in class org.snpeff.reactome.Entity
 
isFormat() - Method in class org.snpeff.vcf.VcfHeaderEntry
 
isFormat() - Method in class org.snpeff.vcf.VcfHeaderFormat
 
isFormatLine(String) - Static method in class org.snpeff.vcf.VcfHeader
 
isFullVersion() - Method in enum class org.snpeff.vcf.EffFormatVersion
Is this format fully specified? I.e.
isFusion() - Method in enum class org.snpeff.snpEffect.EffectType
 
isGene(Marker) - Method in class org.snpeff.snpEffect.VariantEffectStructural
 
isGeneGeneFusion() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
isGreedy() - Method in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
Is this a greedy algorithm?
isHeadeSection() - Method in class org.snpeff.fileIterator.VcfFileIterator
 
isHeterozygous() - Method in class org.snpeff.vcf.VcfGenotype
Is the most likely genotype heterozygous?
isHgvs() - Method in class org.snpeff.snpEffect.Config
 
isHgvs1LetterAA() - Method in class org.snpeff.snpEffect.Config
 
isHgvsOld() - Method in class org.snpeff.snpEffect.Config
 
isHgvsShift() - Method in class org.snpeff.snpEffect.Config
 
isHgvsTrId() - Method in class org.snpeff.snpEffect.Config
 
isHighlyConservedAaSequence() - Method in class org.snpeff.interval.NextProt
 
isHomozygous() - Method in class org.snpeff.ped.PedGenotype
Is this homozygous?
isHomozygous() - Method in class org.snpeff.vcf.VcfGenotype
Is this genotype homozygous? (either REF or ALT)
isHomozygousAlt() - Method in class org.snpeff.vcf.VcfGenotype
Is this genotype homozygous ALT?
isIgnoreChromosomeErrors() - Method in class org.snpeff.fileIterator.MarkerFileIterator
 
isImplicit() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
isImprecise() - Method in class org.snpeff.interval.Variant
 
isInDel() - Method in class org.snpeff.interval.Variant
 
isInfo() - Method in class org.snpeff.vcf.VcfHeaderEntry
 
isInfo() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
isInfoLine(String) - Static method in class org.snpeff.vcf.VcfHeader
 
isIns() - Method in class org.snpeff.interval.Variant
 
isInSync() - Method in class org.snpeff.interval.tree.IntervalTree
Determine whether this interval tree is currently a reflection of all intervals in the interval list
isInSync() - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
isInSync() - Method in class org.snpeff.interval.tree.IntervalTreeOri
Determine whether this interval tree is currently a reflection of all intervals in the interval list
isInSync() - Method in interface org.snpeff.interval.tree.Itree
Is the tree 'in sync'? If false, the tree must be 'build()' before the next query
isInteraction() - Method in class org.snpeff.nextProt.Location
 
isInteraction() - Method in class org.snpeff.nextProt.LocationTargetIsoformInteraction
 
isInteresting(String) - Method in class org.snpeff.geneSets.GeneSets
 
isIntergenic() - Method in class org.snpeff.snpEffect.VariantEffect
 
isInterval() - Method in class org.snpeff.interval.Variant
 
isIntron() - Method in class org.snpeff.snpEffect.VariantEffect
 
isIntron(int) - Method in class org.snpeff.interval.Transcript
 
isIntronPart() - Method in class org.snpeff.interval.SpliceSiteRegion
 
isInv() - Method in class org.snpeff.interval.Variant
 
isIsoform() - Method in class org.snpeff.nextProt.Location
 
isIsoform() - Method in class org.snpeff.nextProt.LocationTargetIsoform
 
isLastFragment() - Method in class org.snpeff.sam.SamEntry
The last fragment in the template
isLeave() - Method in class org.snpeff.geneOntology.GoTerm
Is this GOTerm a leave?
isLeft() - Method in class org.snpeff.interval.VariantBnd
 
isLof() - Method in class org.snpeff.snpEffect.LossOfFunction
Can this collection of effects produce a "Loss of function"
isLof(VariantEffect) - Method in class org.snpeff.snpEffect.LossOfFunction
Is this single change a LOF? Criteria: 1) Core splice sites acceptors or donors (only CORE ones) 2) Stop gained (if this happens at the last part of the protein, we assume it has no effect) 3) Frame shifts
isLofDeletion(VariantEffect) - Method in class org.snpeff.snpEffect.LossOfFunction
Is this deletion a LOF? Criteria: 1) First (coding) exon deleted 2) More than 50% of coding sequence deleted
isMapped() - Method in class org.snpeff.sam.SamEntry
Is this entry mapped to the genome?
isMissing() - Method in class org.snpeff.ped.TfamEntry
Is phenotype 'Missing'?
isMissing() - Method in class org.snpeff.vcf.VcfGenotype
Is genotpye missing (e.g.
isMixed() - Method in class org.snpeff.interval.Variant
 
isMnp() - Method in class org.snpeff.interval.Variant
 
isMostExonsHaveSequence() - Method in class org.snpeff.interval.Genome
Do most exons have sequence? This is an indicator that something went really bad building the database.
isMotif() - Method in class org.snpeff.snpEffect.VariantEffect
 
isMt() - Method in class org.snpeff.interval.Chromosome
Is this a mitochondrial chromosome? Note: This is a wild guess just by looking at the name
isMultiallelic() - Method in class org.snpeff.vcf.VcfEntry
Is this multi-allelic (based ONLY on the number of ALTs) WARINIG: You should use 'calcHetero()' method for a more precise calculation.
isMultipleFragments() - Method in class org.snpeff.sam.SamEntry
Template having multiple fragments in sequencing
isMultipleGenes() - Method in class org.snpeff.snpEffect.VariantEffect
 
isMultipleGenes() - Method in class org.snpeff.snpEffect.VariantEffectStructural
 
isMultipleHits() - Method in class org.snpeff.sam.SamEntry
Is this read mapped to multiple genomic locations?
isMultipleValues(String) - Method in class org.snpeff.fileIterator.GuessTableTypes
Has this field multiple values
isNewFeature(String) - Method in class org.snpeff.genBank.Embl
Has this line a new feature?
isNewFeature(String) - Method in class org.snpeff.genBank.Features
Is there a new feature in this line?
isNewFeature(String) - Method in class org.snpeff.genBank.GenBank
Has this line a new feature?
isNewVersion() - Method in class org.snpeff.logStatsServer.VersionCheck
 
isNextProt() - Method in class org.snpeff.snpEffect.VariantEffect
 
isNextReverseWc() - Method in class org.snpeff.sam.SamEntry
SEQ of the next fragment in the template being reversed
isNextUnmapped() - Method in class org.snpeff.sam.SamEntry
Next fragment in the template unmapped
isNmd() - Method in class org.snpeff.snpEffect.LossOfFunction
Can this collection of effects produce a "Nonsense mediated decay"?
isNmd(VariantEffect) - Method in class org.snpeff.snpEffect.LossOfFunction
Is this single change a LOF? Criteria: 1) Core splice sites acceptors or donors (only CORE ones) 2) Stop gained (if this happens at the last part of the protein, we assume it has no effect) 3) Frame shifts
isNonRef() - Method in class org.snpeff.interval.Variant
 
isNonRef() - Method in class org.snpeff.interval.VariantNonRef
 
isNotQualityControl() - Method in class org.snpeff.sam.SamEntry
Not passing quality controls
isNumberAllAlleles() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
isNumberNumber() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
isNumberOnePerAllele() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
isNumberOnePerGenotype() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
isNumberPerAllele() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
isOk(Apfloat) - Static method in class org.snpeff.probablility.RankSumPdf
Is the value OK? (i.e.
isOnlyRegulation() - Method in class org.snpeff.snpEffect.Config
 
isOpt(String) - Method in class org.snpeff.SnpEff
Is this a command line option (e.g.
isPhased() - Method in class org.snpeff.vcf.VcfGenotype
 
isPowerOfTwo(int) - Static method in class org.snpeff.collections.BitUtil
returns true if v is a power of two or zero
isPowerOfTwo(long) - Static method in class org.snpeff.collections.BitUtil
returns true if v is a power of two or zero
isProperlyAligned() - Method in class org.snpeff.sam.SamEntry
Each fragment properly aligned according to the aligner
isProteinCoding() - Method in enum class org.snpeff.interval.BioType
 
isProteinCoding() - Method in class org.snpeff.interval.Gene
Is any of the transcripts protein coding?
isProteinCoding() - Method in class org.snpeff.interval.Transcript
 
isProteingCoding() - Method in class org.snpeff.interval.GffMarker
Is biotType considered 'protein coding'?
isQuiet() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
isQuiet() - Method in class org.snpeff.snpEffect.Config
 
isRank() - Method in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
Does the algorithm need a rank statistic?
isRanked() - Method in class org.snpeff.geneSets.GeneSets
 
isRanked() - Method in class org.snpeff.geneSets.GeneSetsRanked
 
isRanked(String) - Method in class org.snpeff.geneSets.GeneSetsRanked
 
isReaction() - Method in class org.snpeff.reactome.Entity
 
isReaction() - Method in class org.snpeff.reactome.events.Reaction
 
isRef() - Method in class org.snpeff.vcf.VcfGenotype
Is any genotype different than REF? Note: This is calculated for the most likely genotype (GT field)
isRegulation() - Method in class org.snpeff.snpEffect.VariantEffect
 
isReverseWc() - Method in class org.snpeff.sam.SamEntry
SEQ being reverse complemented
isRibosomalSlippage() - Method in class org.snpeff.genBank.Feature
 
isRibosomalSlippage() - Method in class org.snpeff.interval.Transcript
 
isRunning() - Method in class org.snpeff.osCmd.StreamGobbler
 
isSameChromo(Marker) - Method in class org.snpeff.interval.Interval
 
isSaveStd() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
isSecondaryAlignment() - Method in class org.snpeff.sam.SamEntry
Secondary alignment
isShow(Result) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
Showld we show this result or should the output be filtered?
isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Chromosome
 
isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Downstream
Upstream sites are no included in transcript (by definition).
isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Gene
 
isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Marker
Show an error if parent does not include child?
isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.SpliceSite
Splice sites are not included in Exons, by definition.
isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Upstream
Upstream sites are no included in transcript (by definition).
isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.interval.Variant
 
isShowWarningIfParentDoesNotInclude() - Method in class org.snpeff.vcf.VcfEntry
 
isSingleSnp() - Method in class org.snpeff.vcf.VcfEntry
Is thins a VCF entry with a single SNP?
isSingleton() - Method in class org.snpeff.vcf.VcfEntry
Is this variant a singleton (appears only in one genotype)
isSnp() - Method in class org.snpeff.interval.Variant
 
isSpliceSite() - Method in class org.snpeff.snpEffect.VariantEffect
 
isSpliceSiteCore() - Method in class org.snpeff.snpEffect.VariantEffect
 
isSpliceSiteRegion() - Method in class org.snpeff.snpEffect.VariantEffect
 
isStart(String) - Method in class org.snpeff.codons.CodonTable
Is 'codon' a start codon in this table?
isStarted() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
isStartFirst(String) - Method in class org.snpeff.codons.CodonTable
Is the first codon a 'start' codon?
isStdin(String) - Static method in class org.snpeff.util.Gpr
Empty or '-' means STDIN
isStop(String) - Method in class org.snpeff.codons.CodonTable
Is 'codon' a stop codon in this table?
isStopAa(String) - Method in class org.snpeff.codons.CodonTable
Is there a stop codon in this amino acid sequence
isStrandMinus() - Method in class org.snpeff.interval.Interval
 
isStrandPlus() - Method in class org.snpeff.interval.Interval
 
isStructural() - Method in class org.snpeff.interval.Variant
 
isStructural() - Method in class org.snpeff.interval.VariantBnd
 
isStructuralHuge() - Method in class org.snpeff.interval.Variant
Is this a huge structural variant?
isTranscript(Marker) - Method in class org.snpeff.snpEffect.VariantEffectStructural
 
isTransition(String, String) - Method in class org.snpeff.stats.TsTvStats
Is this a transition?
isTranversion(String, String) - Method in class org.snpeff.stats.TsTvStats
Is this a transversion?
isTreatAllAsProteinCoding() - Method in class org.snpeff.snpEffect.Config
 
isTruncation() - Method in class org.snpeff.interval.Variant
 
isType(Marker, String) - Method in class org.snpeff.coverage.MarkerTypes
 
isUIB(char) - Static method in class org.snpeff.util.IubString
 
isUniqueHit() - Method in class org.snpeff.sam.SamEntry
Is this read mapped to only one genomic locations?
isUnmapped() - Method in class org.snpeff.sam.SamEntry
Fragment unmapped
isUpstream(int) - Method in class org.snpeff.interval.Transcript
 
isUsed(String) - Method in class org.snpeff.geneSets.GeneSets
 
isUsed(String) - Method in class org.snpeff.geneSets.GeneSetsRanked
 
isUsed(GeneSet) - Method in class org.snpeff.geneSets.GeneSets
Is this gene set used? I.e.
isUsed(GeneSet) - Method in class org.snpeff.geneSets.GeneSetsRanked
Is this gene set used? I.e.
isUtr(int) - Method in class org.snpeff.interval.Transcript
 
isUtr(Marker) - Method in class org.snpeff.interval.Transcript
 
isUtr3() - Method in class org.snpeff.snpEffect.VariantEffect
 
isUtr3(int) - Method in class org.snpeff.interval.Transcript
 
isUtr3prime() - Method in class org.snpeff.interval.Utr
 
isUtr3prime() - Method in class org.snpeff.interval.Utr3prime
 
isUtr3prime() - Method in class org.snpeff.interval.Utr5prime
 
isUtr5() - Method in class org.snpeff.snpEffect.VariantEffect
 
isUtr5(int) - Method in class org.snpeff.interval.Transcript
 
isUtr5prime() - Method in class org.snpeff.interval.Utr
 
isUtr5prime() - Method in class org.snpeff.interval.Utr3prime
 
isUtr5prime() - Method in class org.snpeff.interval.Utr5prime
 
isValid() - Method in class org.snpeff.interval.Interval
 
isValid() - Method in class org.snpeff.nextProt.Location
 
isValid() - Method in class org.snpeff.ped.PedGenotype
 
isValidData() - Method in class org.snpeff.stats.IntStats
Do we have any data
isValidInfoKey(String) - Static method in class org.snpeff.vcf.VcfEntry
Make sure the INFO key matches the regular expression (as specified in VCF spec 4.3)
isValidInfoValue(String) - Static method in class org.snpeff.vcf.VcfEntry
Check that this value can be added to an INFO field
isValidIp(String) - Static method in class org.snpeff.util.Gpr
 
isValidRid(int) - Static method in class org.snpeff.util.Gpr
Is this a valid Rid
isVariant() - Method in class org.snpeff.interval.Variant
Is this a change or is ALT actually the same as the reference
isVariant() - Method in class org.snpeff.vcf.VcfEntry
Is this a change or are the ALTs actually the same as the reference
isVariant() - Method in class org.snpeff.vcf.VcfGenotype
Is any genotype different than REF? Note: This is calculated for the most likely genotype (GT field)
isVariant(String) - Method in class org.snpeff.vcf.VcfEntry
Is this ALT string a variant?
isVerbose() - Method in class org.snpeff.snpEffect.Config
 
isWarning() - Method in enum class org.snpeff.snpEffect.ErrorWarningType
 
isWarningStopCodon() - Method in class org.snpeff.interval.Transcript
Is the last codon a STOP codon?
iterator() - Method in class org.snpeff.binseq.GenomicSequences
 
iterator() - Method in class org.snpeff.binseq.indexer.SequenceIndexer
 
iterator() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
 
iterator() - Method in class org.snpeff.codons.CodonTables
 
iterator() - Method in class org.snpeff.fileIterator.BinSeqFileIterator
 
iterator() - Method in class org.snpeff.fileIterator.FastqFileIterator
 
iterator() - Method in class org.snpeff.fileIterator.FileIterator
 
iterator() - Method in class org.snpeff.fileIterator.LineClassFileIterator
 
iterator() - Method in class org.snpeff.fileIterator.LineFileIterator
 
iterator() - Method in class org.snpeff.fileIterator.SamFileIterator
 
iterator() - Method in class org.snpeff.genBank.Feature
 
iterator() - Method in class org.snpeff.genBank.Features
 
iterator() - Method in class org.snpeff.genBank.FeaturesFile
 
iterator() - Method in class org.snpeff.geneOntology.GoTerm
 
iterator() - Method in class org.snpeff.geneOntology.GoTerms
Iterate through each GOterm in this GOTerms
iterator() - Method in class org.snpeff.geneSets.GeneSet
 
iterator() - Method in class org.snpeff.geneSets.GeneSets
Iterate through each GeneSet in this GeneSets
iterator() - Method in class org.snpeff.gtex.Gtex
 
iterator() - Method in class org.snpeff.interval.Custom
 
iterator() - Method in class org.snpeff.interval.Genes
 
iterator() - Method in class org.snpeff.interval.Genome
 
iterator() - Method in class org.snpeff.interval.GffMarker
 
iterator() - Method in class org.snpeff.interval.IntervalAndSubIntervals
 
iterator() - Method in class org.snpeff.interval.IntervalSetIterator
 
iterator() - Method in class org.snpeff.interval.Markers
 
iterator() - Method in class org.snpeff.interval.tree.IntervalForest
 
iterator() - Method in class org.snpeff.interval.tree.IntervalNodeOri
 
iterator() - Method in class org.snpeff.interval.tree.IntervalTree
 
iterator() - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
iterator() - Method in class org.snpeff.interval.tree.IntervalTreeOri
 
iterator() - Method in class org.snpeff.motif.Jaspar
 
iterator() - Method in class org.snpeff.osCmd.OsCmdQueue
 
iterator() - Method in class org.snpeff.ped.PedEntry
 
iterator() - Method in class org.snpeff.ped.PedPedigree
 
iterator() - Method in class org.snpeff.reactome.events.Complex
 
iterator() - Method in class org.snpeff.reactome.events.Pathway
 
iterator() - Method in class org.snpeff.reactome.Reactome
 
iterator() - Method in class org.snpeff.sam.SamHeader
 
iterator() - Method in class org.snpeff.snpEffect.Config
 
iterator() - Method in class org.snpeff.snpEffect.VariantEffects
 
iterator() - Method in class org.snpeff.spliceSites.TranscriptSet
 
iterator() - Method in class org.snpeff.stats.GeneCountByTypeTable
 
iterator() - Method in class org.snpeff.util.CombinatorialIterator
 
iterator() - Method in class org.snpeff.util.Iterator2Iterable
 
iterator() - Method in class org.snpeff.util.IubString
 
iterator() - Method in class org.snpeff.vcf.Pedigree
 
iterator() - Method in class org.snpeff.vcf.VcfEntry
 
Iterator2Iterable<T> - Class in org.snpeff.util
Convert an iterator instance to a (fake) iterable
Iterator2Iterable(Iterator<T>) - Constructor for class org.snpeff.util.Iterator2Iterable
 
iteratorSorted() - Method in class org.snpeff.geneSets.GeneSets
Iterate through each GeneSet in this GeneSets
Itree - Interface in org.snpeff.interval.tree
Interval tree interface
iub2bases(char) - Static method in class org.snpeff.util.IubString
Convert a single IUB code to the corresponding bases IUB codes: M=A/C, R=A/G, W=A/T, S=C/G, Y=C/T, K=G/T and N=A/C/G/T
IubString - Class in org.snpeff.util
Find all bases combinations from a string containing IUB codes
IubString(String) - Constructor for class org.snpeff.util.IubString
 

J

Jaspar - Class in org.snpeff.motif
Load PWM matrices from a Jaspar file
Jaspar() - Constructor for class org.snpeff.motif.Jaspar
 
JOIN - Static variable in class org.snpeff.genBank.Features
 

K

K - Static variable in class org.snpeff.fastq.FastqSplit
 
KB - Static variable in class org.snpeff.util.Gpr
 
keepTranscripts(Set<String>) - Method in class org.snpeff.interval.Gene
Remove all transcripts in trIds
keepTranscriptsProteinCoding() - Method in class org.snpeff.interval.Gene
Keep only protein coding transcripts
keepTranscriptsProteinCoding() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Remove all transcripts that are NOT in the list
key - Variable in class org.snpeff.util.KeyValue
 
KEY_BUNDLE_SUFIX - Static variable in class org.snpeff.snpEffect.Config
 
KEY_CODON_PREFIX - Static variable in class org.snpeff.snpEffect.Config
 
KEY_CODONTABLE_SUFIX - Static variable in class org.snpeff.snpEffect.Config
 
KEY_COORDINATES - Static variable in class org.snpeff.snpEffect.Config
 
KEY_DATA_DIR - Static variable in class org.snpeff.snpEffect.Config
 
KEY_DATABASE_LOCAL - Static variable in class org.snpeff.snpEffect.Config
 
KEY_DATABASE_REPOSITORY - Static variable in class org.snpeff.snpEffect.Config
 
KEY_DATABASE_REPOSITORY_KEY - Static variable in class org.snpeff.snpEffect.Config
 
KEY_DBNSFP_FIELDS - Static variable in class org.snpeff.snpEffect.Config
 
KEY_GENOME_SUFIX - Static variable in class org.snpeff.snpEffect.Config
 
KEY_LOF_DELETE_PROTEIN_CODING_BASES - Static variable in class org.snpeff.snpEffect.Config
 
KEY_LOF_IGNORE_PROTEIN_CODING_AFTER - Static variable in class org.snpeff.snpEffect.Config
 
KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE - Static variable in class org.snpeff.snpEffect.Config
 
KEY_REFERENCE_SUFIX - Static variable in class org.snpeff.snpEffect.Config
 
KEY_SEPARATOR - Static variable in class org.snpeff.snpEffect.PurityChange
 
KEY_VERSIONS_URL - Static variable in class org.snpeff.snpEffect.Config
 
keys() - Method in class org.snpeff.collections.HashLongLongArray
Return an array with all the keys to this hash
keys() - Method in class org.snpeff.snpEffect.Config
 
keySet() - Method in class org.snpeff.geneOntology.GoTerms
 
keySet() - Method in class org.snpeff.geneSets.GeneSets
 
keySet() - Method in class org.snpeff.interval.tree.IntervalForest
 
keySet() - Method in class org.snpeff.ped.PedPedigree
 
keySet() - Method in class org.snpeff.stats.CountByKey
 
keySet() - Method in class org.snpeff.stats.CountByType
 
keysRanked(boolean) - Method in class org.snpeff.stats.CountByType
List all types (sorted by count)
keysSorted() - Method in class org.snpeff.stats.CountByType
List all types (alphabetically sorted)
KeyValue<A,B> - Class in org.snpeff.util
A "key = value" pair
KeyValue(A, B) - Constructor for class org.snpeff.util.KeyValue
 
kill() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
kill() - Method in class org.snpeff.osCmd.OsCmdQueue
Kill all commands
KNOWN_FILE_EXTENSIONS - Static variable in class org.snpeff.util.GprSeq
 
KNOWN_GENES - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
 

L

LAST_BASE_IN_LONGWORD - Static variable in class org.snpeff.binseq.coder.DnaCoder
 
lastBaseinWord() - Method in class org.snpeff.binseq.coder.Coder
Index of the last base coded in a word
lastBaseinWord() - Method in class org.snpeff.binseq.coder.DnaCoder
 
lastIdx - Variable in class org.snpeff.interval.tree.IntervalTreeArray
 
lastIndexOf(String) - Method in class org.snpeff.binseq.DnaAndQualitySequence
Returns the index within this string of the rightmost occurrence of the specified substring
lastNmdPos(Transcript) - Method in class org.snpeff.snpEffect.LossOfFunction
Find the last position where a nonsense mediated decay is supposed to occurr This is 50 bases (MND_BASES_BEFORE_LAST_JUNCTION bases) before the last exon-exon junction.
LEADING_EDGE_FRACTION - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
 
LeadingEdgeFractionAlgorithm - Class in org.snpeff.geneSets.algorithm
Leading edge fraction algorithm References: "Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits" http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001058 See page 12, "Step 4"
LeadingEdgeFractionAlgorithm(GeneSets, int, boolean) - Constructor for class org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
 
left - Variable in class org.snpeff.interval.tree.IntervalTreeArray
 
leftNode - Variable in class org.snpeff.interval.tree.IntervalNode
 
LEN_AFTER_TSS - Static variable in class org.snpeff.PromoterSequences
 
LEN_UPSTREAM - Static variable in class org.snpeff.PromoterSequences
 
length - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
length() - Method in class org.snpeff.binseq.BinarySequence
Get sequence length
length() - Method in class org.snpeff.binseq.DnaAndQualitySequence
Sequence lenth
length() - Method in class org.snpeff.binseq.DnaSequence
Sequence lenth
length() - Method in class org.snpeff.binseq.DnaSequenceByte
Sequence lenth
length() - Method in class org.snpeff.binseq.DnaSequencePe
 
length() - Method in class org.snpeff.interval.Genome
Total genome length: add all chromosomes
length() - Method in class org.snpeff.motif.Pwm
 
length() - Method in class org.snpeff.nmer.Nmer
Get nmer's length
length2words(int) - Method in class org.snpeff.binseq.coder.DnaCoder
Calculate the coded length of a sequence in 'words' (depends on coder)
lengthChange() - Method in class org.snpeff.interval.Variant
Calculate the number of bases of change in length
levels() - Method in class org.snpeff.geneOntology.GoTerms
Calculate each node's level (in DAG)
LIGHT_ROW - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
 
lincRNA - Enum constant in enum class org.snpeff.interval.BioType
 
line - Variable in class org.snpeff.fileIterator.FileIterator
 
line - Variable in class org.snpeff.vcf.FileIndexChrPos.LineAndPos
 
line - Variable in class org.snpeff.vcf.VcfEntry
 
line - Variable in class org.snpeff.vcf.VcfHeaderEntry
 
LINE_COLOR_STROKE - Static variable in class org.snpeff.svg.Svg
 
LINE_STROKE_WIDTH - Static variable in class org.snpeff.svg.Svg
 
LineAndPos() - Constructor for class org.snpeff.vcf.FileIndexChrPos.LineAndPos
 
LINEAR - Enum constant in enum class org.snpeff.reactome.Entity.TransferFunction
 
lineChart - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
 
LineChrPos - Class in org.snpeff.vcf
A simple chr:pos parser Stores using bytes instead of chars
LineChrPos(String) - Constructor for class org.snpeff.vcf.LineChrPos
 
LineClassFileIterator<T> - Class in org.snpeff.fileIterator
Iterate on each line.
LineClassFileIterator(String, Class) - Constructor for class org.snpeff.fileIterator.LineClassFileIterator
 
LineClassFileIterator(String, Class, String) - Constructor for class org.snpeff.fileIterator.LineClassFileIterator
 
LineFileIterator - Class in org.snpeff.fileIterator
Iterate on each line in this file
LineFileIterator(String) - Constructor for class org.snpeff.fileIterator.LineFileIterator
 
LineFileIterator(String, boolean) - Constructor for class org.snpeff.fileIterator.LineFileIterator
 
LineFilter - Interface in org.snpeff.osCmd
Filter a line before processing
lineNum - Variable in class org.snpeff.fileIterator.FileIterator
 
lineNum - Variable in class org.snpeff.vcf.VcfEntry
 
LineSeqFileIterator - Class in org.snpeff.fileIterator
One line per sequence.
LineSeqFileIterator(String) - Constructor for class org.snpeff.fileIterator.LineSeqFileIterator
 
listTopTerms(int) - Method in class org.snpeff.geneOntology.GoTerms
Select a number of GOTerms
listTopTerms(int) - Method in class org.snpeff.geneSets.GeneSets
Select a number of GeneSets
load() - Method in class org.snpeff.binseq.GenomicSequences
Load sequences for all 'small chromosomes" (from "sequence.bin" file)
load() - Method in class org.snpeff.fileIterator.FileIterator
Load all elements from a file into a list
load() - Method in class org.snpeff.fileIterator.TableFile
Load all data into memory
load() - Method in class org.snpeff.SnpEff
 
load() - Method in class org.snpeff.Zzz
 
load(String) - Method in class org.snpeff.binseq.GenomicSequences
Load sequences for a single chromosome (from "sequence.chr.bin" file)
load(String) - Static method in class org.snpeff.genotypes.Genotypes
Read from a file
load(String) - Method in class org.snpeff.interval.Markers
 
load(String) - Method in class org.snpeff.motif.Jaspar
Load matrix file
load(String) - Method in class org.snpeff.pdb.IdMapper
 
load(String) - Method in class org.snpeff.ped.PedPedigree
Load a pedigree from a PED and MAP file pair
load(String) - Method in class org.snpeff.reactome.GeneIds
Load data from file
load(String) - Method in class org.snpeff.serializer.MarkerSerializer
Load data from file
load(String) - Method in class org.snpeff.stats.ReadsOnMarkersModel
Load data from a file
load(String, boolean) - Static method in class org.snpeff.fileIterator.BedFileIterator
 
load(String, String) - Method in class org.snpeff.gtex.Gtex
 
load(String, String) - Method in class org.snpeff.reactome.Reactome
 
load(String, Genome) - Method in class org.snpeff.interval.Markers
 
load(String, Genome) - Method in class org.snpeff.interval.tree.IntervalTree
 
load(String, Genome) - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
load(String, Genome) - Method in class org.snpeff.interval.tree.IntervalTreeOri
 
load(String, Genome) - Method in interface org.snpeff.interval.tree.Itree
Load intervals from file
load(Config) - Static method in class org.snpeff.snpEffect.SnpEffectPredictor
Load predictor from a binary file
loadCatalystActivity() - Method in class org.snpeff.reactome.Reactome
Load catalyst activity to molecule mapping
loadComplex2HasComponent() - Method in class org.snpeff.reactome.Reactome
Load complexes
loadConfig() - Method in class org.snpeff.SnpEff
Read config file
loadCustomFile(String) - Method in class org.snpeff.SnpEff
Read a custom interval file
loadData(String) - Method in class org.snpeff.gtex.Gtex
Load data: Experimental (sometimes normalized) values
loadDatabaseObjects() - Method in class org.snpeff.reactome.Reactome
Load objects table (populate objectType and objectName maps)
loadDb() - Method in class org.snpeff.SnpEff
Load database
loadExperimentalValues(String, boolean) - Method in class org.snpeff.geneSets.GeneSets
Reads a file with a list of genes and experimental values.
loadExperimentalValues(String, boolean) - Method in class org.snpeff.geneSets.GeneSetsRanked
Reads a file with a list of genes and experimental values.
loadGeneIds(String) - Method in class org.snpeff.reactome.Reactome
Load Gene IDs data, then map geneIDs <-> Entities
loadIdMapper() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
loadMap(String, String, HashMap<String, String>) - Method in class org.snpeff.reactome.Reactome
Load a two-column file into a Hash
loadMarkers() - Method in class org.snpeff.fileIterator.MarkerFileIterator
 
loadMarkers(String) - Method in class org.snpeff.SnpEff
Read markers file Supported formats: BED, TXT, BigBed, GFF
loadMSigDb(String, boolean) - Method in class org.snpeff.geneSets.GeneSets
Read an MSigDBfile and add every Gene set (do not add relationships between nodes in DAG)
loadOrCreateFromGenome(String) - Method in class org.snpeff.binseq.GenomicSequences
Load sequences from genomic sequence file or (if not file is available) generate some sequences from exons.
loadPathway2HasEvent() - Method in class org.snpeff.reactome.Reactome
Load pathway events
loadPhysicalEntity2Compartment() - Method in class org.snpeff.reactome.Reactome
Load compartment information
loadReactionlikeEvent2CatalystActivity() - Method in class org.snpeff.reactome.Reactome
Load reaction catalyst
loadReactionlikeEvent2Input() - Method in class org.snpeff.reactome.Reactome
Load reaction inputs
loadReactionlikeEvent2Output() - Method in class org.snpeff.reactome.Reactome
Load reaction outputs
loadRegulation() - Method in class org.snpeff.reactome.Reactome
Load reaction regulation
loadSamples(String) - Method in class org.snpeff.gtex.Gtex
Load samples names
loadSnpEffectPredictor() - Method in class org.snpeff.snpEffect.Config
Load a snpEff predictor WARNING: 'genome' object get replaced upon loading a snpEffectPredictor (this is a dangerous side effect)
loadSnpEffectPredictor(String, boolean) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Load predictor and create interval forest
loadTfam(String) - Method in class org.snpeff.ped.PedPedigree
Load a TFAM file
loadVcf() - Method in class org.snpeff.genotypes.Genotypes
Load data
Location - Class in org.snpeff.nextProt
A location (i.e.
Location() - Constructor for class org.snpeff.nextProt.Location
 
Location(String) - Constructor for class org.snpeff.nextProt.Location
 
Location(String, int, int) - Constructor for class org.snpeff.nextProt.Location
 
locationBeginPos(Attributes) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
locationEnd() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
End of location tag
locationEndPos(Attributes) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
locationIsoformStart(String) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
locationStart(Attributes) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
LocationTargetIsoform - Class in org.snpeff.nextProt
A location respect to an isoform
LocationTargetIsoform(String) - Constructor for class org.snpeff.nextProt.LocationTargetIsoform
 
LocationTargetIsoform(String, int, int) - Constructor for class org.snpeff.nextProt.LocationTargetIsoform
 
LocationTargetIsoformInteraction - Class in org.snpeff.nextProt
A location respect to two locations within an isoform In this case "start" and "end" are not really an interval, but an interaction between two locations (e.g.
LocationTargetIsoformInteraction(String, int, int) - Constructor for class org.snpeff.nextProt.LocationTargetIsoformInteraction
 
LocationTargetIsoformInteraction(LocationTargetIsoform) - Constructor for class org.snpeff.nextProt.LocationTargetIsoformInteraction
 
log - Variable in class org.snpeff.logStatsServer.LogStats
 
log - Variable in class org.snpeff.SnpEff
 
Log - Class in org.snpeff.util
Logging
Log() - Constructor for class org.snpeff.util.Log
 
LOG_THREAD_WAIT_TIME - Static variable in class org.snpeff.logStatsServer.LogStats
 
LOG_THREAD_WAIT_TIME - Static variable in class org.snpeff.logStatsServer.VersionCheck
 
LOG_THREAD_WAIT_TIME_REPEAT - Static variable in class org.snpeff.logStatsServer.LogStats
 
LOG_THREAD_WAIT_TIME_REPEAT - Static variable in class org.snpeff.logStatsServer.VersionCheck
 
Log.FatalErrorBehabiour - Enum Class in org.snpeff.util
 
log2(double) - Static method in class org.snpeff.motif.MotifLogo
Log base 2
LOG2 - Static variable in class org.snpeff.geneSets.GeneSets
 
LOG2 - Static variable in class org.snpeff.spliceSites.AcgtTree
 
LogStats - Class in org.snpeff.logStatsServer
Log basic usage information to a server (for feedback and stats) This information an always be suppressed (no info sent at all)
LogStats(String, String, String) - Constructor for class org.snpeff.logStatsServer.LogStats
Constructor
LogStats.RequestResult - Enum Class in org.snpeff.logStatsServer
 
LossOfFunction - Class in org.snpeff.snpEffect
Analyze if a set of effects are can create a "Loss Of Function" and "Nonsense mediated decays" effects.
LossOfFunction(Config, Collection<VariantEffect>) - Constructor for class org.snpeff.snpEffect.LossOfFunction
 
LOW - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
 
LowFrequency - Enum constant in enum class org.snpeff.vcf.VcfEntry.AlleleFrequencyType
 

M

M - Static variable in class org.snpeff.fastq.FastqSplit
 
mac() - Method in class org.snpeff.vcf.VcfEntry
Calculate Minor allele count
macro_lncRNA - Enum constant in enum class org.snpeff.interval.BioType
 
maf() - Method in class org.snpeff.vcf.VcfEntry
Calculate Minor allele frequency
main(String[]) - Static method in class org.snpeff.fastq.FastqSplit
Main
main(String[]) - Static method in class org.snpeff.Fastq2Fastq
 
main(String[]) - Static method in class org.snpeff.genotypes.Genotypes
 
main(String[]) - Static method in class org.snpeff.probablility.Hypergeometric
 
main(String[]) - Static method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
main(String[]) - Static method in class org.snpeff.probablility.RankSumPdf
 
main(String[]) - Static method in class org.snpeff.PromoterSequences
 
main(String[]) - Static method in class org.snpeff.Qseq2Fastq
 
main(String[]) - Static method in class org.snpeff.reactome.Reactome
Main
main(String[]) - Static method in class org.snpeff.SnpEff
Main
main(String[]) - Static method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
 
main(String[]) - Static method in class org.snpeff.snpEffect.IntHisto
 
main(String[]) - Static method in class org.snpeff.snpEffect.PurityChange
 
main(String[]) - Static method in class org.snpeff.snpEffect.testCases.integration.CompareToEnsembl
Main
main(String[]) - Static method in class org.snpeff.snpEffect.testCases.integration.CreateSpliceSiteTestCase
 
main(String[]) - Static method in class org.snpeff.Zzz
 
Male - Enum constant in enum class org.snpeff.ped.Sex
 
mark(int) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
MARK - Static variable in class org.snpeff.genotypes.Genotypes
 
MARK - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
marker - Variable in class org.snpeff.snpEffect.Hgvs
 
marker - Variable in class org.snpeff.snpEffect.VariantEffect
 
marker() - Method in class org.snpeff.svg.Svg
 
Marker - Class in org.snpeff.interval
An interval intended as a mark
Marker() - Constructor for class org.snpeff.interval.Marker
 
Marker(Marker, int, int) - Constructor for class org.snpeff.interval.Marker
 
Marker(Marker, int, int, boolean, String) - Constructor for class org.snpeff.interval.Marker
 
MarkerFileIterator<M extends Marker> - Class in org.snpeff.fileIterator
Opens a Marker file and iterates over all markers
MarkerFileIterator(BufferedReader, int) - Constructor for class org.snpeff.fileIterator.MarkerFileIterator
 
MarkerFileIterator(String, int) - Constructor for class org.snpeff.fileIterator.MarkerFileIterator
 
MarkerFileIterator(String, Genome, int) - Constructor for class org.snpeff.fileIterator.MarkerFileIterator
 
markerId() - Method in class org.snpeff.svg.Svg
 
MarkerParentId - Class in org.snpeff.interval
This is a marker used as a 'fake' parent during data serialization
MarkerParentId(int) - Constructor for class org.snpeff.interval.MarkerParentId
 
markers - Variable in class org.snpeff.interval.Markers
 
markers - Variable in class org.snpeff.interval.tree.IntervalTreeArray
 
markers - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
markers - Variable in class org.snpeff.snpEffect.testCases.unity.TestGenome
 
markers() - Method in class org.snpeff.interval.Gene
 
markers() - Method in class org.snpeff.interval.IntervalAndSubIntervals
A list of all markers in this transcript
markers() - Method in class org.snpeff.interval.Transcript
A list of all markers in this transcript
Markers - Class in org.snpeff.interval
A collection of markers
Markers() - Constructor for class org.snpeff.interval.Markers
 
Markers(String) - Constructor for class org.snpeff.interval.Markers
 
Markers(Collection) - Constructor for class org.snpeff.interval.Markers
 
Markers(Markers) - Constructor for class org.snpeff.interval.Markers
 
MarkerSeq - Class in org.snpeff.interval
Marker with a DNA sequence
MarkerSeq() - Constructor for class org.snpeff.interval.MarkerSeq
 
MarkerSeq(Marker, int, int, boolean, String) - Constructor for class org.snpeff.interval.MarkerSeq
 
MarkerSeq(Marker, int, int, String) - Constructor for class org.snpeff.interval.MarkerSeq
 
MarkerSerializer - Class in org.snpeff.serializer
Serialize markers to (and from) file
MarkerSerializer(Genome) - Constructor for class org.snpeff.serializer.MarkerSerializer
 
MarkerTypes - Class in org.snpeff.coverage
Create a list of marker types (names or labels for markers)
MarkerTypes() - Constructor for class org.snpeff.coverage.MarkerTypes
 
markerTypesClass() - Method in class org.snpeff.coverage.MarkerTypes
List of markers whose types are based on class names
MarkerUtil - Class in org.snpeff.interval
Generic utility methods for Markers
MarkerUtil() - Constructor for class org.snpeff.interval.MarkerUtil
 
MarkerWithFrame - Interface in org.snpeff.interval
A Marker that has 'frame' information (Exon and Cds)
markSupported() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
mask - Static variable in class org.snpeff.genotypes.GenotypeVector
 
mask(int) - Method in class org.snpeff.binseq.coder.Coder
Bitmask for a base in a word
mask(int) - Method in class org.snpeff.binseq.coder.DnaCoder
 
MASK - Static variable in class org.snpeff.binseq.DnaSequenceByte
 
MASK_ALL_WORD - Static variable in class org.snpeff.binseq.coder.DnaCoder
 
MASK_BASE - Variable in class org.snpeff.binseq.coder.DnaCoder
 
MASK_FIRST_BASE - Static variable in class org.snpeff.binseq.coder.DnaCoder
 
MASK_HIGH - Variable in class org.snpeff.binseq.coder.DnaCoder
 
MASK_LOW - Variable in class org.snpeff.binseq.coder.DnaCoder
 
MAT_PEPTIDE - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
matrix - Variable in class org.snpeff.fileIterator.MatrixEntry
 
MatrixEntry - Class in org.snpeff.fileIterator
A simple entry in a 'Matrix' file
MatrixEntry() - Constructor for class org.snpeff.fileIterator.MatrixEntry
 
MatrixEntryFileIterator - Class in org.snpeff.fileIterator
Iterate on each line of a file, creating a MatrixEntry
MatrixEntryFileIterator(String) - Constructor for class org.snpeff.fileIterator.MatrixEntryFileIterator
 
max() - Method in class org.snpeff.gsa.ScoreList
Get minimum pvalue
max() - Method in class org.snpeff.nmer.NmerCount
Max nmer count
max() - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
 
max() - Method in class org.snpeff.stats.CountByKey
Maximum count
max() - Method in class org.snpeff.stats.CountByType
Maximum count
max(double) - Method in class org.snpeff.stats.CounterDouble
 
max(NmerCount) - Method in class org.snpeff.nmer.NmerCount
Max nmer count
MAX - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
 
MAX_ALIGN_LENGTH - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
 
MAX_CODON_SEQUENCE_LEN - Static variable in class org.snpeff.snpEffect.VariantEffect
 
MAX_CONVERGENCE_DIFFERENCE - Static variable in class org.snpeff.reactome.Reactome
 
MAX_DATA_POINTS - Static variable in class org.snpeff.stats.plot.GooglePlot
 
MAX_DATA_POINTS - Static variable in class org.snpeff.stats.plot.GooglePlotInt
 
MAX_DIFF - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare
 
MAX_DIFF - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest
 
MAX_DIFF - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric
 
MAX_ENTROPY - Static variable in class org.snpeff.spliceSites.AcgtTree
 
MAX_ERROR_RATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
 
MAX_ERROR_RATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
MAX_ERRORS - Static variable in class org.snpeff.util.Log
 
MAX_EXONS - Static variable in class org.snpeff.interval.ExonSpliceCharacterizer
 
MAX_EXONS_CHART - Static variable in class org.snpeff.coverage.CountReadsOnMarkers
 
MAX_ITERATIONS - Static variable in class org.snpeff.align.VariantRealign
 
MAX_ITERATIONS - Static variable in class org.snpeff.binseq.GenomicSequences
 
MAX_ITERATIONS - Static variable in class org.snpeff.reactome.Reactome
 
MAX_IUB_BASES - Static variable in class org.snpeff.util.IubString
 
MAX_LEN_TO_SHOW - Static variable in class org.snpeff.genBank.Features
 
MAX_LINES_DIFF - Static variable in class org.snpeff.snpEffect.testCases.integration.IntegrationTest
 
MAX_MAC - Static variable in class org.snpeff.stats.AlleleCountStats
 
MAX_MAC - Static variable in class org.snpeff.stats.VariantTypeStats
 
MAX_NMER_SIZE - Static variable in class org.snpeff.nmer.Nmer
 
MAX_NORM_DOUBLE - Static variable in class org.snpeff.probablility.NormalDistribution
 
MAX_QUALITY - Static variable in class org.snpeff.binseq.coder.DnaQualityCoder
 
MAX_SEQUENCE_LEN_HGVS - Static variable in class org.snpeff.snpEffect.Hgvs
 
MAX_SIZE - Static variable in class org.snpeff.align.VcfRefAltAlign
 
MAX_SMALL_MARKER_SIZE - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
MAX_SPLICE_SIZE - Static variable in class org.snpeff.spliceSites.SpliceTypes
 
MAX_TRANSCRIPTS_PER_GENE - Static variable in class org.snpeff.spliceSites.TranscriptSet
 
MAX_WARNINGS - Static variable in class org.snpeff.util.Log
 
MAX_WARNS - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
 
MAX_WEIGHT_SUM - Static variable in class org.snpeff.reactome.events.Reaction
 
maxExons - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
maxGeneLen - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
maxPvalue - Variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
 
maxPvalueAjusted - Variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
 
maxRankSum(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Maximum possible rank sum
maxRankSum(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
Maximum possible rank sum
maxTranscripts - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
maxTranscriptSupportLevel - Variable in class org.snpeff.SnpEff
 
MB - Static variable in class org.snpeff.util.Gpr
 
mean(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
mean(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Mean value for a given N and N_T
mean(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
Mean value for a given N and N_T
mean(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
Calculate the mean References: http://en.wikipedia.org/wiki/Hypergeometric_distribution
merge() - Method in class org.snpeff.interval.Markers
Merge overlapping intervals This is the same as 'union()' method, but the algorithm is more efficient
message - Variable in class org.snpeff.snpEffect.VariantEffect
 
method - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
MICRO_RNA - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
MicroCosmEntry - Class in org.snpeff.fileIterator.microCosm
Entry in a MicroCosm (miRNA target prediction) file
MicroCosmEntry() - Constructor for class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
MicroCosmFileIterator - Class in org.snpeff.fileIterator.microCosm
Iterate on each line of a MicroCosm predictions References: http://www.ebi.ac.uk/enright-srv/microcosm/
MicroCosmFileIterator(String) - Constructor for class org.snpeff.fileIterator.microCosm.MicroCosmFileIterator
 
MicroRnaBindingSite - Class in org.snpeff.interval
miRna binding site (usually this was predicted by some algorithm)
MicroRnaBindingSite() - Constructor for class org.snpeff.interval.MicroRnaBindingSite
 
MicroRnaBindingSite(Marker, int, int, boolean, String, double) - Constructor for class org.snpeff.interval.MicroRnaBindingSite
 
mid - Variable in class org.snpeff.interval.tree.IntervalTreeArray
 
min() - Method in class org.snpeff.gsa.ScoreList
Get minimum pvalue
min() - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
 
min() - Method in class org.snpeff.stats.CountByKey
Minimum count
min() - Method in class org.snpeff.stats.CountByType
Minimum count
min(double) - Method in class org.snpeff.stats.CounterDouble
 
MIN - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
 
MIN_COUNT_CODON - Static variable in class org.snpeff.snpEffect.PurityChange
 
MIN_LINES - Static variable in class org.snpeff.fileIterator.GuessTableTypes
 
MIN_MARKERS_PER_LEAF - Static variable in class org.snpeff.interval.tree.IntervalTreeArray
 
MIN_QUALITY - Static variable in class org.snpeff.binseq.coder.DnaQualityCoder
 
MIN_TOTAL_FRAME_COUNT - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
MineMarkerIntervals - Class in org.snpeff.stats
Mine marker intervals: I.e.
MineMarkerIntervals(Markers) - Constructor for class org.snpeff.stats.MineMarkerIntervals
 
MineTwoMarkerIntervals - Class in org.snpeff.stats
Mine marker intervals: I.e.
MineTwoMarkerIntervals(Markers, Markers) - Constructor for class org.snpeff.stats.MineTwoMarkerIntervals
 
minExons - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
minRankSum(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Minimum possible rank sum
minRankSum(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
Minimum possible rank sum
minus(Marker) - Method in class org.snpeff.interval.Marker
Return the difference between two markers
minus(Marker) - Method in class org.snpeff.interval.Markers
Calculate 'set minus' using one interval
minus(Markers) - Method in class org.snpeff.interval.Markers
Returns the result of this set minus 'intervals'
miRNA - Enum constant in enum class org.snpeff.interval.BioType
 
miRnaName - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
MISC_FEATURE - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
misc_RNA - Enum constant in enum class org.snpeff.interval.BioType
 
MISC_RNA - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
mismatch - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
MISSENSE - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
 
MISSING - Static variable in class org.snpeff.fileIterator.VcfFileIterator
 
MIXED - Enum constant in enum class org.snpeff.interval.Variant.VariantType
 
MND_BASES_BEFORE_LAST_JUNCTION - Static variable in class org.snpeff.snpEffect.LossOfFunction
Number of bases before last exon-exon junction that nonsense mediated decay is supposed to occur
MNP - Enum constant in enum class org.snpeff.interval.Variant.VariantType
 
MODERATE - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
 
MODIFIER - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
 
Monitor - Class in org.snpeff.reactome
 
Monitor() - Constructor for class org.snpeff.reactome.Monitor
 
mother - Variable in class org.snpeff.vcf.PedigreeEntry
 
motherNum - Variable in class org.snpeff.vcf.PedigreeEntry
 
motif - Variable in class org.snpeff.SnpEff
 
Motif - Class in org.snpeff.interval
Regulatory elements
Motif() - Constructor for class org.snpeff.interval.Motif
 
Motif(Marker, int, int, boolean, String, String, String) - Constructor for class org.snpeff.interval.Motif
 
MOTIF - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
MOTIF_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
MotifFileIterator - Class in org.snpeff.fileIterator
Opens a regulation file and create Motif elements.
MotifFileIterator(String, Genome, Jaspar) - Constructor for class org.snpeff.fileIterator.MotifFileIterator
 
MotifLogo - Class in org.snpeff.motif
Create a DNA logo for a PWM References: - See WebLogo http://weblogo.berkeley.edu/ - "WebLogo: A Sequence Logo Generator"
MotifLogo(Pwm) - Constructor for class org.snpeff.motif.MotifLogo
 
mRna() - Method in class org.snpeff.interval.Transcript
Retrieve coding sequence AND the UTRs (mRNA = 5'UTR + CDS + 3'UTR) I.e.
MRNA - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
msg - Variable in class org.snpeff.logStatsServer.LogStats
 
Mt_rRNA - Enum constant in enum class org.snpeff.interval.BioType
 
Mt_tRNA - Enum constant in enum class org.snpeff.interval.BioType
 
multiThreaded - Variable in class org.snpeff.SnpEff
 
MultivalueHashMap<K,V> - Class in org.snpeff.collections
A Hash that can hold multiple values for each key
MultivalueHashMap() - Constructor for class org.snpeff.collections.MultivalueHashMap
 
MUTUALLY_EXCLUSIVE - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
 

N

N - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesCds
 
N - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesDel
 
N - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesDels
 
N - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIns
 
N - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant
 
N - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesMnps
 
N - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesSnps
 
N - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite
 
NA_VALUE - Static variable in class org.snpeff.gtex.Gtex
 
name - Variable in class org.snpeff.interval.Markers
 
name - Variable in class org.snpeff.reactome.Entity
 
name - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
 
name() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
Return an annotation "name" Clean up characters to make them compatible with VCF annotations
NCACTIVITY - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
 
NCCAT - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
 
NCCONS - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
 
NCELEMENT - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
 
NCFACTOR - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
 
NCMARK - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
 
NeedlemanWunsch - Class in org.snpeff.align
Needleman-Wunsch (global sequence alignment) algorithm for sequence alignment (short strings, since it's not memory optimized)
NeedlemanWunsch(String, String) - Constructor for class org.snpeff.align.NeedlemanWunsch
 
NeedlemanWunschOverlap - Class in org.snpeff.align
Needleman-Wunsch algorithm for string alignment (short strings, since it's not memory optimized)
NeedlemanWunschOverlap(String, String) - Constructor for class org.snpeff.align.NeedlemanWunschOverlap
 
NegativeRegulation - Enum constant in enum class org.snpeff.reactome.events.Reaction.RegulationType
 
netCdsChange() - Method in class org.snpeff.interval.codonChange.CodonChange
We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exons
netCdsChange() - Method in class org.snpeff.interval.codonChange.CodonChangeMnp
We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exons
netChange(boolean) - Method in class org.snpeff.interval.Variant
Return the change (always compared to 'referenceStrand')
netChange(Marker) - Method in class org.snpeff.interval.Variant
Only the part of the change that overlaps with a marker Return the change (always in positive strand)
newItree() - Method in class org.snpeff.interval.tree.IntervalForest
Create new tree.
newItree(Markers) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
newItree(Markers) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray
 
newItree(Markers) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri
 
newNode(Markers) - Method in class org.snpeff.interval.tree.IntervalNode
Create a new node
next - Variable in class org.snpeff.fileIterator.FileIterator
 
next() - Method in class org.snpeff.fileIterator.BinSeqFileIterator
 
next() - Method in class org.snpeff.fileIterator.FastqFileIterator
 
next() - Method in class org.snpeff.fileIterator.FileIterator
 
next() - Method in class org.snpeff.fileIterator.VariantTxtFileIterator
 
next() - Method in class org.snpeff.genBank.FeaturesFile
 
next() - Method in class org.snpeff.interval.IntervalSetIterator
 
next() - Method in class org.snpeff.util.CombinatorialIterator
 
next() - Method in class org.snpeff.util.IubString
 
NEXT_PROT - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
nextHighestPowerOfTwo(int) - Static method in class org.snpeff.collections.BitUtil
returns the next highest power of two, or the current value if it's already a power of two or zero
nextHighestPowerOfTwo(long) - Static method in class org.snpeff.collections.BitUtil
returns the next highest power of two, or the current value if it's already a power of two or zero
nextLine - Variable in class org.snpeff.fileIterator.FileIterator
 
nextProt - Variable in class org.snpeff.SnpEff
 
nextProt(Transcript, String, String, int, int) - Method in class org.snpeff.nextProt.NextProtMarkerFactory
Create a single NextProt marker
nextProt(Transcript, NextProtXmlAnnotation, Location) - Method in class org.snpeff.nextProt.NextProtMarkerFactory
Create a list of NextProt markers according to this annotation
NextProt - Class in org.snpeff.interval
NextProt annotation marker
NextProt() - Constructor for class org.snpeff.interval.NextProt
 
NextProt(Transcript, int, int, String) - Constructor for class org.snpeff.interval.NextProt
 
NextProt(Transcript, int, int, String, String) - Constructor for class org.snpeff.interval.NextProt
 
NextProtDb - Class in org.snpeff.nextProt
Parse NetxProt XML file and build a database
NextProtDb(String, Config) - Constructor for class org.snpeff.nextProt.NextProtDb
 
NextProtHandler - Class in org.snpeff.nextProt
Handler used in XML parsing for NextProt database It keeps track of the tags and saves state data to create Markers using NextProtMarkerFactory http://www.nextprot.org/
NextProtHandler(NextProtMarkerFactory) - Constructor for class org.snpeff.nextProt.NextProtHandler
 
nextProtKeepAllTrs - Variable in class org.snpeff.SnpEff
 
NextProtMarkerFactory - Class in org.snpeff.nextProt
Creates Markers from nextprot XML annotations
NextProtMarkerFactory(Config) - Constructor for class org.snpeff.nextProt.NextProtMarkerFactory
 
NextProtSequenceConservation - Class in org.snpeff.nextProt
A simple analysis of sequence conservation for each entry type Why? Many NextProt annotations are only a few amino acids long (or only 1 AA) and often they only involve very specific sequences If the sequence is highly conserved and a non-synonymous mutation occurs, then this might be disruptive (i.e.
NextProtSequenceConservation() - Constructor for class org.snpeff.nextProt.NextProtSequenceConservation
 
NextProtXmlAnnotation - Class in org.snpeff.nextProt
Mimics the 'annotation' tag in a NextProt XML file
NextProtXmlAnnotation(NextProtXmlEntry, String) - Constructor for class org.snpeff.nextProt.NextProtXmlAnnotation
 
NextProtXmlEntry - Class in org.snpeff.nextProt
Mimics the 'entry' in a NextProt XML file
NextProtXmlEntry(String, NextProtHandler) - Constructor for class org.snpeff.nextProt.NextProtXmlEntry
 
NextProtXmlIsoform - Class in org.snpeff.nextProt
Mimics the 'isoform-mapping' in a NextProt XML file
NextProtXmlIsoform(String) - Constructor for class org.snpeff.nextProt.NextProtXmlIsoform
 
NextProtXmlNode - Class in org.snpeff.nextProt
Mimics a node in NextProt XML file
NextProtXmlNode(String) - Constructor for class org.snpeff.nextProt.NextProtXmlNode
 
nextSetBit(int) - Method in class org.snpeff.collections.OpenBitSet
Returns the index of the first set bit starting at the index specified.
nextSetBit(long) - Method in class org.snpeff.collections.OpenBitSet
Returns the index of the first set bit starting at the index specified.
Nmer - Class in org.snpeff.nmer
Binary packed N-mer (i.e.
Nmer(int) - Constructor for class org.snpeff.nmer.Nmer
 
Nmer(String) - Constructor for class org.snpeff.nmer.Nmer
 
NMER_SIZE - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
 
NmerCount - Class in org.snpeff.nmer
Mark if an Nmer has been 'seen' It only count up to 255 (one byte per counter)
NmerCount(int) - Constructor for class org.snpeff.nmer.NmerCount
 
NmerCountWc - Class in org.snpeff.nmer
Create a counter that can count Nmers as well as their WC complements That means that given an Nmer, the nmer and the Watson-Crick complement are counted the same.
NmerCountWc(int) - Constructor for class org.snpeff.nmer.NmerCountWc
 
NO_VARIANT - Static variable in class org.snpeff.interval.Variant
 
noGenome - Variable in class org.snpeff.SnpEff
 
NOINFO - Enum constant in enum class org.snpeff.logStatsServer.LogStats.RequestResult
 
non_coding - Enum constant in enum class org.snpeff.interval.BioType
 
NON_CODING - Enum constant in enum class org.snpeff.interval.Gene.GeneType
 
NON_CODING - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.Coding
 
non_stop_decay - Enum constant in enum class org.snpeff.interval.BioType
 
NON_SYNONYMOUS_CODING - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
NON_SYNONYMOUS_START - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
NON_SYNONYMOUS_STOP - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
NONE - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
 
NONE - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
 
NONE - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
NONE - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
 
NoneAlgorithm - Class in org.snpeff.geneSets.algorithm
An algorithm that does nothing
NoneAlgorithm(GeneSets) - Constructor for class org.snpeff.geneSets.algorithm.NoneAlgorithm
 
NONSENSE - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
 
nonsense_mediated_decay - Enum constant in enum class org.snpeff.interval.BioType
 
NormalDistribution - Class in org.snpeff.probablility
Calculate Normal distribution (PDF & CDF) using more precision if required
NormalDistribution() - Constructor for class org.snpeff.probablility.NormalDistribution
 
noSpaces(String) - Static method in class org.snpeff.util.Gpr
Remove spaces and tabs from string.
ntz(int) - Static method in class org.snpeff.collections.BitUtil
Returns number of trailing zeros in a 32 bit int value.
ntz(long) - Static method in class org.snpeff.collections.BitUtil
Returns number of trailing zeros in a 64 bit long value.
ntz2(long) - Static method in class org.snpeff.collections.BitUtil
returns 0 based index of first set bit (only works for x!=0)
This is an alternate implementation of ntz()
ntz3(long) - Static method in class org.snpeff.collections.BitUtil
returns 0 based index of first set bit
This is an alternate implementation of ntz()
ntzTable - Static variable in class org.snpeff.collections.BitUtil
table of number of trailing zeros in a byte
NullReader - Class in org.snpeff.fileIterator
A buffered reader for a file.
NullReader() - Constructor for class org.snpeff.fileIterator.NullReader
 
NUM_CORES - Static variable in class org.snpeff.util.Gpr
 
NUM_DEL_TEST - Static variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCutsomIntervals
 
NUM_DEL_TEST - Static variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLof
 
NUM_LARGE_INTERVALS - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
NUM_SMALL_INTERVALS - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
number - Variable in class org.snpeff.vcf.VcfHeaderInfo
 
number(String) - Static method in class org.snpeff.interval.Chromosome
Convert to chromosome number (return '0' if it cannot be converted)
NUMBER - Enum constant in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
 
NUMBER_OF_COMPARISSONS - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
 
numberOfInterestingSymbols() - Method in class org.snpeff.geneOntology.GoTerms
Calculate how many interesting symbol-IDs in are there in all these GOTerms
numberOfNodes() - Method in class org.snpeff.geneOntology.GoTerms
Number of nodes in this DAG
numberOfNodesWithOneInterestingSymbol() - Method in class org.snpeff.geneOntology.GoTerms
Calculate the number of nodes in that have at least one interesting symbol
numberOfNodesWithOneSymbol() - Method in class org.snpeff.geneOntology.GoTerms
Calculate the number of nodes in that have at least one annotated symbol
numberOfSymbols() - Method in class org.snpeff.geneOntology.GoTerms
Calculate how many symbol-IDs in are there in all these GOTerms
numChilds() - Method in class org.snpeff.interval.IntervalAndSubIntervals
 
numGenes - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
numWorkers - Variable in class org.snpeff.SnpEff
 

O

observed(String) - Method in class org.snpeff.stats.ObservedOverExpected
 
observed(String) - Method in class org.snpeff.stats.ObservedOverExpectedCHG
Count the number of CHH in this sequence
observed(String) - Method in class org.snpeff.stats.ObservedOverExpectedCHH
Count the number of CHH in this sequence
observed(String) - Method in class org.snpeff.stats.ObservedOverExpectedCpG
Count the number of CpG in this sequence
observed(Exon) - Method in class org.snpeff.stats.ObservedOverExpected
Observed sequence (average between plus and minus strand)
observed(Gene) - Method in class org.snpeff.stats.ObservedOverExpected
Observed sequence (average between plus and minus strand)
observed(Transcript) - Method in class org.snpeff.stats.ObservedOverExpected
Observed sequence (average between plus and minus strand)
observedChg(String) - Method in class org.snpeff.stats.ObservedOverExpected
Count the number of CHG in this sequence
ObservedOverExpected - Class in org.snpeff.stats
Observed over expected values (o/e) ratios E.g.: CpG dinucleotides in a sequence
ObservedOverExpected() - Constructor for class org.snpeff.stats.ObservedOverExpected
 
ObservedOverExpectedCHG - Class in org.snpeff.stats
Observed over expected values (o/e) of CHG in a sequence
ObservedOverExpectedCHG() - Constructor for class org.snpeff.stats.ObservedOverExpectedCHG
 
ObservedOverExpectedCHH - Class in org.snpeff.stats
Observed over expected values (o/e) of CHH in a sequence
ObservedOverExpectedCHH() - Constructor for class org.snpeff.stats.ObservedOverExpectedCHH
 
ObservedOverExpectedCpG - Class in org.snpeff.stats
Observed over expected values (o/e) of CpG in a sequence
ObservedOverExpectedCpG() - Constructor for class org.snpeff.stats.ObservedOverExpectedCpG
 
oe(String) - Method in class org.snpeff.stats.ObservedOverExpected
Observed over expected ratio
oe(Exon) - Method in class org.snpeff.stats.ObservedOverExpected
Observed over expected ratio
oe(Gene) - Method in class org.snpeff.stats.ObservedOverExpected
Observed over expected ratio
oe(Transcript) - Method in class org.snpeff.stats.ObservedOverExpected
Observed over expected ratio
OFFSET - Static variable in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
 
OK - Enum constant in enum class org.snpeff.logStatsServer.LogStats.RequestResult
 
ONE - Static variable in class org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
 
onlyMinusStrand - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
onlyOneError - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
 
onlyOneError - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
onlyPlusStrand - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
onlyProtein - Variable in class org.snpeff.SnpEff
 
onlyRegulation - Variable in class org.snpeff.SnpEff
 
onlyTranscriptsFile - Variable in class org.snpeff.SnpEff
 
open() - Method in class org.snpeff.svg.Svg
 
open() - Method in class org.snpeff.vcf.FileIndexChrPos
Open file and initiate mappings
open(String) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
open(String) - Method in class org.snpeff.genBank.Features
Open a file
open(String) - Method in class org.snpeff.genBank.FeaturesFile
Open a file
OpenBitSet - Class in org.snpeff.collections
An "open" BitSet implementation that allows direct access to the array of words storing the bits.
OpenBitSet() - Constructor for class org.snpeff.collections.OpenBitSet
 
OpenBitSet(long) - Constructor for class org.snpeff.collections.OpenBitSet
Constructs an OpenBitSet large enough to hold numBits.
OpenBitSet(long[], int) - Constructor for class org.snpeff.collections.OpenBitSet
Constructs an OpenBitSet from an existing long[].
opposite() - Method in enum class org.snpeff.ped.Sex
Return the opposite sex
or(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
 
ORDER - Static variable in class org.snpeff.genBank.Features
 
org.snpeff - package org.snpeff
 
org.snpeff.align - package org.snpeff.align
 
org.snpeff.binseq - package org.snpeff.binseq
 
org.snpeff.binseq.coder - package org.snpeff.binseq.coder
 
org.snpeff.binseq.comparator - package org.snpeff.binseq.comparator
 
org.snpeff.binseq.indexer - package org.snpeff.binseq.indexer
 
org.snpeff.codons - package org.snpeff.codons
 
org.snpeff.collections - package org.snpeff.collections
 
org.snpeff.complexity - package org.snpeff.complexity
 
org.snpeff.coverage - package org.snpeff.coverage
 
org.snpeff.fastq - package org.snpeff.fastq
 
org.snpeff.fileIterator - package org.snpeff.fileIterator
 
org.snpeff.fileIterator.microCosm - package org.snpeff.fileIterator.microCosm
 
org.snpeff.fileIterator.parser - package org.snpeff.fileIterator.parser
 
org.snpeff.filter - package org.snpeff.filter
 
org.snpeff.genBank - package org.snpeff.genBank
 
org.snpeff.geneOntology - package org.snpeff.geneOntology
 
org.snpeff.geneSets - package org.snpeff.geneSets
 
org.snpeff.geneSets.algorithm - package org.snpeff.geneSets.algorithm
 
org.snpeff.genotypes - package org.snpeff.genotypes
 
org.snpeff.gsa - package org.snpeff.gsa
 
org.snpeff.gtex - package org.snpeff.gtex
 
org.snpeff.interval - package org.snpeff.interval
 
org.snpeff.interval.codonChange - package org.snpeff.interval.codonChange
 
org.snpeff.interval.tree - package org.snpeff.interval.tree
 
org.snpeff.logStatsServer - package org.snpeff.logStatsServer
 
org.snpeff.motif - package org.snpeff.motif
 
org.snpeff.nextProt - package org.snpeff.nextProt
 
org.snpeff.nmer - package org.snpeff.nmer
 
org.snpeff.osCmd - package org.snpeff.osCmd
 
org.snpeff.outputFormatter - package org.snpeff.outputFormatter
 
org.snpeff.overlap - package org.snpeff.overlap
 
org.snpeff.pdb - package org.snpeff.pdb
 
org.snpeff.ped - package org.snpeff.ped
 
org.snpeff.probablility - package org.snpeff.probablility
 
org.snpeff.probablility.bootstrap - package org.snpeff.probablility.bootstrap
 
org.snpeff.reactome - package org.snpeff.reactome
 
org.snpeff.reactome.events - package org.snpeff.reactome.events
 
org.snpeff.sam - package org.snpeff.sam
 
org.snpeff.serializer - package org.snpeff.serializer
 
org.snpeff.snpEffect - package org.snpeff.snpEffect
 
org.snpeff.snpEffect.commandLine - package org.snpeff.snpEffect.commandLine
 
org.snpeff.snpEffect.factory - package org.snpeff.snpEffect.factory
 
org.snpeff.snpEffect.testCases - package org.snpeff.snpEffect.testCases
 
org.snpeff.snpEffect.testCases.integration - package org.snpeff.snpEffect.testCases.integration
 
org.snpeff.snpEffect.testCases.unity - package org.snpeff.snpEffect.testCases.unity
 
org.snpeff.spliceSites - package org.snpeff.spliceSites
 
org.snpeff.stats - package org.snpeff.stats
 
org.snpeff.stats.plot - package org.snpeff.stats.plot
 
org.snpeff.svg - package org.snpeff.svg
 
org.snpeff.util - package org.snpeff.util
 
org.snpeff.vcf - package org.snpeff.vcf
 
OsCmdQueue - Class in org.snpeff.osCmd
A queue of commands to be run.
OsCmdQueue() - Constructor for class org.snpeff.osCmd.OsCmdQueue
 
OsCmdRunner - Class in org.snpeff.osCmd
Run an OS command as a thread
OsCmdRunner(String, String[]) - Constructor for class org.snpeff.osCmd.OsCmdRunner
 
output - Variable in class org.snpeff.reactome.Entity
 
output - Variable in class org.snpeff.SnpEff
 
OutputFormatter - Class in org.snpeff.outputFormatter
Formats output How is this used: - newSection(); // Create a new 'section' on the output format (e.g.
OutputFormatter() - Constructor for class org.snpeff.outputFormatter.OutputFormatter
 
outputs - Variable in class org.snpeff.reactome.events.Reaction
 
overlap(BinarySequence, int) - Method in class org.snpeff.binseq.BinarySequence
Creates a new sequence by overlapping 'this' and 'sequence' E.g.
overlap(BinarySequence, int) - Method in class org.snpeff.binseq.DnaAndQualitySequence
Creates a new sequence by overlapping 'this' and 'sequence' E.g.
overlap(BinarySequence, int) - Method in class org.snpeff.binseq.DnaSequence
Creates a new sequence by overlapping 'this' and 'sequence' E.g.
overlap(DnaSequence, DnaSequence) - Method in class org.snpeff.overlap.OverlapDnaSeq
 
overlap(S, S) - Method in class org.snpeff.overlap.Overlap
Calculate the best overlap between two sequences
overlap(T) - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
Find the best possible overlap and join the sequences or just add add the sequence to the index
Overlap<S extends BinarySequence> - Class in org.snpeff.overlap
Calculates the best overlap between two sequences Note: An overlap is a simple 'alignment' which can only contain gaps at the beginning or at the end of the sequences.
Overlap() - Constructor for class org.snpeff.overlap.Overlap
 
OverlapDnaSeq - Class in org.snpeff.overlap
 
OverlapDnaSeq() - Constructor for class org.snpeff.overlap.OverlapDnaSeq
 
OverlapFilter<T extends BinarySequence> - Interface in org.snpeff.binseq.indexer
Indicate whether an overlap between two sequences should be considered or not
OverlapFilterCompareAllAll - Class in org.snpeff.binseq.indexer
Only allow overlaps between sequences mapped to same/different partition
OverlapFilterCompareAllAll() - Constructor for class org.snpeff.binseq.indexer.OverlapFilterCompareAllAll
 
OverlapFilterDnaId - Class in org.snpeff.binseq.indexer
Only allow sequences with different IDs to be overlapped
OverlapFilterDnaId() - Constructor for class org.snpeff.binseq.indexer.OverlapFilterDnaId
 
OverlapRessult<T extends BinarySequence> - Class in org.snpeff.binseq.indexer
An object used to store overlap parameters
OverlapRessult() - Constructor for class org.snpeff.binseq.indexer.OverlapRessult
 

P

p(int[], int[], double[]) - Method in class org.snpeff.probablility.CochranArmitageTest
 
P - Static variable in class org.snpeff.fastq.FastqSplit
 
P_VALUE_THRESHOLD - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
padN(String, int) - Static method in class org.snpeff.util.GprSeq
 
pAll(int) - Method in class org.snpeff.spliceSites.AcgtTree
 
pAll(int, List<Double>) - Method in class org.snpeff.spliceSites.AcgtTree
 
parent - Variable in class org.snpeff.interval.Interval
 
parse() - Method in class org.snpeff.nextProt.NextProtDb
Parse all XML files in a directory
parse() - Method in class org.snpeff.vcf.VcfEntry
Parse a 'line' from a 'vcfFileIterator'
parse() - Method in class org.snpeff.vcf.VcfHeader
Parse header lines
parse(String) - Method in interface org.snpeff.fileIterator.parser.Parser
 
parse(String) - Method in class org.snpeff.fileIterator.VcfFileIterator
 
parse(String) - Static method in enum class org.snpeff.genBank.Feature.Type
Parse a string into a Feature.Type
parse(String) - Method in class org.snpeff.gtex.GtexExperiment
 
parse(String) - Static method in enum class org.snpeff.interval.BioType
Parse a BioType
parse(String) - Static method in enum class org.snpeff.interval.GffType
 
parse(String) - Static method in enum class org.snpeff.interval.TranscriptSupportLevel
 
parse(String) - Method in class org.snpeff.logStatsServer.VersionCheck
Parse versions page Format: One entry per line Line format: "softwareName \t version \t date \t URL \n"
parse(String) - Method in class org.snpeff.ped.PedEntry
 
parse(String) - Method in class org.snpeff.ped.TfamEntry
Parse a line form a TFAM file
parse(String) - Method in class org.snpeff.sam.SamHeaderRecord
Parse a line for this record type
parse(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Parse a line
parse(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22
 
parse(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
 
parse(String) - Static method in enum class org.snpeff.vcf.VcfInfoType
 
parse(String[]) - Method in class org.snpeff.genotypes.Genotypes
Parse command line arguments
parse(String[]) - Method in class org.snpeff.ped.PedEntry
 
parse(String[]) - Method in class org.snpeff.ped.TfamEntry
Parse fields form a line
parse(Genome, String) - Method in class org.snpeff.interval.GffMarker
Parse an entry (line) from a GFF file
parse(EffFormatVersion, String) - Static method in enum class org.snpeff.snpEffect.EffectType
Parse a string to an EffectType
parse(VcfConsequenceHeader, String) - Static method in class org.snpeff.vcf.VcfConsequence
 
parse(VcfConsequenceHeader, VcfEntry) - Static method in class org.snpeff.vcf.VcfConsequence
 
parseArgs(String[]) - Method in class org.snpeff.fastq.FastqSplit
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.SnpEff
Parse command line arguments
parseArgs(String[]) - Method in interface org.snpeff.snpEffect.commandLine.CommandLine
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuildNextProt
 
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCount
Parse
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
 
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDownload
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDump
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
 
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdLen
 
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdSeq
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdShow
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
Parse command line arguments
parseArgs(String[]) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
 
parseArgs(String[]) - Method in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
parseAttributes(String) - Method in class org.snpeff.interval.GffMarker
Parse attributes (key-value pairs) from a line in a GFF file
parseAttributes(String) - Method in class org.snpeff.interval.Gtf2Marker
Parse attributes
parseBoolSafe(String) - Static method in class org.snpeff.util.Gpr
Equivalent to Boolean.parseBoolean, except it returns 0 on invalid integer (NumberFormatException)
parsedHeader() - Method in class org.snpeff.fileIterator.GuessTableTypes
 
parseDoubleSafe(String) - Static method in class org.snpeff.util.Gpr
Equivalent to Double.parseDouble(), except it returns 0 on invalid double (NumberFormatException)
parseFeatures() - Method in class org.snpeff.genBank.Features
Parse features
parseField(String, String) - Method in class org.snpeff.sam.SamHeaderRecord
Parse a field for this record
parseField(String, String) - Method in class org.snpeff.sam.SamHeaderRecordSq
 
parseFieldLine(String, String, int) - Method in class org.snpeff.genBank.Embl
Parse a feature line Line types: ID - identification (begins each entry; 1 per entry) AC - accession number (>=1 per entry) PR - project identifier (0 or 1 per entry) DT - date (2 per entry) DE - description (>=1 per entry) KW - keyword (>=1 per entry) OS - organism species (>=1 per entry) OC - organism classification (>=1 per entry) OG - organelle (0 or 1 per entry) RN - reference number (>=1 per entry) RC - reference comment (>=0 per entry) RP - reference positions (>=1 per entry) RX - reference cross-reference (>=0 per entry) RG - reference group (>=0 per entry) RA - reference author(s) (>=0 per entry) RT - reference title (>=1 per entry) RL - reference location (>=1 per entry) DR - database cross-reference (>=0 per entry) CC - comments or notes (>=0 per entry) AH - assembly header (0 or 1 per entry) AS - assembly information (0 or >=1 per entry) FH - feature table header (2 per entry) FT - feature table data (>=2 per entry) XX - spacer line (many per entry) SQ - sequence header (1 per entry) CO - contig/construct line (0 or >=1 per entry) bb - (blanks) sequence data (>=1 per entry) // - termination line (ends each entry; 1 per entry)
parseFieldLine(String, String, int, int) - Method in class org.snpeff.genBank.GenBank
Parse a feature line
parseFloatSafe(String) - Static method in class org.snpeff.util.Gpr
Equivalent to Float.parseFloat(), except it returns 0 on invalid double (NumberFormatException)
parseId() - Method in class org.snpeff.interval.GffMarker
Obtain or create an ID
parseInt(char[]) - Static method in class org.snpeff.collections.ArrayUtil
Parses the string argument as if it was an int value and returns the result.
parseInt(char[], int, int) - Static method in class org.snpeff.collections.ArrayUtil
Parses a char array into an int.
parseInt(char[], int, int, int) - Static method in class org.snpeff.collections.ArrayUtil
Parses the string argument as if it was an int value and returns the result.
parseIntSafe(String) - Static method in class org.snpeff.util.Gpr
Equivalent to Integer.parseInt, except it returns 0 on invalid integer (NumberFormatException)
parseLof() - Method in class org.snpeff.vcf.VcfEntry
Parse LOF from VcfEntry
parseLongSafe(String) - Static method in class org.snpeff.util.Gpr
Equivalent to Integer.parseInt, except it returns 0 on invalid integer (NumberFormatException)
parseNmd() - Method in class org.snpeff.vcf.VcfEntry
Parse NMD from VcfEntry
parsePosition(String) - Method in class org.snpeff.fileIterator.MarkerFileIterator
Parse a string as a 'position'.
parsePosition(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Parse a string as a 'position'.
Parser<T> - Interface in org.snpeff.fileIterator.parser
Parse a string and return a collection of objects.
parseSampleNames() - Method in class org.snpeff.vcf.VcfHeader
 
parseSampleNum() - Method in class org.snpeff.vcf.VcfHeader
 
parseSnpEffectFile(String) - Method in class org.snpeff.snpEffect.testCases.integration.CompareEffects
Parse a variant file and return a list
parseTranscript(String) - Static method in class org.snpeff.snpEffect.Hgvs
 
parseVcfLine(String) - Method in class org.snpeff.fileIterator.VcfFileIterator
Parse a line from a VCF file
path(String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
path(String) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
pathClassName() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
pathClassName() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
pathMigrate(String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Used to migrate test files in old path
Pathway - Class in org.snpeff.reactome.events
A Reactome pathway
Pathway(int, String) - Constructor for class org.snpeff.reactome.events.Pathway
 
Pcingola - Class in org.snpeff
Author's data
Pcingola() - Constructor for class org.snpeff.Pcingola
 
pdb() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
PDB analysis
PDB_EXT - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
PDB_EXT_GZ - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
PDB_EXTS - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
pdbAaLen - Variable in class org.snpeff.pdb.IdMapperEntry
 
pdbAnalysis() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
Check that protein sequences form PDB matches sequences from Genome Return an IdMapped of confirmed entries (i.e.
pdbAnalysis(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
Analyze a PDB file
pdbChainId - Variable in class org.snpeff.pdb.IdMapperEntry
 
pdbChainId1 - Variable in class org.snpeff.pdb.DistanceResult
 
pdbChainId2 - Variable in class org.snpeff.pdb.DistanceResult
 
PdbFile - Class in org.snpeff.pdb
A structure that reads PDB files This code is similar to 'PDBFileReader' from BioJava, but the BioJava version doesn't close file descriptors and eventually produces a crash when reading many files.
PdbFile() - Constructor for class org.snpeff.pdb.PdbFile
 
pdbId - Variable in class org.snpeff.pdb.DistanceResult
 
pdbId - Variable in class org.snpeff.pdb.IdMapperEntry
 
pdf(double, double, double) - Static method in class org.snpeff.probablility.NormalDistribution
 
pdf(double, int, int) - Method in class org.snpeff.probablility.Binomial
Probability density function
pdf(int, int, int) - Static method in class org.snpeff.probablility.RankSumPdf
Probability density function (pdf)
pdf(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Probability of getting a rank sum equal to 'r' when adding the ranks of 'nt' selected items.
pdfApfloat(double, double, double) - Static method in class org.snpeff.probablility.NormalDistribution
 
pdfExact(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Probability of getting a rank sum equal to 'r' when adding the ranks of 'nt' selected items.
pdfExact(int, int, long, long, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Probability density function (pdf): Exact calculation
pdfLog(double, int, int) - Method in class org.snpeff.probablility.Binomial
 
pdfNormal(int, int, int) - Static method in class org.snpeff.probablility.RankSumPdf
Normal approximation to rank sum statistic
pdfNormal(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Normal approximation to rank sum statistic
pdfTriangle(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Uniform 'approximation' to rank sum statistic
pdfUniform(int, int, long) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Uniform 'approximation' to rank sum statistic
PedEntry - Class in org.snpeff.ped
An entry in a PED table.
PedEntry(PlinkMap, String) - Constructor for class org.snpeff.ped.PedEntry
 
PedEntry(PlinkMap, String, String, String, String, Sex, double, String[]) - Constructor for class org.snpeff.ped.PedEntry
 
PedFamily - Class in org.snpeff.ped
A family: A group of Tfams with the same familyId
PedFamily() - Constructor for class org.snpeff.ped.PedFamily
 
PedFileIterator - Class in org.snpeff.ped
PED file iterator (PED file from PLINK) Reference: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
PedFileIterator(String, String) - Constructor for class org.snpeff.ped.PedFileIterator
 
PedGenotype - Class in org.snpeff.ped
A Simple genotype implementation for PED files
PedGenotype(String[]) - Constructor for class org.snpeff.ped.PedGenotype
 
PedGenotype(String[], String, int) - Constructor for class org.snpeff.ped.PedGenotype
 
Pedigree - Class in org.snpeff.vcf
A pedigree for cancer samples
Pedigree(VcfFileIterator) - Constructor for class org.snpeff.vcf.Pedigree
 
Pedigree(VcfFileIterator, String) - Constructor for class org.snpeff.vcf.Pedigree
 
PEDIGREE_PREFIX - Static variable in class org.snpeff.vcf.VcfHeader
 
PedigreeEntry - Class in org.snpeff.vcf
Pedigree entry in a VCF file header E.g.: ##PEDIGREE=<Derived=Patient_01_Somatic,Original=Patient_01_Germline> or ##PEDIGREE=<Child=CHILD-GENOME-ID,Mother=MOTHER-GENOME-ID,Father=FATHER-GENOME-ID>
PedigreeEntry(String, String) - Constructor for class org.snpeff.vcf.PedigreeEntry
 
PedigreeEntry(String, String, String) - Constructor for class org.snpeff.vcf.PedigreeEntry
 
PedPedigree - Class in org.snpeff.ped
A pedigree of PedEntries
PedPedigree() - Constructor for class org.snpeff.ped.PedPedigree
 
PedPedigree(String) - Constructor for class org.snpeff.ped.PedPedigree
 
percent(String) - Method in class org.snpeff.stats.CountByType
Percentage by type
percentColumns() - Method in class org.snpeff.stats.plot.GoogleBarChart
Scale columns to their respective counts
percentColumns(ArrayList<String>) - Method in class org.snpeff.stats.plot.GoogleBarChart
Scale column to total sum
phase - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
PHASE - Enum constant in enum class org.snpeff.interval.FrameType
 
PHENOTYPE_CASE - Static variable in class org.snpeff.ped.TfamEntry
From PLINK's manual: Affection status, by default, should be coded: -9 missing 0 missing 1 unaffected 2 affected
PHENOTYPE_CONTROL - Static variable in class org.snpeff.ped.TfamEntry
 
PHENOTYPE_MISSING - Static variable in class org.snpeff.ped.TfamEntry
 
pident - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
PlinkMap - Class in org.snpeff.ped
PLINK MAP file References: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
PlinkMap() - Constructor for class org.snpeff.ped.PlinkMap
 
PlinkMap(String) - Constructor for class org.snpeff.ped.PlinkMap
 
plodity() - Method in class org.snpeff.vcf.VcfGenotype
Genotype plodity (i.e.
Polymerisation - Class in org.snpeff.reactome.events
A polymerization event
Polymerisation(int, String) - Constructor for class org.snpeff.reactome.events.Polymerisation
 
polymorphic_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
pop(long) - Static method in class org.snpeff.collections.BitUtil
Returns the number of bits set in the long
pop_andnot(long[], long[], int, int) - Static method in class org.snpeff.collections.BitUtil
Returns the popcount or cardinality of A & ~B Neither array is modified.
pop_array(long[], int, int) - Static method in class org.snpeff.collections.BitUtil
Returns the number of set bits in an array of longs.
pop_intersect(long[], long[], int, int) - Static method in class org.snpeff.collections.BitUtil
Returns the popcount or cardinality of the two sets after an intersection.
pop_union(long[], long[], int, int) - Static method in class org.snpeff.collections.BitUtil
Returns the popcount or cardinality of the union of two sets.
pop_xor(long[], long[], int, int) - Static method in class org.snpeff.collections.BitUtil
 
pos - Variable in class org.snpeff.fileIterator.MatrixEntry
 
pos() - Method in class org.snpeff.snpEffect.HgvsDna
Genomic position for exonic variants
pos(int) - Method in class org.snpeff.snpEffect.HgvsDna
HGVS position base on genomic coordinates (chr is assumed to be the same as in transcript/marker).
pos(int) - Method in class org.snpeff.snpEffect.HgvsProtein
Protein position
pos(int, int) - Method in class org.snpeff.snpEffect.HgvsProtein
 
pos(String) - Method in class org.snpeff.vcf.FileIndexChrPos
The position argument of a line (second column in tab-separated format).
pos(Transcript, int) - Method in class org.snpeff.snpEffect.HgvsProtein
Protein position
pos(Transcript, int, int) - Method in class org.snpeff.snpEffect.HgvsProtein
Position string given two coordinates
POS_OFFSET - Static variable in class org.snpeff.vcf.FileIndexChrPos
 
pos1 - Variable in class org.snpeff.pdb.DistanceResult
 
pos2 - Variable in class org.snpeff.pdb.DistanceResult
 
posArray() - Method in class org.snpeff.stats.ChrPosStats
 
posDel() - Method in class org.snpeff.snpEffect.HgvsProtein
Position for deletions
posDelIns() - Method in class org.snpeff.snpEffect.HgvsProtein
Position for 'delins'
posDownstream(int) - Method in class org.snpeff.snpEffect.HgvsDna
Position downstream of the transcript
posDup() - Method in class org.snpeff.snpEffect.HgvsProtein
Position for 'duplications' (a special kind of insertion)
posExon(int) - Method in class org.snpeff.snpEffect.HgvsDna
Convert genomic position to HGVS compatible (DNA) position
posFs() - Method in class org.snpeff.snpEffect.HgvsProtein
Frame shifts ....are described using ...
posIns() - Method in class org.snpeff.snpEffect.HgvsProtein
Position for insertions
posIntron(int, Intron) - Method in class org.snpeff.snpEffect.HgvsDna
Intronic position
position - Variable in class org.snpeff.vcf.FileIndexChrPos.LineAndPos
 
PositiveRegulation - Enum constant in enum class org.snpeff.reactome.events.Reaction.RegulationType
 
posSnpOrMnp() - Method in class org.snpeff.snpEffect.HgvsProtein
Position: SNP or NMP
PosStats - Class in org.snpeff.stats
How many changes per position do we have in a chromosome.
PosStats() - Constructor for class org.snpeff.stats.PosStats
 
PosStats(String) - Constructor for class org.snpeff.stats.PosStats
 
PosStats(String, int) - Constructor for class org.snpeff.stats.PosStats
 
posUpstream(int) - Method in class org.snpeff.snpEffect.HgvsDna
Position upstream of the transcript Note: How to calculate Upstream position: If strand is '-' as for NM_016176.3, "genomicTxStart" being the rightmost tx coord: cDotUpstream = -(cdsStart + variantPos - genomicTxStart) Instead of "-(variantPos - genomicCdsStart)": The method that stays in transcript space until extending beyond the transcript is correct because of these statements on http://varnomen.hgvs.org/bg-material/numbering/: * nucleotides upstream (5') of the ATG-translation initiation codon (start) are marked with a "-" (minus) and numbered c.-1, c.-2, c.-3, etc.
posUtr3(int) - Method in class org.snpeff.snpEffect.HgvsDna
Position within 3'UTR
posUtr5(int) - Method in class org.snpeff.snpEffect.HgvsDna
Position within 5'UTR
PREFERRED_CONFIG_FILE - Static variable in class org.snpeff.snpEffect.Config
 
prefixes - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
prefixes - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
prefixTranslocation() - Method in class org.snpeff.snpEffect.HgvsDna
Translocation nomenclature.
prependEachLine(String, Object) - Static method in class org.snpeff.util.Gpr
Prepend a message to each line
prependSequenceToFirstExon(String) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
Prepend first's exons sequence with a given one
prime3_overlapping_ncrna - Enum constant in enum class org.snpeff.interval.BioType
 
print() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Dump to sdtout
print(String) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
print(String) - Method in class org.snpeff.outputFormatter.OutputFormatter
Print a "raw" string to a file
PRINT_SOMETHING_TIME - Static variable in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
PRINT_SOMETHING_TIME - Static variable in class org.snpeff.geneSets.GeneSets
 
printSection(Marker) - Method in class org.snpeff.outputFormatter.OutputFormatter
End this section and print results
printSequences() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
 
probabilityTable(CountByType) - Method in class org.snpeff.coverage.CountReadsOnMarkers
Show probabilities
processed_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
processed_transcript - Enum constant in enum class org.snpeff.interval.BioType
 
progress() - Method in class org.snpeff.osCmd.ExecuteOsCommand
Report progress
progress() - Method in interface org.snpeff.osCmd.Progress
 
Progress - Interface in org.snpeff.osCmd
 
PROGRESSIVE_BASES_EXTRA - Static variable in class org.snpeff.align.VariantRealign
 
PROGRESSIVE_BASES_MULTIPLIER - Static variable in class org.snpeff.align.VariantRealign
 
PromoterSequences - Class in org.snpeff
Get promoter sequences from genes
PromoterSequences(String, String, List<String>) - Constructor for class org.snpeff.PromoterSequences
 
protein() - Method in class org.snpeff.interval.Transcript
Protein sequence (amino acid sequence produced by this transcripts)
protein_coding - Enum constant in enum class org.snpeff.interval.BioType
 
PROTEIN_INTERACTION_FILE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
PROTEIN_PROTEIN_INTERACTION_LOCUS - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
PROTEIN_STRUCTURAL_INTERACTION_LOCUS - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
ProteinInteractionLocus - Class in org.snpeff.interval
Protein interaction: An amino acid that is "in contact" with another amino acid.
ProteinInteractionLocus() - Constructor for class org.snpeff.interval.ProteinInteractionLocus
 
ProteinInteractionLocus(Transcript, int, int, String) - Constructor for class org.snpeff.interval.ProteinInteractionLocus
 
ProteinProteinInteractionLocus - Class in org.snpeff.interval
Protein interaction: An amino acid that is "in contact" with another amino acid within the same protein.
ProteinProteinInteractionLocus() - Constructor for class org.snpeff.interval.ProteinProteinInteractionLocus
 
ProteinProteinInteractionLocus(Transcript, int, int, Transcript, String) - Constructor for class org.snpeff.interval.ProteinProteinInteractionLocus
 
ProteinStructuralInteractionLocus - Class in org.snpeff.interval
Protein interaction: An amino acid that is "in contact" with another amino acid.
ProteinStructuralInteractionLocus() - Constructor for class org.snpeff.interval.ProteinStructuralInteractionLocus
 
ProteinStructuralInteractionLocus(Transcript, int, int, String) - Constructor for class org.snpeff.interval.ProteinStructuralInteractionLocus
 
pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
PurityChange - Class in org.snpeff.snpEffect
Analize purity changes in codons and amino acids
PurityChange(CodonTable) - Constructor for class org.snpeff.snpEffect.PurityChange
 
put(long, long) - Method in class org.snpeff.collections.HashLongLongArray
Insert a <key, value> pair How does it work? - bucket_number = hash.get( key ) - bu = bucket[ bucket_number ] - append 'value' to 'bu'
pValue - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
pValueBonferroni() - Method in class org.snpeff.gsa.ScoreList
Minimum p-value corrected using Bonferroni
pValueDown(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
 
pValueDown(int, int, int, int, double) - Method in class org.snpeff.probablility.FisherExactTest
Pvalue for 'k' or less Note: Includes 'k' It also compares to a 'threshold' value to speedup the process.
pValueFdr(double) - Method in class org.snpeff.gsa.ScoreList
Combine p-values using FDR procedure References: http://en.wikipedia.org/wiki/False_discovery_rate
pValueFisherChi2() - Method in class org.snpeff.gsa.ScoreList
Combine p-values using Fisher's method References: http://en.wikipedia.org/wiki/Fisher's_method
pValueSimes() - Method in class org.snpeff.gsa.ScoreList
Combine p-values using Simes's procedure References: http://biomet.oxfordjournals.org/content/73/3/751
PvaluesList - Class in org.snpeff.gsa
A list of pvalues (i.e.
PvaluesList() - Constructor for class org.snpeff.gsa.PvaluesList
 
pValueUp(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
 
pValueUp(int, int, int, int, double) - Method in class org.snpeff.probablility.FisherExactTest
Fisher's exact test for more than 'k' It also compares to a 'threshold' value to speedup the process.
pValueZScore() - Method in class org.snpeff.gsa.ScoreList
Combine p-values using Stouffer's Z-score method References: http://en.wikipedia.org/wiki/Fisher's_method (scroll down to Stouffer's method)
Pwm - Class in org.snpeff.motif
Create a DNA motif count matrix Refrence http://en.wikipedia.org/wiki/Position-specific_scoring_matrix
Pwm(int) - Constructor for class org.snpeff.motif.Pwm
 
Pwm(String) - Constructor for class org.snpeff.motif.Pwm
 
PwmAndSeqs - Class in org.snpeff.motif
Create a DNA motif count matrix and also count the number of sequences in that contribute to this motif.
PwmAndSeqs(int) - Constructor for class org.snpeff.motif.PwmAndSeqs
 

Q

qend - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
Qseq2Fastq - Class in org.snpeff
Convert qseq file to fastq
Qseq2Fastq() - Constructor for class org.snpeff.Qseq2Fastq
 
qseqid - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
qstart - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
quality - Variable in class org.snpeff.vcf.VcfEntry
 
qualityToBits(int) - Method in class org.snpeff.binseq.coder.Coder
Encode a quality using a binary representation
qualityToBits(int) - Method in class org.snpeff.binseq.coder.DnaQualityCoder
WARNING: This implementation transforms the quality to a range [0, ..., 63] (in order to use 6 bits)
qualtityArray(Fastq) - Static method in class org.snpeff.fastq.FastqTools
Create an array of integers describing quality
quantile(double) - Method in class org.snpeff.gsa.ScoreList
Get pvalue quantile
quantile(double) - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
Smallest number whose CDF is larger than a given quantile.
query(Interval) - Method in class org.snpeff.interval.tree.IntervalNode
Perform an interval intersection query on the node
query(Interval) - Method in class org.snpeff.interval.tree.IntervalNodeOri
Perform an interval intersection query on the node
query(Interval) - Method in class org.snpeff.interval.tree.IntervalTree
Perform an interval query, returning the intervals that intersect with 'interval'
query(Interval) - Method in class org.snpeff.interval.tree.IntervalTreeArray
Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'
query(Interval) - Method in class org.snpeff.interval.tree.IntervalTreeOri
Perform an interval query, returning the intervals that intersect with 'interval'
query(Interval) - Method in interface org.snpeff.interval.tree.Itree
Perform an interval query, returning the intervals that intersect with 'interval'
query(Interval, int, Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'
query(Marker) - Method in class org.snpeff.interval.CytoBands
 
query(Marker) - Method in class org.snpeff.interval.Exon
Query all genomic regions that intersect 'marker'
query(Marker) - Method in class org.snpeff.interval.IntervalAndSubIntervals
Query all genomic regions that intersect 'marker'
query(Marker) - Method in class org.snpeff.interval.Intron
Query all genomic regions that intersect 'marker'
query(Marker) - Method in class org.snpeff.interval.Marker
Query all genomic regions that intersect 'marker' (this makes sense in Gene, Transcript, Exon, etc.)
query(Marker) - Method in class org.snpeff.interval.Transcript
Query all genomic regions that intersect 'marker'
query(Marker) - Method in class org.snpeff.interval.tree.IntervalForest
Query all intervals that intersect with 'interval'
query(Marker) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Return a collection of intervals that intersect 'marker'
query(Markers) - Method in class org.snpeff.interval.tree.IntervalForest
Query all intervals that intersect with any interval in 'intervals'
query(IntervalForest) - Method in class org.snpeff.interval.Marker
Return a collection of intervals that intersect this marker
query(IntervalForest) - Method in class org.snpeff.interval.VariantBnd
Return a collection of intervals that intersect both ends of this variant
queryClosestGene(Marker) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Find closest gene to this marker
queryDeep(Marker) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Return a collection of intervals that intersect 'marker' Query resulting genes, transcripts and exons to get ALL types of intervals possible
queryExon(Marker) - Method in class org.snpeff.interval.Transcript
Return the first exon that intersects 'interval' (null if not found)
queryIntersects(Interval, int, Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
Query entries intersecting 'marker' at node 'idx'
queryMarkerSequence(Marker) - Method in class org.snpeff.binseq.GenomicSequences
Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form database
queryNaive(Marker) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
Naively find all intervals intersecting 'marker'
querySequence(Marker) - Method in class org.snpeff.binseq.GenomicSequences
Get sequence for a marker
queryUnique(Markers) - Method in class org.snpeff.interval.tree.IntervalForest
Query unique intervals that intersect with any interval in 'markers' I.e.: Return a set of intervals that intersects (at least once) with any interval in 'markers'
quiet - Variable in class org.snpeff.SnpEff
 

R

rand - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
rand - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMarkerSeq
 
rand - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
rand - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
rand() - Method in class org.snpeff.interval.Markers
Return a random interval within this collection
rand(int) - Method in class org.snpeff.probablility.RandMarker
Create a random marker of size readLen
rand(int, int) - Method in class org.snpeff.stats.PosStats
Create random counts (used for debugging)
rand(Random) - Static method in enum class org.snpeff.ped.Sex
Random sex
randBase(Random) - Static method in class org.snpeff.util.GprSeq
Random base
randDnaSeqGetBasesTest(int, int, int, long) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
Create random sequences and store them in a DnaNSequence.
randDnaSeqGetBasesTest(int, int, int, long) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
Create random sequences and store them in a DnaSequence.
randDnaSeqGetBaseTest(int, int, int, long) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
Create random sequences and store them in a DnaNSequence.
randDnaSeqGetBaseTest(int, int, int, long) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
Create random sequences and store them in a DnaSequence.
randDnaSeqTest(int, int, long) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
Create random sequences and compare to storing them in a DnaNSequence
randDnaSeqTest(int, int, long) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
Create random sequences and compare to storing them in a DnaSequence
RandMarker - Class in org.snpeff.probablility
Create random markers using a uniform distribution
RandMarker(Genome) - Constructor for class org.snpeff.probablility.RandMarker
 
RandMarker(Genome, int) - Constructor for class org.snpeff.probablility.RandMarker
 
random(int) - Method in class org.snpeff.nmer.NmerCount
Create random sequences and count nmers This is used to create a null distribution
randomIntervals(int, int, int, int) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Create a random set of intervals
randomizeSamples() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
Shufle samples (random ranks)
randomSampling(int, int, int) - Method in class org.snpeff.stats.ReadsOnMarkersModel
Sample and calculate the probability of hitting each type of marker (marker.class).
randReplaceBaseTest(int, int, int, long) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
Create random sequences and store them in a DnaNSequence.
randReplaceBaseTest(int, int, int, long) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
Create random sequences and store them in a DnaSequence.
randSeed - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMarkerSeq
 
randSeed - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
randSequence(Random, int) - Static method in class org.snpeff.util.GprSeq
Random sequence
randTestQual(int, int, long) - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
Create random sequences (and qualities) and compare to storing them in a DnaAndQuality
rankByValue(boolean) - Method in class org.snpeff.geneSets.GeneSetsRanked
Rank genes by value
rankExons() - Method in class org.snpeff.interval.Transcript
Assign ranks to exons
ranks(boolean) - Method in class org.snpeff.stats.CountByType
A map: key -> rank(counts)
rankSum() - Method in class org.snpeff.geneSets.GeneSet
Calculate rankSum, rankedSymbols and maxRank
rankSum() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
Calculate rankSums
RANKSUM - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
 
RANKSUM_GREEDY - Enum constant in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
 
RankSumNoReplacementPdf - Class in org.snpeff.probablility
Calculate rank sum probability distribution function (pdf) and cumulative distribution function (cdf).
RankSumNoReplacementSimulate - Class in org.snpeff.probablility
Calculate rank sum probability distribution function (pdf) and cumulative distribution function (cdf).
RankSumNoReplacementSimulate(int, int) - Constructor for class org.snpeff.probablility.RankSumNoReplacementSimulate
 
RankSumPdf - Class in org.snpeff.probablility
Calculate rank sum probability distribution function (pdf) and cumulative distribution function (cdf).
RankSumPdf() - Constructor for class org.snpeff.probablility.RankSumPdf
 
RankSumPValueAlgorithm - Class in org.snpeff.geneSets.algorithm
 
RankSumPValueAlgorithm(GeneSetsRanked, int) - Constructor for class org.snpeff.geneSets.algorithm.RankSumPValueAlgorithm
 
RankSumPValueGreedyAlgorithm - Class in org.snpeff.geneSets.algorithm
 
RankSumPValueGreedyAlgorithm(GeneSetsRanked, int) - Constructor for class org.snpeff.geneSets.algorithm.RankSumPValueGreedyAlgorithm
 
Rare - Enum constant in enum class org.snpeff.vcf.VcfEntry.AlleleFrequencyType
 
RARE_AMINO_ACID - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
RARE_THRESHOLD - Static variable in class org.snpeff.codons.FindRareAaIntervals
 
RareAminoAcid - Class in org.snpeff.interval
Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.
RareAminoAcid() - Constructor for class org.snpeff.interval.RareAminoAcid
 
RareAminoAcid(Marker, int, int, String) - Constructor for class org.snpeff.interval.RareAminoAcid
 
ratio(String) - Method in class org.snpeff.complexity.SequenceComplexity
Measure string's complexity ratio.
Reaction - Class in org.snpeff.reactome.events
A reaction
Reaction(int, String) - Constructor for class org.snpeff.reactome.events.Reaction
 
Reaction.RegulationType - Enum Class in org.snpeff.reactome.events
Reaction regulation types
Reactome - Class in org.snpeff.reactome
Load reactome data from TXT files
Reactome() - Constructor for class org.snpeff.reactome.Reactome
 
read() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
read(char[]) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
read(char[], int, int) - Method in class org.snpeff.fileIterator.NullReader
 
read(char[], int, int) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
read(DataInputStream) - Method in class org.snpeff.binseq.BinarySequence
Read a sequence from a data stream
read(DataInputStream) - Method in class org.snpeff.binseq.DnaAndQualitySequence
Read data in binary format
read(DataInputStream) - Method in class org.snpeff.binseq.DnaNSequence
Read data in binary format
read(DataInputStream) - Method in class org.snpeff.binseq.DnaSequence
Read data in binary format
read(DataInputStream) - Method in class org.snpeff.binseq.DnaSequenceId
Read data in binary format
read(DataInputStream) - Method in class org.snpeff.binseq.DnaSequencePe
Read data in binary format
read(InputStream) - Method in class org.snpeff.nmer.Nmer
 
read(InputStream) - Static method in class org.snpeff.util.Gpr
Read an input stream
read(String) - Method in class org.snpeff.ped.PlinkMap
Reads MAP file MAP file format (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) Space separated or tab columns: chromosome (1-22, X, Y or 0 if unplaced) rs# or snp identifier Genetic distance (morgans) Base-pair position (bp units)
read(CharBuffer) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
READ_INPUT_SHOW_EVERY - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
 
readCacheFile() - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Read cache file
readDataStream(DataInputStream) - Method in class org.snpeff.binseq.BinarySequence
 
readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaAndQualitySequence
Read data in binary format
readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaAndQualitySequenceWithId
Read data in binary format
readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaNSequence
Read data in binary format
readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaSequence
Read data in binary format
readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaSequenceId
Read data in binary format
readDataStream(DataInputStream) - Method in class org.snpeff.binseq.DnaSequencePe
Read data in binary format
reader - Variable in class org.snpeff.fileIterator.FileIterator
 
reader(String) - Static method in class org.snpeff.util.Gpr
Try to open a file (BufferedReader) using either the file or a gzip file (appending '.gz' to fileName)
reader(String, boolean) - Static method in class org.snpeff.util.Gpr
Try to open a file (BufferedReader) using either the file or a gzip file (appending '.gz' to fileName)
readExonSequences() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Read exon sequences from a FASTA file
readExonSequences() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
 
readExonSequencesGff(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Read chromosome sequence from GFF3 file and extract exons' sequences
readField(String[], int) - Method in class org.snpeff.fileIterator.VcfFileIterator
Read a field an return a value
readFile() - Method in class org.snpeff.genBank.Embl
Load and parse the contents of a data file
readFile() - Method in class org.snpeff.genBank.Features
Load and parse the contents of a data file previously opened by 'open()' method.
readFile() - Method in class org.snpeff.genBank.GenBank
Load and parse the contents of a data file
readFile(String) - Static method in class org.snpeff.util.Gpr
Read a file as a String.
readFile(String, boolean) - Static method in class org.snpeff.util.Gpr
Read a file as a String.
readFile(RegulationFileIterator) - Method in class org.snpeff.RegulationFileConsensus
Read a file and add all regulation intervals
readFileSerialized(String) - Static method in class org.snpeff.util.Gpr
Read an object from a file (supposing an object was previously serialized to that file)
readFileSerializedGz(String) - Static method in class org.snpeff.util.Gpr
Read an object from a file (supposing an object was previously serialized to that file) Note: The file is compressed using GZIP
readFileSerializedGzThrow(String) - Static method in class org.snpeff.util.Gpr
Read an object from a file (supposing an object was previously serialized to that file) Note: Same as 'readFileSerializedGz' but it throws all the exceptions
readGeneAssocFile(String, boolean) - Method in class org.snpeff.geneOntology.GoTerms
Reads a file containing every gene (names and ids) associated GO terms
readGenomeSequence(String) - Method in class org.snpeff.interval.Genome
Read the whole genome sequence into memory
readGff() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Read GFF file from the beginning looking for 'typeToRead' elements
readHeader() - Method in class org.snpeff.fileIterator.VcfFileIterator
Read only header info
readId(String) - Static method in class org.snpeff.util.GprSeq
Create an ID: Remove everything after the first space char.
readInterestingSymbolIdsFile(String) - Method in class org.snpeff.geneOntology.GoTerms
Reads a file with a list of 'interesting' genes (one per line)
readLine() - Method in class org.snpeff.fileIterator.FileIterator
Read a line from reader
readLine() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
readMarkers(String) - Static method in class org.snpeff.interval.Markers
Read markers from a file Supported formats: BED, BigBed, VCF, TXT
readNext() - Method in class org.snpeff.fileIterator.BedFileIterator
 
readNext() - Method in class org.snpeff.fileIterator.BigBedFileIterator
 
readNext() - Method in class org.snpeff.fileIterator.FastaFileIterator
Read a sequence from the file
readNext() - Method in class org.snpeff.fileIterator.FileIterator
Read next element
readNext() - Method in class org.snpeff.fileIterator.GenericMarkerFileIterator
 
readNext() - Method in class org.snpeff.fileIterator.Gff3FileIterator
 
readNext() - Method in class org.snpeff.fileIterator.LineClassFileIterator
Read a sequence from the file
readNext() - Method in class org.snpeff.fileIterator.LineFileIterator
Read a sequence from the file
readNext() - Method in class org.snpeff.fileIterator.MotifFileIterator
 
readNext() - Method in class org.snpeff.fileIterator.RegulationBedFileIterator
 
readNext() - Method in class org.snpeff.fileIterator.RegulationGffFileIterator
 
readNext() - Method in class org.snpeff.fileIterator.SamFileIterator
Read a sequence from the file
readNext() - Method in class org.snpeff.fileIterator.VariantTxtFileIterator
 
readNext() - Method in class org.snpeff.fileIterator.VcfFileIterator
 
readNext() - Method in class org.snpeff.fileIterator.VcfHapMapFileIterator
 
readNext() - Method in class org.snpeff.ped.PedFileIterator
 
readOboFile(String, boolean) - Method in class org.snpeff.geneOntology.GoTerms
Read an OBO file
readPdbFile(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
Read and parse PDB file
readRefSeqFile() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
Read and parse genes file
readRefSeqFile() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRefSeq
Read and parse RefSeq file
ReadsOnMarkersModel - Class in org.snpeff.stats
Calculate the maximum interval length by type, for all markers in a genome Create a probability model based on binomial ditribution.
ReadsOnMarkersModel(SnpEffectPredictor) - Constructor for class org.snpeff.stats.ReadsOnMarkersModel
 
readTxt(String, int, Genome, int) - Method in class org.snpeff.interval.Marker
Parse a line (form a file) Format: "chromosome \t start \t end \t id \n"
readTxt(String, Genome, int) - Static method in class org.snpeff.interval.MarkerUtil
Read intervals from a file using a simplt TXT format Format: chr \t start \t end \t id Note: Zero-based positions
ready() - Method in class org.snpeff.fileIterator.FileIterator
Is reader ready? I.e.
ready() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
realign() - Method in class org.snpeff.align.VariantRealign
Realign variant
realignLeft() - Method in class org.snpeff.interval.Variant
Create a new variant realigning it towards the leftmost position
realignLeft() - Method in class org.snpeff.interval.VariantBnd
 
realignLeft() - Method in class org.snpeff.interval.VariantNonRef
 
realignSeqs() - Method in class org.snpeff.align.VariantRealign
Realignment
RECT_COLOR_FILL - Static variable in class org.snpeff.svg.Svg
 
RECT_COLOR_STROKE - Static variable in class org.snpeff.svg.Svg
 
RECT_HEIGHT - Static variable in class org.snpeff.svg.Svg
 
RECT_STROKE_WIDTH - Static variable in class org.snpeff.svg.Svg
 
rectangle() - Method in class org.snpeff.svg.Svg
 
rectangle(double, double, double, double, boolean) - Method in class org.snpeff.svg.Svg
 
redundant(Collection<? extends Marker>) - Static method in class org.snpeff.interval.MarkerUtil
Redundant markers in a list: Find intervals that are totally included in other intervals in the list
ref - Variable in class org.snpeff.fileIterator.MatrixEntry
 
ref - Variable in class org.snpeff.interval.Variant
 
ref - Variable in class org.snpeff.vcf.VcfEntry
 
ref() - Method in class org.snpeff.snpEffect.HgvsDna
 
REFSEQ - Enum constant in enum class org.snpeff.SnpEff.GeneDatabaseFormat
 
regions(Marker, boolean, boolean) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Name of the regions hit by a marker
regions(Marker, boolean, boolean, String) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Name of the regions hit by a marker
Regulation - Class in org.snpeff.interval
Regulatory elements
Regulation() - Constructor for class org.snpeff.interval.Regulation
 
Regulation(Marker, int, int, boolean, String, String, String) - Constructor for class org.snpeff.interval.Regulation
 
REGULATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
RegulationBedFileIterator - Class in org.snpeff.fileIterator
Opens a GFF3 file and create regulatory elements.
RegulationBedFileIterator(String, String, String) - Constructor for class org.snpeff.fileIterator.RegulationBedFileIterator
 
RegulationBedFileIterator(String, Genome, String, String) - Constructor for class org.snpeff.fileIterator.RegulationBedFileIterator
 
RegulationConsensusMultipleBed - Class in org.snpeff
Create a regulation consensus from multiple BED files
RegulationConsensusMultipleBed(String, String) - Constructor for class org.snpeff.RegulationConsensusMultipleBed
 
RegulationFileConsensus - Class in org.snpeff
Create a regulation consensus from a regulation file.
RegulationFileConsensus() - Constructor for class org.snpeff.RegulationFileConsensus
 
RegulationFileIterator - Class in org.snpeff.fileIterator
Opens a regulation file and create Regulation elements.
RegulationFileIterator(String, int) - Constructor for class org.snpeff.fileIterator.RegulationFileIterator
 
RegulationFileIterator(String, Genome, int) - Constructor for class org.snpeff.fileIterator.RegulationFileIterator
 
RegulationFileSplitBytType - Class in org.snpeff
Split regulation files into smaller files (one per 'regulation type') Regulation files can be quite large and we cannot read them into memory.
RegulationFileSplitBytType() - Constructor for class org.snpeff.RegulationFileSplitBytType
 
RegulationGffFileIterator - Class in org.snpeff.fileIterator
Opens a GFF3 file and create regulatory elements.
RegulationGffFileIterator(String) - Constructor for class org.snpeff.fileIterator.RegulationGffFileIterator
 
RegulationGffFileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.RegulationGffFileIterator
 
regulationTracks - Variable in class org.snpeff.SnpEff
 
regulator - Variable in class org.snpeff.reactome.events.Reaction
 
remove() - Method in class org.snpeff.fileIterator.BinSeqFileIterator
 
remove() - Method in class org.snpeff.fileIterator.FastqFileIterator
 
remove() - Method in class org.snpeff.fileIterator.FileIterator
 
remove() - Method in class org.snpeff.genBank.FeaturesFile
 
remove() - Method in class org.snpeff.interval.IntervalSetIterator
 
remove() - Method in class org.snpeff.util.CombinatorialIterator
 
remove() - Method in class org.snpeff.util.IubString
 
remove(Object) - Method in class org.snpeff.interval.Markers
 
remove(String) - Method in class org.snpeff.stats.CountByType
Remove this entry type
remove(String) - Method in class org.snpeff.vcf.VcfHeader
Remove header line starting with a prefix
remove(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
Remove all elements set in other.
remove(GeneSet) - Method in class org.snpeff.geneSets.GeneSets
 
remove(Chromosome) - Method in class org.snpeff.interval.Genome
Remove a chromosome WARINIG: Doesn't check any dependencies!
remove(T) - Method in class org.snpeff.interval.IntervalAndSubIntervals
Remove a subinterval
removeAll(Collection<?>) - Method in class org.snpeff.interval.Markers
 
removeBackslashR(String) - Static method in class org.snpeff.util.Gpr
Remove trailing '\r'
removeExt(String) - Static method in class org.snpeff.util.Gpr
 
removeExt(String) - Static method in class org.snpeff.util.GprSeq
 
removeExt(String, String[]) - Static method in class org.snpeff.util.Gpr
Remove extension from a file (if matches one of 'fileExtensions[]')
removeGeneSet(String) - Method in class org.snpeff.geneSets.GeneSets
Remove a GeneSet
removeGOTerm(String) - Method in class org.snpeff.geneOntology.GoTerms
Remove a GOTerm
removeInfo(String) - Method in class org.snpeff.vcf.VcfEntry
Remove INFO field
removeInfo(String) - Method in class org.snpeff.vcf.VcfHeader
Remove header line matching an INFO field
removeNonCanonical(String) - Method in class org.snpeff.interval.Gene
Remove all non-canonical transcripts
removeNonCanonical(String) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Remove all non-canonical transcripts If a file is provided, read "Gene => canonical_transcript" mapping from file
removeTranscript(String) - Static method in class org.snpeff.snpEffect.Hgvs
 
removeUnusedSets() - Method in class org.snpeff.geneSets.GeneSets
Remove unused gene sets
removeUnverified() - Method in class org.snpeff.interval.Gene
Remove unverified or corrected transcripts
removeUnverified() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Remove all unverified transcripts
repeat(char, int) - Static method in class org.snpeff.util.Gpr
Create a string of n time 'c'
REPEAT_REGION - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
REPEAT_UNIT - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
replace(long, long, long) - Method in class org.snpeff.collections.HashLongLongArray
Replace a value with newValue
replaceBase(long, int, char) - Method in class org.snpeff.binseq.coder.DnaCoder
Decode bits from a given position
replaceQuality(byte, int) - Method in class org.snpeff.binseq.coder.DnaQualityCoder
Replace quality value in a given code
replaceSeq(String) - Method in class org.snpeff.sam.SamEntry
Replace a sequence WARNING: Doing this might invalidate the CIGAR field
replaceTranscript(Transcript, Transcript) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
report(String, String, String, boolean, boolean, String[], String, HashMap<String, String>) - Static method in class org.snpeff.logStatsServer.LogStats
Report stats to server
REPORT_TEMPLATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
 
reportValues() - Method in class org.snpeff.SnpEff
Additional values to be reported
reportValues() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
Requirement - Enum constant in enum class org.snpeff.reactome.events.Reaction.RegulationType
 
resample(int) - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
Re-sample 'iterations' times
ReSampleInt - Class in org.snpeff.probablility.bootstrap
Re-sample statistic Statistic is a sum of a set of integer numbers (e.g.
ReSampleInt(int[], int) - Constructor for class org.snpeff.probablility.bootstrap.ReSampleInt
 
ReSampleMap - Class in org.snpeff.probablility.bootstrap
Resample statistic
ReSampleMap(HashMap<String, Integer>, int) - Constructor for class org.snpeff.probablility.bootstrap.ReSampleMap
 
ReSampleMapRank - Class in org.snpeff.probablility.bootstrap
Re-sample statistic using ranks of scores (scores are double)
ReSampleMapRank(HashMap<String, Double>, int) - Constructor for class org.snpeff.probablility.bootstrap.ReSampleMapRank
 
reset() - Method in class org.snpeff.binseq.GenomicSequences
 
reset() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
reset() - Method in class org.snpeff.geneSets.GeneSets
Reset every 'interesting' gene or ranked gene (on every single GeneSet in this GeneSets)
reset() - Method in class org.snpeff.geneSets.GeneSetsRanked
Reset every 'interesting' gene or ranked gene (on every single GeneSet in this GeneSets)
reset() - Method in class org.snpeff.interval.Exon
 
reset() - Method in class org.snpeff.interval.IntervalAndSubIntervals
Remove all intervals
reset() - Method in class org.snpeff.interval.Intron
 
reset() - Method in class org.snpeff.interval.Transcript
 
reset() - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
reset() - Method in class org.snpeff.reactome.Entity
 
reset() - Method in class org.snpeff.reactome.Reactome
Reset all nodes in the circuit
reset() - Static method in class org.snpeff.snpEffect.Config
 
reset() - Method in class org.snpeff.stats.Average
 
reset() - Method in class org.snpeff.stats.AverageInt
 
reset() - Method in class org.snpeff.stats.Counter
 
reset() - Method in class org.snpeff.stats.CounterDouble
 
reset() - Static method in class org.snpeff.util.Log
Reset all parameters, warning counters, silenced warningis, etc.
resetBuffer() - Method in class org.snpeff.osCmd.StreamGobbler
 
resetBuffers() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
resetCache() - Method in class org.snpeff.interval.Transcript
 
resetExons() - Method in class org.snpeff.interval.Transcript
 
resetInterestingSymbolIds() - Method in class org.snpeff.geneOntology.GoTerms
Reset every 'interesting' symbolId (on every single GOTerm in this GOTerms)
Result - Class in org.snpeff.geneSets
Store a result form a greedy search algorithm
Result() - Constructor for class org.snpeff.geneSets.Result
 
Result(List<GeneSet>, double) - Constructor for class org.snpeff.geneSets.Result
 
Result(GeneSet, Apfloat, int) - Constructor for class org.snpeff.geneSets.Result
 
Result(Result) - Constructor for class org.snpeff.geneSets.Result
 
retainAll(Collection<?>) - Method in class org.snpeff.interval.Markers
 
retainAllTranscripts(Set<String>) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Remove all transcripts that are NOT in the list
RETAINED - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
 
retained_intron - Enum constant in enum class org.snpeff.interval.BioType
 
reverse() - Method in class org.snpeff.interval.Variant
Reverse variant (e.g.
reverse(String) - Static method in class org.snpeff.util.GprSeq
Reverse of a string (sequence)
reverseBases(long) - Method in class org.snpeff.binseq.coder.DnaCoder
Reverse all bases in 'code'
reverseMask - Static variable in class org.snpeff.genotypes.GenotypeVector
 
reverseWc() - Method in class org.snpeff.binseq.BinarySequence
Reverse Watson-Cricks complement
reverseWc() - Method in class org.snpeff.binseq.DnaAndQualitySequence
 
reverseWc() - Method in class org.snpeff.binseq.DnaNSequence
 
reverseWc() - Method in class org.snpeff.binseq.DnaSequence
 
reverseWc() - Method in class org.snpeff.binseq.DnaSequencePe
 
reverseWc(String) - Static method in class org.snpeff.util.GprSeq
Reverse Watson-Cricks complement
reverseWC - Variable in class org.snpeff.binseq.indexer.OverlapRessult
 
REVISION - Static variable in class org.snpeff.SnpEff
 
ribozyme - Enum constant in enum class org.snpeff.interval.BioType
 
right - Variable in class org.snpeff.interval.tree.IntervalTreeArray
 
rightNode - Variable in class org.snpeff.interval.tree.IntervalNode
 
rmInfo(String) - Method in class org.snpeff.vcf.VcfEntry
Parse INFO fields
rol(char) - Method in class org.snpeff.nmer.Nmer
Rotate sequence left and append a base at the end Note: The first base is dropped, so the total length is still 'n'
rootNode() - Method in class org.snpeff.geneOntology.GoTerm
Get the root node
rootNodes() - Method in class org.snpeff.geneOntology.GoTerms
 
rotate(int) - Method in class org.snpeff.overlap.SequenceRotator
Rotate left
rRNA - Enum constant in enum class org.snpeff.interval.BioType
 
RRNA - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
run() - Method in class org.snpeff.fastq.FastqSplit
Run command
run() - Method in class org.snpeff.logStatsServer.LogStats
Run thread in background
run() - Method in class org.snpeff.logStatsServer.VersionCheck
Run thread in background
run() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
run() - Method in class org.snpeff.osCmd.OsCmdQueue
Run commands
run() - Method in class org.snpeff.osCmd.OsCmdRunner
 
run() - Method in class org.snpeff.osCmd.StreamGobbler
 
run() - Method in class org.snpeff.PromoterSequences
 
run() - Method in class org.snpeff.RegulationConsensusMultipleBed
Main method: Creates the consensus from multiple files
run() - Method in class org.snpeff.SnpEff
Run according to command line options
run() - Method in interface org.snpeff.snpEffect.commandLine.CommandLine
Run the command
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
Run command
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
Build database
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuildNextProt
Run main analysis
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
Run command
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
Run command
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCount
Run
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
 
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDownload
Download database from server
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDump
Run according to command line options
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
Run according to command line options
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
 
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
Run command
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdLen
Run
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
Run command
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdSeq
Run according to command line options
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdShow
Run according to command line options
run() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
 
run() - Method in class org.snpeff.snpEffect.testCases.integration.CreateSpliceSiteTestCase
 
run() - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
 
run() - Method in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
run() - Method in class org.snpeff.stats.ReadsOnMarkersModel
Run
run(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
Run according to command line options
run(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
run(GtexExperiment) - Method in class org.snpeff.reactome.Reactome
Run some simulations
run(Gtex, String) - Method in class org.snpeff.reactome.Reactome
Run all experiments on gtex
run(SnpEff, String[], StringBuilder) - Method in class org.snpeff.SnpEff
Run a SnpEff (usually a sub-class)
runAnalisis() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
Run command
runAnalisisRand() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
Run enrichment analysis using random scores
runCommands() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
Read "command" lines from file.
runIfNotExists(String[], String, boolean) - Static method in class org.snpeff.osCmd.OsCmdRunner
Run an OS command only if the output files does not exists.
runIfNotExists(String, boolean) - Method in class org.snpeff.osCmd.OsCmdRunner
Run a command only if 'outputFile' does not exist

S

SamEntry - Class in org.snpeff.sam
An entry in a SAM file References: http://samtools.sourceforge.net/SAM-1.3.pdf
SamEntry(String) - Constructor for class org.snpeff.sam.SamEntry
Create an entry give a line from a file
SamFileIterator - Class in org.snpeff.fileIterator
Reads a SAM file Note: This is a very 'rustic' reader (we should use Picard's API instead)
SamFileIterator(String) - Constructor for class org.snpeff.fileIterator.SamFileIterator
 
SamHeader - Class in org.snpeff.sam
Sam header
SamHeader() - Constructor for class org.snpeff.sam.SamHeader
 
SamHeaderRecord - Class in org.snpeff.sam
Sam header record
SamHeaderRecord(String, String) - Constructor for class org.snpeff.sam.SamHeaderRecord
 
SamHeaderRecordSq - Class in org.snpeff.sam
SQ header: Reference sequence dictionary.
SamHeaderRecordSq(String) - Constructor for class org.snpeff.sam.SamHeaderRecordSq
 
samLine2Id(String) - Static method in class org.snpeff.sam.SamEntry
Get an ID from a SAM line
sample(double) - Method in class org.snpeff.stats.FloatStats
 
sample(int) - Method in class org.snpeff.stats.ChrPosStats
Use 'num' as a sample
sample(int) - Method in class org.snpeff.stats.IntStats
Use 'num' as a sample
sample(Gene, Transcript, String, VariantEffect) - Method in class org.snpeff.stats.GeneCountByTypeTable
Sample this <gene, marker, type, variant> tuple to update statistics
sample(Marker, Marker) - Method in class org.snpeff.stats.PosStats
Use 'num' as a sample
sample(Variant) - Method in class org.snpeff.stats.VariantStats
Use this sample to perform statistics
sample(VariantEffect) - Method in class org.snpeff.stats.VariantEffectStats
 
sample(VcfEntry) - Method in class org.snpeff.stats.AlleleCountStats
Update MAC counters
sample(VcfEntry) - Method in class org.snpeff.stats.GenotypeStats
Update counters
sample(VcfEntry) - Method in class org.snpeff.stats.HomHetStats
Update Hom/Het counters
sample(VcfEntry) - Method in class org.snpeff.stats.TsTvStats
Update Ts and Tv counters Only for SNPs
sample(VcfEntry) - Method in class org.snpeff.stats.VariantTypeStats
Update MAC counters
sample(VcfEntry) - Method in class org.snpeff.stats.VcfStats
 
sample(T) - Method in interface org.snpeff.stats.SamplingStats
Analyze one sample
sampleMean(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
Calculate the mean rankSum for a given 'N_T' (number of ranks to add)
sampleNumbers(List<String>) - Method in class org.snpeff.vcf.PedigreeEntry
Find sample numbers in a list of sample names
sampleVariance(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
Calculate the variance of rankSum for a given 'N_T' (number of ranks to add)
SamplingStats<T> - Interface in org.snpeff.stats
Perform stats by analyzing some samples
sanityCheck() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
Perform consistency checks
sanityCheck(Variant) - Method in class org.snpeff.interval.Exon
Check that the base in the exon corresponds with the one in the SNP
sanityCheck(Variant) - Method in class org.snpeff.interval.Transcript
Perfom some baseic chekcs, return error type, if any
sanityCheckChromo(String, Chromosome) - Method in class org.snpeff.fileIterator.MarkerFileIterator
Sanity check
sanityzeFileName(String) - Static method in class org.snpeff.util.Gpr
 
sanityzeName(String) - Static method in class org.snpeff.util.Gpr
 
save() - Method in class org.snpeff.RegulationFileConsensus
Save databases (one file per regType)
save(Iterable<Marker>) - Method in class org.snpeff.serializer.MarkerSerializer
Save all markers
save(String) - Method in class org.snpeff.fileIterator.TableFile
Save this object to a binary file (using Java serialization)
save(String) - Method in class org.snpeff.genotypes.Genotypes
Save to file
save(String) - Method in class org.snpeff.interval.Genome
Save genome to file
save(String) - Method in class org.snpeff.interval.Markers
Save to a file using a serializer
save(String) - Method in class org.snpeff.reactome.Monitor
 
save(String) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Save predictor to a binary file
save(String) - Method in class org.snpeff.stats.ReadsOnMarkersModel
Save model to file
save(String, String) - Method in class org.snpeff.interval.Markers
Save to a file using a serializer Only save one chromosome ('chr') Note: This is used to save only markers related to one chromosome (e.g.
save(String, Markers) - Method in class org.snpeff.serializer.MarkerSerializer
Save data to file
save(Marker) - Method in class org.snpeff.serializer.MarkerSerializer
Save a marker
save(Config) - Method in class org.snpeff.binseq.GenomicSequences
Save genomic sequence into separate files (per chromosome)
save(Config) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Save predictor to a binary file (specified by the configuration)
saveDatabase() - Method in class org.snpeff.nextProt.NextProtDb
 
saveDatabase() - Method in class org.snpeff.nextProt.NextProtMarkerFactory
Save nextprot markers as databases
saveGseaGeneSets(String) - Method in class org.snpeff.geneOntology.GoTerms
Save gene sets file for GSEA analysis Format specification: http://www.broad.mit.edu/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29
saveGseaGeneSets(String) - Method in class org.snpeff.geneSets.GeneSets
Save gene sets file for GSEA analysis Format specification: http://www.broad.mit.edu/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29
saveOutput - Variable in class org.snpeff.SnpEff
 
saveTfam(String) - Method in class org.snpeff.ped.PedPedigree
Save pedigree as a TFAM file
SCALE - Static variable in class org.snpeff.motif.Pwm
 
SCALE_HEIGHT - Static variable in class org.snpeff.svg.SvgScale
 
SCALE_TICK_HEIGHT - Static variable in class org.snpeff.svg.SvgScale
 
scaleWeights() - Method in class org.snpeff.reactome.events.Reaction
Scale weights so that they add to 1
scaRNA - Enum constant in enum class org.snpeff.interval.BioType
 
score - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
score(long[], long[], int, int, int) - Method in class org.snpeff.binseq.coder.DnaCoder
Calculate a 'score' for a sequence (dst) and a sub-sequence (src).
score(String) - Method in class org.snpeff.motif.Pwm
Calculate PWM score for a string
score(Collection<String>) - Method in class org.snpeff.probablility.bootstrap.ReSampleMap
 
score(Collection<String>) - Method in class org.snpeff.probablility.bootstrap.ReSampleMapRank
 
score(DnaAndQualitySequence, int, DnaAndQualitySequence, int) - Method in class org.snpeff.binseq.comparator.DnaQualSubsequenceComparator
 
score(DnaSequence, int, DnaSequence, int) - Method in class org.snpeff.binseq.comparator.DnaSubsequenceComparator
 
score(ScoreList.ScoreSummary) - Method in class org.snpeff.gsa.ScoreList
Create a single pValue representing the gene
score(T, int, T, int) - Method in class org.snpeff.binseq.comparator.SubsequenceComparator
 
SCORE_CUTOFF_QUANTILE_DEFAULT - Static variable in class org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
 
SCORE_THRESHOLD - Static variable in class org.snpeff.interval.Motif
 
ScoreList - Class in org.snpeff.gsa
A list of scores
ScoreList() - Constructor for class org.snpeff.gsa.ScoreList
 
ScoreList.ScoreSummary - Enum Class in org.snpeff.gsa
 
scoreSlow(DnaSequence, int, DnaSequence, int) - Method in class org.snpeff.binseq.comparator.DnaSubsequenceComparator
This method is used when none of the indexes is zero.
scRNA - Enum constant in enum class org.snpeff.interval.BioType
 
second - Variable in class org.snpeff.util.Tuple
 
seek(long) - Method in class org.snpeff.fileIterator.FileIterator
Seek to 'pos' (jump to byte number 'pos' in the file
seek(long) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
Seek to a position in the file
SeekableBufferedReader - Class in org.snpeff.fileIterator
A buffered reader for a file.
SeekableBufferedReader(String) - Constructor for class org.snpeff.fileIterator.SeekableBufferedReader
 
SeekableBufferedReader(String, int) - Constructor for class org.snpeff.fileIterator.SeekableBufferedReader
 
select() - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
Select the 'best' gene sets
select() - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
Select the 'best' gene sets
send - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
sense_intronic - Enum constant in enum class org.snpeff.interval.BioType
 
sense_overlapping - Enum constant in enum class org.snpeff.interval.BioType
 
separator - Variable in class org.snpeff.fileIterator.LineClassFileIterator
 
separator - Variable in class org.snpeff.fileIterator.TableFile
 
separator() - Method in enum class org.snpeff.vcf.EffFormatVersion
Multiple effect separator
separatorSplit() - Method in enum class org.snpeff.vcf.EffFormatVersion
Multiple effect separator: Split regex
seqConservation() - Method in class org.snpeff.spliceSites.AcgtTree
 
SEQUENCE - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
SequenceComplexity - Class in org.snpeff.complexity
Measures the complexity of a sequence Ideally we'd like to measure the Kolmogorov complexity of the sequence.
SequenceComplexity() - Constructor for class org.snpeff.complexity.SequenceComplexity
 
SequenceIndexer<T extends BinarySequence> - Class in org.snpeff.binseq.indexer
A collection of sequences that are indexed using some algorithm Note: The ID is just the position in the array.
SequenceIndexer(SubsequenceComparator<T>) - Constructor for class org.snpeff.binseq.indexer.SequenceIndexer
 
SequenceReference - Class in org.snpeff.binseq.comparator
A reference to a sequence.
SequenceReference() - Constructor for class org.snpeff.binseq.comparator.SequenceReference
 
SequenceRotator - Class in org.snpeff.overlap
Rotates a binary packed sequence WARNING: We only rotate up to Coder.basesPerWord() because after that the sequences are the same (with an integer offset) NOTE: Left rotation 'n' is the same as a right rotation 'Coder.basesPerWord() - n'
SequenceRotator(DnaSequence) - Constructor for class org.snpeff.overlap.SequenceRotator
 
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Cds
 
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Chromosome
Parse a line from a serialized file
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Exon
Parse a line from a serialized file
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Gene
Parse a line from a serialized file
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Genome
Parse a line from a serialized file
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.IntervalAndSubIntervals
Parse a line from a serialized file
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Intron
 
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Marker
Parse a line from a serialized file
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.MarkerSeq
Parse a line from a serialized file
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Motif
 
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.NextProt
 
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Regulation
Parse a line from a serialized file
serializeParse(MarkerSerializer) - Method in class org.snpeff.interval.Transcript
Parse a line from a serialized file
serializeParse(MarkerSerializer) - Method in interface org.snpeff.serializer.TxtSerializable
 
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Cds
Create a string to serialize to a file
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Chromosome
 
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Exon
Create a string to serialize to a file
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Gene
Create a string to serialize to a file
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Genome
Create a string to serialize to a file
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.IntervalAndSubIntervals
Create a string to serialize to a file
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Intron
Create a string to serialize to a file
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Marker
Create a string to serialize to a file
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.MarkerSeq
Create a string to serialize to a file
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Motif
Create a string to serialize to a file
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.NextProt
 
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Regulation
Create a string to serialize to a file
serializeSave(MarkerSerializer) - Method in class org.snpeff.interval.Transcript
Create a string to serialize to a file
serializeSave(MarkerSerializer) - Method in interface org.snpeff.serializer.TxtSerializable
 
set(boolean) - Method in class org.snpeff.stats.BooleanMutable
 
set(char, AcgtTree) - Method in class org.snpeff.spliceSites.AcgtTree
Set a node
set(double) - Method in class org.snpeff.stats.CounterDouble
 
set(int, int) - Method in class org.snpeff.genotypes.GenotypeVector
Set genotype code Codes {0, 1, 2, 3} => Genotypes { 0/0, 0/1, 1/0, 1/1 }
set(int, int, int) - Method in class org.snpeff.util.CombinatorialIterator
 
set(int, int, VcfGenotype) - Method in class org.snpeff.genotypes.Genotypes
Set an entry
set(int, VcfGenotype) - Method in class org.snpeff.genotypes.GenotypeVector
Set genotype
set(long) - Method in class org.snpeff.collections.OpenBitSet
sets a bit, expanding the set size if necessary
set(long) - Method in class org.snpeff.stats.Counter
 
set(long, long) - Method in class org.snpeff.collections.OpenBitSet
Sets a range of bits, expanding the set size if necessary
set(String) - Method in class org.snpeff.binseq.BinarySequence
Set sequence from a string
set(String) - Method in class org.snpeff.binseq.DnaAndQualitySequence
Set sequence
set(String) - Method in class org.snpeff.binseq.DnaNSequence
 
set(String) - Method in class org.snpeff.binseq.DnaSequence
Set sequence
set(String) - Method in class org.snpeff.binseq.DnaSequenceByte
Set sequence
set(String) - Method in class org.snpeff.binseq.DnaSequencePe
 
set(String) - Method in class org.snpeff.motif.Pwm
Set PWM as a perfect match to a dna sequence
set(String) - Method in class org.snpeff.nmer.Nmer
Set nmer's sequence
set(String, boolean) - Method in class org.snpeff.binseq.DnaSequence
 
set(String, String) - Method in class org.snpeff.vcf.VcfGenotype
Set a genotype field value
set(String, String, FastqVariant) - Method in class org.snpeff.binseq.DnaAndQualitySequence
Set sequence
set(List<GeneSet>, Apfloat) - Method in class org.snpeff.geneSets.Result
Ser a new list and pvalue
set(Genome, CodonTable) - Method in class org.snpeff.codons.CodonTables
Set a codon table for a all chromosomes in a genome I.e.: Default genome-wide chromosome table
set(Genome, Chromosome, CodonTable) - Method in class org.snpeff.codons.CodonTables
Set a codon table for a given genome & chromosome
set(Marker, EffectType, VariantEffect.EffectImpact, String) - Method in class org.snpeff.snpEffect.VariantEffect
 
setAa(String) - Method in class org.snpeff.vcf.VcfEffect
 
setAa1(AminoAcid) - Method in class org.snpeff.pdb.DistanceResult
 
setAa2(AminoAcid) - Method in class org.snpeff.pdb.DistanceResult
 
setAaCheck(boolean) - Method in class org.snpeff.interval.Transcript
 
setAaIdx(int, int) - Method in class org.snpeff.interval.Exon
 
setAaLen(int) - Method in class org.snpeff.vcf.VcfEffect
 
setAcc(String) - Method in class org.snpeff.geneOntology.GoTerm
 
setAddUtrs(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
 
setAdjustedPvalue(boolean) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
 
setAlert(String) - Method in class org.snpeff.osCmd.StreamGobbler
 
setAlertNotify(Object) - Method in class org.snpeff.osCmd.StreamGobbler
 
setAlignLeft() - Method in class org.snpeff.align.VariantRealign
 
setAlignRight() - Method in class org.snpeff.align.VariantRealign
 
setAutoClose(boolean) - Method in class org.snpeff.fileIterator.FileIterator
 
setBarSpace(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
 
setBarWidth(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
 
setBase(int, char) - Method in class org.snpeff.binseq.DnaNSequence
Replace a base in the sequence
setBase(int, char) - Method in class org.snpeff.binseq.DnaSequence
Replace a base in the sequence
setBaseY(int) - Method in class org.snpeff.svg.Svg
 
setBinary(boolean) - Method in class org.snpeff.osCmd.StreamGobbler
 
setBinaryStderr(boolean) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setBinaryStdout(boolean) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setBioType(BioType) - Method in class org.snpeff.interval.Gene
 
setBioType(BioType) - Method in class org.snpeff.interval.Transcript
 
setBioType(BioType) - Method in class org.snpeff.vcf.VcfEffect
 
setBits(long[]) - Method in class org.snpeff.collections.OpenBitSet
Expert: sets a new long[] to use as the bit storage
setCacheFile(String) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
 
setCanonical(boolean) - Method in class org.snpeff.interval.Transcript
 
setCanonical(boolean) - Method in class org.snpeff.SnpEff
 
setCellType(String) - Method in class org.snpeff.RegulationConsensusMultipleBed
 
setCheckNumOk(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
 
setCheckNumOk(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
 
setCheckNumOk(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
setChilds(HashSet<GoTerm>) - Method in class org.snpeff.geneOntology.GoTerm
 
setChromo(Chromosome) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
 
setChromosomeNameOri(String) - Method in class org.snpeff.interval.Interval
 
setChrStr(String) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setCircular(boolean) - Method in class org.snpeff.interval.Chromosome
 
setCircularCorrectLargeGap(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
setCodes(long[]) - Method in class org.snpeff.binseq.DnaSequence
 
setCoding(VariantEffect.Coding) - Method in class org.snpeff.vcf.VcfEffect
 
setCodon(String) - Method in class org.snpeff.vcf.VcfEffect
 
setCodons(String, String, int, int) - Method in class org.snpeff.snpEffect.VariantEffect
Set codon change.
setCodonsAround(String, String) - Method in class org.snpeff.snpEffect.VariantEffect
Set values for codons around change.
setColumnSeparator(String) - Method in class org.snpeff.fileIterator.GuessTableTypes
 
setCommandArgs(String[]) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setCommandLineStr(String) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setCompareHgvs() - Method in class org.snpeff.snpEffect.testCases.integration.CompareToVep
 
setCompareHgvsDna(boolean) - Method in class org.snpeff.snpEffect.testCases.integration.CompareToVep
 
setCompareHgvsProt(boolean) - Method in class org.snpeff.snpEffect.testCases.integration.CompareToVep
 
setCompartment(Compartment) - Method in class org.snpeff.reactome.Entity
 
setConfig(Config) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setConfig(Config) - Method in class org.snpeff.SnpEff
 
setConfig(Config) - Method in interface org.snpeff.snpEffect.VcfAnnotator
Set configuration
setConfig(Config) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
 
setConfigFile(String) - Method in class org.snpeff.SnpEff
 
setCorrectLargeGap(boolean) - Method in class org.snpeff.interval.CircularCorrection
 
setCounts(char, int[]) - Method in class org.snpeff.motif.Pwm
Set counts for one base
setCreateChromos(boolean) - Method in class org.snpeff.fileIterator.MarkerFileIterator
 
setCreateChromos(boolean) - Method in class org.snpeff.fileIterator.VcfFileIterator
 
setCreateRandSequences(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
setCvTerm(CvTerm) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
setDebug(boolean) - Method in class org.snpeff.align.VariantRealign
 
setDebug(boolean) - Method in class org.snpeff.fileIterator.FileIterator
 
setDebug(boolean) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
setDebug(boolean) - Method in class org.snpeff.interval.CircularCorrection
 
setDebug(boolean) - Method in class org.snpeff.interval.tree.IntervalForest
 
setDebug(boolean) - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
setDebug(boolean) - Method in class org.snpeff.nextProt.NextProtDb
 
setDebug(boolean) - Method in class org.snpeff.SnpEff
 
setDebug(boolean) - Method in class org.snpeff.snpEffect.Config
 
setDebug(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
setDebug(boolean) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
setDebug(boolean) - Method in interface org.snpeff.snpEffect.VcfAnnotator
Set debug mode
setDebug(boolean) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
 
setDebug(boolean) - Method in class org.snpeff.spliceSites.SpliceTypes
 
setDebug(boolean) - Method in class org.snpeff.spliceSites.TranscriptSet
 
setDebug(boolean) - Method in class org.snpeff.util.Download
 
setDebug(boolean) - Method in class org.snpeff.vcf.FileIndexChrPos
 
setDebug(boolean) - Method in class org.snpeff.vcf.Pedigree
 
setDefaultWaitTime(long) - Method in class org.snpeff.osCmd.OsCmdRunner
 
setDeletion(int) - Method in class org.snpeff.align.NeedlemanWunsch
 
setDeletion(int) - Method in class org.snpeff.align.NeedlemanWunschOverlap
 
setDescription(String) - Method in class org.snpeff.geneSets.GeneSet
 
setDescription(String) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
setDisableLoad(boolean) - Method in class org.snpeff.binseq.GenomicSequences
 
setDistance(int) - Method in class org.snpeff.snpEffect.VariantEffect
 
setDistanceThresholdNon(double) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
setDnaCheck(boolean) - Method in class org.snpeff.interval.Transcript
 
setDoNotAddIfNotInGeneSet(boolean) - Method in class org.snpeff.geneSets.GeneSets
 
setEffect(EffectType) - Method in class org.snpeff.snpEffect.VariantEffect
Set effect using default impact
setEffectDetails(String) - Method in class org.snpeff.vcf.VcfEffect
 
setEffectImpact(VariantEffect.EffectImpact) - Method in class org.snpeff.snpEffect.VariantEffect
 
setEffectType(EffectType) - Method in class org.snpeff.snpEffect.VariantEffect
 
setEffectType(EffectType) - Method in class org.snpeff.vcf.VcfEffect
 
setEnd(int) - Method in class org.snpeff.interval.Interval
 
setErrorChromoHit(boolean) - Method in class org.snpeff.snpEffect.Config
 
setErrorIfUnsorted(boolean) - Method in class org.snpeff.fileIterator.VcfFileIterator
 
setErrorOnMissingChromo(boolean) - Method in class org.snpeff.snpEffect.Config
 
setExonId(String) - Method in class org.snpeff.vcf.VcfEffect
 
setExpandIub(boolean) - Method in class org.snpeff.fileIterator.VcfFileIterator
 
setExpandIub(boolean) - Method in class org.snpeff.snpEffect.Config
 
setFalse() - Method in class org.snpeff.stats.BooleanMutable
 
setFastaFile(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
setFatalErrorBehabiour(Log.FatalErrorBehabiour) - Static method in class org.snpeff.util.Log
 
setFileName(String) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
setFilter(String) - Method in class org.snpeff.vcf.VcfEntry
 
setFilterOutputGeneSets(Set<String>) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
setFixedOutput(double) - Method in class org.snpeff.reactome.Entity
 
setForceNegativeStrand(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
 
setForcePositiveStrand(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
 
setFormat(String) - Method in class org.snpeff.vcf.VcfEntry
 
setFormatVersion(EffFormatVersion) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
 
setFormatVersion(EffFormatVersion) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
setFormatVersion(EffFormatVersion) - Method in class org.snpeff.vcf.VcfEffect
 
setFrame(int) - Method in class org.snpeff.interval.Cds
Frame can be {-1, 0, 1, 2}, where '-1' means unknown
setFrame(int) - Method in class org.snpeff.interval.Exon
Frame can be {-1, 0, 1, 2}, where '-1' means unknown
setFrame(int) - Method in interface org.snpeff.interval.MarkerWithFrame
 
setFunClass(VariantEffect.FunctionalClass) - Method in class org.snpeff.vcf.VcfEffect
 
setGap(int) - Method in class org.snpeff.binseq.DnaSequencePe
 
setGatk(boolean) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
 
setGeneId(String) - Method in class org.snpeff.gsa.ScoreList
 
setGeneId(String) - Method in class org.snpeff.vcf.VcfEffect
 
setGeneName(String) - Method in class org.snpeff.vcf.VcfEffect
 
setGeneSetByName(HashMap<String, GeneSet>) - Method in class org.snpeff.geneSets.GeneSets
 
setGeneSetCount(List<Integer>) - Method in class org.snpeff.geneSets.Result
 
setGeneSetCountLast(int) - Method in class org.snpeff.geneSets.Result
 
setGeneSets(List<GeneSet>) - Method in class org.snpeff.geneSets.Result
Assign geneSets
setGeneSets(GeneSets) - Method in class org.snpeff.geneSets.GeneSet
 
setGenesSet(HashSet<String>) - Method in class org.snpeff.geneOntology.GoTerm
 
setGenomeFasta(String) - Method in class org.snpeff.spliceSites.SpliceTypes
 
setGenomeVer(String) - Method in class org.snpeff.SnpEff
 
setGenotype(String) - Method in class org.snpeff.interval.Variant
 
setGenotype(String) - Method in class org.snpeff.vcf.VcfEffect
 
setGenotype(String) - Method in class org.snpeff.vcf.VcfGenotype
Set genotype value
setGenotypeStr(String) - Method in class org.snpeff.vcf.VcfEntry
 
setGoTerms(GoTerms) - Method in class org.snpeff.geneOntology.GoTerm
 
sethAxis(String) - Method in class org.snpeff.stats.plot.GoogleLineChart
 
setHeight(int) - Method in class org.snpeff.stats.plot.GoogleLineChart
 
setHgvsOld(boolean) - Method in class org.snpeff.snpEffect.Config
 
setHgvsOneLetterAA(boolean) - Method in class org.snpeff.snpEffect.Config
 
setHgvsShift(boolean) - Method in class org.snpeff.snpEffect.Config
 
setHgvsTrId(boolean) - Method in class org.snpeff.snpEffect.Config
 
setHighlyConservedAaSequence(boolean) - Method in class org.snpeff.interval.NextProt
 
setHtmlTable(boolean) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
setId(String) - Method in class org.snpeff.interval.Interval
 
setId(String) - Method in class org.snpeff.motif.Pwm
 
setId(String) - Method in class org.snpeff.vcf.VcfHeaderEntry
 
setIgnoreCase(boolean) - Method in class org.snpeff.util.Diff
 
setIgnoreChromosomeErrors(boolean) - Method in class org.snpeff.fileIterator.MarkerFileIterator
 
setIgnoreSpaces(boolean) - Method in class org.snpeff.util.Diff
 
setImpact(VariantEffect.EffectImpact) - Method in class org.snpeff.vcf.VcfEffect
 
setImplicit(boolean) - Method in class org.snpeff.vcf.VcfHeaderInfo
 
setImprecise(boolean) - Method in class org.snpeff.interval.Variant
 
setInitialSize(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
 
setInOffset(int) - Method in class org.snpeff.fileIterator.MarkerFileIterator
 
setInOffset(int) - Method in class org.snpeff.fileIterator.VcfFileIterator
 
setInterestingGenes(HashSet<String>) - Method in class org.snpeff.geneSets.GeneSets
 
setInterestingSymbolIdSet(HashSet<String>) - Method in class org.snpeff.geneOntology.GoTerm
 
setLabel(String) - Method in class org.snpeff.geneOntology.GoTerms
 
setLabel(String) - Method in class org.snpeff.interval.Custom
 
setLength(int) - Method in class org.snpeff.interval.Chromosome
 
setLength(int) - Method in class org.snpeff.nmer.Nmer
Set nmer's length
setLevel(int) - Method in class org.snpeff.geneOntology.GoTerm
 
setLine(String) - Method in class org.snpeff.interval.GenericMarker
 
setLineFilter(LineFilter) - Method in class org.snpeff.osCmd.StreamGobbler
 
setLineNum(int) - Method in class org.snpeff.vcf.VcfEntry
 
setLog(boolean) - Method in class org.snpeff.SnpEff
 
setLossOfFunction(boolean) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
 
setMarker(Marker) - Method in class org.snpeff.snpEffect.VariantEffect
Set marker.
setMarker(Marker) - Method in class org.snpeff.snpEffect.VariantEffects
 
setMarkerTypes(MarkerTypes) - Method in class org.snpeff.coverage.CountReads
 
setMarkerTypes(MarkerTypes) - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
setMaskDownloadException(boolean) - Method in class org.snpeff.util.Download
 
setMatch(int) - Method in class org.snpeff.align.NeedlemanWunsch
 
setMatch(int) - Method in class org.snpeff.align.NeedlemanWunschOverlap
 
setMaxBins(int) - Method in class org.snpeff.stats.IntStats
 
setMaxBins(int) - Method in class org.snpeff.stats.plot.GoogleHistogram
 
setMaxErrorRate(double) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
 
setMaxErrorRate(double) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
setMaxGeneSetSize(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
setMaxGeneSetSize(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
 
setMaxPvalue(double) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
 
setMaxPValue(double) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
setMaxPvalueAdjusted(double) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
setMaxPvalueAjusted(double) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
 
setMaxRank(int) - Method in class org.snpeff.geneOntology.GoTerm
 
setMaxRank(int) - Method in class org.snpeff.geneSets.GeneSet
 
setMinExons(int) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
 
setMinGeneSetSize(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
setMinGeneSetSize(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
 
setMinOverlap(int) - Method in class org.snpeff.overlap.OverlapDnaSeq
 
setMinus(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
Perform a 'set minus' between this term and 'goTerm' (set minus for 'symbolIdSet' and 'interestingSymbolIdSet').
setMinus(GeneSet) - Method in class org.snpeff.geneSets.GeneSet
Perform a 'set minus' between this term and 'geneSet' (set minus for 'geneSet' and 'interestingGeneSet').
setMissMatch(int) - Method in class org.snpeff.align.NeedlemanWunsch
 
setMissMatch(int) - Method in class org.snpeff.align.NeedlemanWunschOverlap
 
setMonitorTrace(Monitor) - Method in class org.snpeff.reactome.Reactome
 
setN(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
setName(String) - Method in class org.snpeff.geneSets.GeneSet
 
setName(String) - Method in class org.snpeff.interval.Markers
 
setName(String) - Method in class org.snpeff.interval.tree.IntervalForest
 
setName(String) - Method in class org.snpeff.motif.Pwm
 
setNameSpace(String) - Method in class org.snpeff.geneOntology.GoTerm
 
setNextProt(boolean) - Method in class org.snpeff.SnpEff
 
setNextProtKeepAllTrs(boolean) - Method in class org.snpeff.SnpEff
 
setNmer(long) - Method in class org.snpeff.nmer.Nmer
Set nmer (binary coded)
setNumber(int) - Method in class org.snpeff.vcf.VcfHeaderInfo
 
setNumber(String) - Method in class org.snpeff.vcf.VcfHeaderInfo
 
setNumberLabelsXaxis(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
 
setNumberOfSamples(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
setNumGenes(int) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
 
setNumIterations(int) - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
setNumReads(int) - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
setNumThreads(int) - Method in class org.snpeff.osCmd.OsCmdQueue
 
setNumWords(int) - Method in class org.snpeff.collections.OpenBitSet
Expert: sets the number of longs in the array that are in use
setObjetcToNotify(Object) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setOnlyOneTranscript(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
 
setOnlyProtein(boolean) - Method in class org.snpeff.snpEffect.testCases.integration.CompareToVep
 
setOnlyRegulation(boolean) - Method in class org.snpeff.snpEffect.Config
 
setOrderDescending(boolean) - Method in class org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
 
setOutOffset(int) - Method in class org.snpeff.outputFormatter.BedOutputFormatter
 
setOutOffset(int) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setOutOffset(int) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
 
setOutputDir(String) - Method in class org.snpeff.RegulationFileConsensus
 
setOutputFile(String) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setOverlapFilter(OverlapFilter<T>) - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
 
setParent(Interval) - Method in class org.snpeff.interval.Interval
 
setParents(HashSet<GoTerm>) - Method in class org.snpeff.geneOntology.GoTerm
 
setParseNow(boolean) - Method in class org.snpeff.fileIterator.VcfFileIterator
Should we parse vcfEntries later? (lazy parsing)
setPlotMaxData(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
 
setPlotSizeX(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
 
setPlotSizeY(int) - Method in class org.snpeff.stats.plot.GooglePlotInt
 
setProgress(Progress) - Method in class org.snpeff.osCmd.StreamGobbler
 
setProteinByTrId(Map<String, String>) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
setProteinCoding(boolean) - Method in class org.snpeff.interval.Transcript
 
setPvalue(double) - Method in class org.snpeff.geneSets.Result
 
setPvalue(Apfloat) - Method in class org.snpeff.geneSets.Result
 
setpValueCutOffQuantile(double) - Method in class org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
 
setPwd(String) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setPwm(Pwm) - Method in class org.snpeff.interval.Motif
 
setQuality(int, int) - Method in class org.snpeff.binseq.BinarySequence
Set the quality at position 'index'
setQuiet(boolean) - Method in class org.snpeff.snpEffect.Config
 
setQuiet(boolean, boolean) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setQuietMode() - Method in class org.snpeff.osCmd.StreamGobbler
 
setRandom(Random) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
setRank(int) - Method in class org.snpeff.interval.Exon
 
setRank(int) - Method in class org.snpeff.interval.Intron
 
setRankedSymbols(int) - Method in class org.snpeff.geneOntology.GoTerm
 
setRankSum(int) - Method in class org.snpeff.geneOntology.GoTerm
 
setRankSum(long[][]) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
setRareThreshold(double) - Method in class org.snpeff.codons.FindRareAaIntervals
 
setReadLength(int) - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
setReadSequences(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Read sequences? Note: This is only used for debugging and testing
setRedirectStderr(String) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setRedirectStdout(String) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setRedirectTo(String) - Method in class org.snpeff.osCmd.StreamGobbler
 
setRedirectToOutput(boolean) - Method in class org.snpeff.osCmd.OsCmdQueue
 
setRibosomalSlippage(boolean) - Method in class org.snpeff.interval.Transcript
 
setSamples(int[][]) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
setSaveLinesInMemory(boolean) - Method in class org.snpeff.osCmd.StreamGobbler
 
setSaveStd(boolean) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setSaveStd(boolean) - Method in class org.snpeff.osCmd.OsCmdRunner
 
setScore(double) - Method in class org.snpeff.interval.Custom
 
setScore(double) - Method in class org.snpeff.interval.VariantWithScore
 
setScore(String, double) - Method in class org.snpeff.stats.CountByType
 
setSeparator(String) - Method in class org.snpeff.fileIterator.LineClassFileIterator
 
setSequence(String) - Method in class org.snpeff.interval.Chromosome
Set sequence for this chromosome
setSequence(String) - Method in class org.snpeff.interval.MarkerSeq
Set sequence WARNING: Sequence is always according to coding strand.
setSequence(String) - Method in class org.snpeff.nextProt.NextProtXmlIsoform
Add an Isoform sequence
setSequenceAlt(String) - Method in class org.snpeff.align.VariantRealign
 
setSequenceRef(String) - Method in class org.snpeff.align.VariantRealign
 
setSescription(String) - Method in class org.snpeff.geneOntology.GoTerm
 
setShiftHgvs(boolean) - Method in class org.snpeff.SnpEff
 
setShiftHgvs(boolean) - Method in class org.snpeff.snpEffect.testCases.integration.CompareToVep
 
setShowExceptions(boolean) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setShowHeader(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setShowOnlyDifferentLines(boolean) - Method in class org.snpeff.util.Diff
 
setSizeGrowthFactor(int) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
 
setSnpEffectPredictor(SnpEffectPredictor) - Method in class org.snpeff.snpEffect.Config
 
setSnpEffectPredictor(SnpEffectPredictor) - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
setSpliceRegionExonSize(int) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
setSpliceRegionIntronMax(int) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
setSpliceRegionIntronMin(int) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
setSpliceSiteSize(int) - Method in class org.snpeff.SnpEff
 
setSpliceSiteSize(int) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
setStacked(boolean) - Method in class org.snpeff.stats.plot.GoogleLineChart
 
setStart(int) - Method in class org.snpeff.interval.Interval
 
setStdoutAlert(String) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setStdoutAlertNotify(Object) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setStdOutFilter(LineFilter) - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
setStoreAlignments(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
 
setStoreAlignments(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
 
setStoreAlignments(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
setStoreSequences(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
setStrandMinus(boolean) - Method in class org.snpeff.interval.Interval
 
setStrandMinus(boolean) - Method in class org.snpeff.interval.IntervalAndSubIntervals
 
setStrict(boolean) - Method in class org.snpeff.snpEffect.testCases.integration.CompareToVep
 
setString(String, String) - Method in class org.snpeff.snpEffect.Config
 
setSubfieldSeparator(String) - Method in class org.snpeff.fileIterator.GuessTableTypes
 
setSupressOutput(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setSupressOutput(boolean) - Method in class org.snpeff.SnpEff
 
setSvgPlot(String) - Method in class org.snpeff.stats.TranslocationReport
 
setSymbolIdSet(HashSet<String>) - Method in class org.snpeff.geneOntology.GoTerm
 
setTitle(String) - Method in class org.snpeff.stats.plot.GoogleLineChart
 
setTitle(String) - Method in class org.snpeff.stats.plot.GooglePlotInt
 
setTr1(Transcript) - Method in class org.snpeff.pdb.DistanceResult
 
setTr2(Transcript) - Method in class org.snpeff.pdb.DistanceResult
 
setTranscriptId(String) - Method in class org.snpeff.vcf.VcfEffect
 
setTranscriptSet(TranscriptSet) - Method in class org.snpeff.spliceSites.SpliceTypes
 
setTranscriptSupportLevel(TranscriptSupportLevel) - Method in class org.snpeff.interval.Transcript
 
setTreatAllAsProteinCoding(boolean) - Method in class org.snpeff.snpEffect.Config
 
setTrue() - Method in class org.snpeff.stats.BooleanMutable
 
setUpdate(boolean) - Method in class org.snpeff.util.Download
 
setUpDownStreamLength(int) - Method in class org.snpeff.SnpEff
 
setUpDownStreamLength(int) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
setUseAaNoNum(boolean) - Method in class org.snpeff.snpEffect.testCases.integration.CompareEffects
 
setUseChromosomes(boolean) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
setUseFirstEffect(boolean) - Method in class org.snpeff.vcf.VcfEffect
 
setUseGeneId(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setUseGeneId(boolean) - Method in class org.snpeff.vcf.VcfEffect
 
setUseHgvs(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setUseHgvs(boolean) - Method in class org.snpeff.snpEffect.Config
 
setUseHgvs(boolean) - Method in class org.snpeff.vcf.VcfEffect
 
setUseMiliSecs(boolean) - Method in class org.snpeff.util.Timer
 
setUseOicr(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setUseSequenceOntology(boolean) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setUseSequenceOntology(boolean) - Method in class org.snpeff.stats.VariantEffectStats
 
setUseSpace(boolean) - Method in class org.snpeff.align.NeedlemanWunsch
 
setValue(String, double) - Method in class org.snpeff.geneSets.GeneSets
Set experimental value for this gene
setVariantEffectResutFilter(VariantEffectFilter) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setVariantRef(Variant) - Method in class org.snpeff.interval.VariantNonRef
 
setVariantType(Variant.VariantType) - Method in class org.snpeff.align.VcfRefAltAlign
 
setVariantType(Variant.VariantType) - Method in class org.snpeff.interval.Variant
 
setvAxis(String) - Method in class org.snpeff.stats.plot.GoogleLineChart
 
setVcfFileName(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
 
setVcfHeader(VcfHeader) - Method in class org.snpeff.fileIterator.VcfFileIterator
Set header
setVcfInfoNumber(VcfHeaderInfo.VcfInfoNumber) - Method in class org.snpeff.vcf.VcfHeaderInfo
 
setVcfInfoType(VcfInfoType) - Method in class org.snpeff.vcf.VcfHeaderInfo
 
setVerbose(boolean) - Method in class org.snpeff.binseq.GenomicSequences
 
setVerbose(boolean) - Method in class org.snpeff.codons.FindRareAaIntervals
 
setVerbose(boolean) - Method in class org.snpeff.coverage.CountReads
 
setVerbose(boolean) - Method in class org.snpeff.coverage.CountReadsOnMarkers
 
setVerbose(boolean) - Method in class org.snpeff.fastq.FastqSplit
 
setVerbose(boolean) - Method in class org.snpeff.fileIterator.FileIterator
 
setVerbose(boolean) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
 
setVerbose(boolean) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
 
setVerbose(boolean) - Method in class org.snpeff.geneSets.GeneSets
 
setVerbose(boolean) - Method in class org.snpeff.gtex.Gtex
 
setVerbose(boolean) - Method in class org.snpeff.interval.ExonSpliceCharacterizer
 
setVerbose(boolean) - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
setVerbose(boolean) - Method in class org.snpeff.motif.Jaspar
 
setVerbose(boolean) - Method in class org.snpeff.nextProt.NextProtDb
 
setVerbose(boolean) - Method in class org.snpeff.osCmd.OsCmdQueue
 
setVerbose(boolean) - Method in class org.snpeff.pdb.IdMapper
 
setVerbose(boolean) - Method in class org.snpeff.ped.PedPedigree
 
setVerbose(boolean) - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
 
setVerbose(boolean) - Method in class org.snpeff.reactome.Reactome
 
setVerbose(boolean) - Method in class org.snpeff.RegulationConsensusMultipleBed
 
setVerbose(boolean) - Method in class org.snpeff.RegulationFileConsensus
 
setVerbose(boolean) - Method in class org.snpeff.RegulationFileSplitBytType
 
setVerbose(boolean) - Method in class org.snpeff.SnpEff
 
setVerbose(boolean) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
 
setVerbose(boolean) - Method in class org.snpeff.snpEffect.Config
 
setVerbose(boolean) - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
setVerbose(boolean) - Method in class org.snpeff.snpEffect.testCases.integration.CompareToEnsembl
 
setVerbose(boolean) - Method in interface org.snpeff.snpEffect.VcfAnnotator
Set verbose mode
setVerbose(boolean) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
 
setVerbose(boolean) - Method in class org.snpeff.spliceSites.SpliceTypes
 
setVerbose(boolean) - Method in class org.snpeff.spliceSites.TranscriptSet
 
setVerbose(boolean) - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
setVerbose(boolean) - Method in class org.snpeff.util.Download
 
setVerbose(boolean) - Method in class org.snpeff.vcf.FileIndexChrPos
 
setVerbose(boolean) - Method in class org.snpeff.vcf.Pedigree
 
setVersion(String) - Method in class org.snpeff.interval.Transcript
 
setVersion(String) - Method in class org.snpeff.outputFormatter.OutputFormatter
 
setWeight(double) - Method in class org.snpeff.reactome.Entity
 
setWidth(int) - Method in class org.snpeff.stats.plot.GoogleLineChart
 
setxAxisLabel(String) - Method in class org.snpeff.stats.plot.GooglePlotInt
 
setxLables(ArrayList<String>) - Method in class org.snpeff.stats.plot.GoogleLineChart
 
Sex - Enum Class in org.snpeff.ped
 
shiftArgs - Variable in class org.snpeff.SnpEff
 
shiftCoordinates(int) - Method in class org.snpeff.interval.Interval
 
shiftCoordinates(int) - Method in class org.snpeff.interval.IntervalAndSubIntervals
 
shiftHgvs - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
shiftHgvs - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
shouldApply(Variant) - Method in class org.snpeff.interval.Marker
True if the variant should be applied to the marker
show(Object) - Static method in class org.snpeff.util.Timer
Show absolute timer value and a message
SHOW_EVERY - Static variable in class org.snpeff.coverage.CountReads
 
SHOW_EVERY - Static variable in class org.snpeff.coverage.CountReadsOnMarkers
 
SHOW_EVERY - Static variable in class org.snpeff.Fastq2Fastq
 
SHOW_EVERY - Static variable in class org.snpeff.interval.ExonSpliceCharacterizer
 
SHOW_EVERY - Static variable in class org.snpeff.Qseq2Fastq
 
SHOW_EVERY - Static variable in class org.snpeff.reactome.Reactome
 
SHOW_EVERY - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
SHOW_EVERY - Static variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
 
SHOW_EVERY - Static variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
SHOW_EVERY - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesReactome
 
showChromoNamesDifferences() - Method in class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
Shw differences in chromosome names
showCodonChange - Static variable in class org.snpeff.interval.codonChange.CodonChange
 
showCommand(CommandLine) - Method in class org.snpeff.snpEffect.testCases.integration.IntegrationTest
Show command (as a command line)
showDiff(String, String) - Method in class org.snpeff.snpEffect.testCases.integration.IntegrationTest
Show the difference between who string (multi-line strings)
showDiffLine(String, String) - Method in class org.snpeff.snpEffect.testCases.integration.IntegrationTest
Show difference between two lines
showGenes() - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
Show genes in BED format
showMark(int, int) - Static method in class org.snpeff.util.Gpr
Show a mark
showMark(int, int, String) - Static method in class org.snpeff.util.Gpr
Show a mark
showMarkStderr(int, int) - Static method in class org.snpeff.util.Gpr
Show a mark (on STDERR)
showMismatch(String, String, String) - Static method in class org.snpeff.util.GprSeq
Show differences between two sequences
showStackTrace(int) - Static method in class org.snpeff.util.Gpr
 
showStackTrace(int, int) - Static method in class org.snpeff.util.Gpr
Prints a stack trace for a number of steps
showStdErr(Object) - Static method in class org.snpeff.util.Timer
Show absolute timer value and a message on STDERR
showTranscripts(Genome) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
showTranscripts(Genome, boolean) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Show a genome in a 'standard' way
shrink(byte[], int) - Static method in class org.snpeff.collections.ArrayUtil
 
shrink(int[], int) - Static method in class org.snpeff.collections.ArrayUtil
 
shrink(long[], int) - Static method in class org.snpeff.collections.ArrayUtil
 
SIGM - Enum constant in enum class org.snpeff.reactome.Entity.TransferFunction
 
SIGM_PLUS_MINUS - Enum constant in enum class org.snpeff.reactome.Entity.TransferFunction
 
sigma(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Wrapper to Sqrt(variance)
sigma(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
Wrapper to Sqrt(variance)
SIGN_WIDTH - Static variable in class org.snpeff.svg.SvgIntron
 
SIGNIFICANCE_LEVEL_95 - Static variable in class org.snpeff.gsa.ScoreList
 
silenceWarning(ErrorWarningType) - Static method in class org.snpeff.util.Log
 
SILENT - Enum constant in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
 
SIMES - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
 
simpleName(String) - Static method in class org.snpeff.interval.Chromosome
Simplify chromosome name
simpleName(String) - Method in class org.snpeff.interval.ChromosomeSimpleName
Simplify chromosome name
simpleNameCache(String) - Method in class org.snpeff.interval.ChromosomeSimpleName
Query cache before simplifying name
size - Variable in class org.snpeff.fileIterator.TableFile
 
size() - Method in class org.snpeff.binseq.indexer.SequenceIndexer
Number of sequences in this index
size() - Method in class org.snpeff.collections.OpenBitSet
Returns the current capacity of this set.
size() - Method in class org.snpeff.fileIterator.TableFile
Array size
size() - Method in class org.snpeff.geneSets.GeneSet
 
size() - Method in class org.snpeff.genotypes.GenotypeVector
 
size() - Method in class org.snpeff.gsa.ChrPosScoreList
 
size() - Method in class org.snpeff.gsa.ScoreList
 
size() - Method in class org.snpeff.gtex.GtexExperiment
 
size() - Method in class org.snpeff.interval.Genes
 
size() - Method in class org.snpeff.interval.Interval
 
size() - Method in class org.snpeff.interval.Markers
 
size() - Method in class org.snpeff.interval.tree.IntervalForest
 
size() - Method in class org.snpeff.interval.tree.IntervalTree
Size: number of entries in the interval list
size() - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
size() - Method in class org.snpeff.interval.tree.IntervalTreeOri
Size: number of entries in the interval list
size() - Method in interface org.snpeff.interval.tree.Itree
Size: number of entries in this tree
size() - Method in class org.snpeff.nmer.NmerCount
 
size() - Method in class org.snpeff.osCmd.OsCmdQueue
 
size() - Method in class org.snpeff.ped.PedEntry
Number of phenotypes
size() - Method in class org.snpeff.ped.PedGenotype
 
size() - Method in class org.snpeff.ped.PedPedigree
 
size() - Method in class org.snpeff.ped.PlinkMap
 
size() - Method in class org.snpeff.reactome.events.Complex
 
size() - Method in class org.snpeff.reactome.events.Pathway
 
size() - Method in class org.snpeff.reactome.Monitor
 
size() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
size() - Method in class org.snpeff.snpEffect.VariantEffects
 
size() - Method in class org.snpeff.stats.ChrPosStats
 
size() - Method in class org.snpeff.stats.CountByKey
 
size() - Method in class org.snpeff.stats.PosStats
 
size() - Method in class org.snpeff.vcf.FileIndexChrPos
File size
SIZE_BRANCH - Static variable in class org.snpeff.spliceSites.SpliceTypes
 
SIZE_CONSENSUS_ACCEPTOR - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
SIZE_CONSENSUS_DONOR - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
sizeEffective() - Method in class org.snpeff.geneSets.GeneSet
Number of genes that have a value
sizeof(String) - Method in class org.snpeff.interval.Gene
Size of a genetic region for a given gene
sizeResults() - Method in class org.snpeff.reactome.Monitor
 
skip(long) - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
SKIPPED - Enum constant in enum class org.snpeff.interval.Exon.ExonSpliceType
 
SMALL - Static variable in class org.snpeff.probablility.RankSumPdf
A small number
SMALL_VARIANT_SIZE_THRESHOLD - Static variable in class org.snpeff.snpEffect.SnpEffectPredictor
 
SmithWaterman - Class in org.snpeff.align
Smith-Waterman (local sequence alignment) algorithm for sequence alignment (short strings, since it's not memory optimized)
SmithWaterman(String, String) - Constructor for class org.snpeff.align.SmithWaterman
 
snoRNA - Enum constant in enum class org.snpeff.interval.BioType
 
SNP - Enum constant in enum class org.snpeff.interval.Variant.VariantType
 
SnpEff - Class in org.snpeff
SnpEff's main command line program
SnpEff() - Constructor for class org.snpeff.SnpEff
 
SnpEff(String[]) - Constructor for class org.snpeff.SnpEff
 
SnpEff.GeneDatabaseFormat - Enum Class in org.snpeff
Available gene database formats
SnpEff.InputFormat - Enum Class in org.snpeff
Available input formats
SnpEff.OutputFormat - Enum Class in org.snpeff
Available output formats
snpEffCmd - Variable in class org.snpeff.SnpEff
 
SnpEffCmdAcat - Class in org.snpeff.snpEffect.commandLine
ACAT: Create ACAT score for T2D project Note: This is just used to compile 'ACAT' score in T2D-GENES project, not useful at all for general audience.
SnpEffCmdAcat() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
 
SnpEffCmdBuild - Class in org.snpeff.snpEffect.commandLine
Command line program: Build database
SnpEffCmdBuild() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
 
SnpEffCmdBuildNextProt - Class in org.snpeff.snpEffect.commandLine
Parse NetxProt XML file and build a database http://www.nextprot.org/
SnpEffCmdBuildNextProt() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdBuildNextProt
 
SnpEffCmdCds - Class in org.snpeff.snpEffect.commandLine
Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structures
SnpEffCmdCds() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
 
SnpEffCmdCds(String, String, String) - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
 
SnpEffCmdCds(Config) - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
 
SnpEffCmdClosest - Class in org.snpeff.snpEffect.commandLine
Command line: Find closes marker to each variant
SnpEffCmdClosest() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
 
SnpEffCmdClosest(Config) - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
 
SnpEffCmdCount - Class in org.snpeff.snpEffect.commandLine
Count reads from a BAM file given a list of intervals
SnpEffCmdCount() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdCount
 
SnpEffCmdDatabases - Class in org.snpeff.snpEffect.commandLine
Show all databases configures in snpEff.config Create an HTML 'download' table based on the config file Also creates a list of genome for Galaxy menu
SnpEffCmdDatabases() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
 
SnpEffCmdDownload - Class in org.snpeff.snpEffect.commandLine
Command line program: Download and install a (pre built) database
SnpEffCmdDownload() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdDownload
 
SnpEffCmdDump - Class in org.snpeff.snpEffect.commandLine
Command line program: Build database
SnpEffCmdDump() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdDump
 
SnpEffCmdDump.DumpFormat - Enum Class in org.snpeff.snpEffect.commandLine
 
SnpEffCmdEff - Class in org.snpeff.snpEffect.commandLine
Command line program: Predict variant effects
SnpEffCmdEff() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
SnpEffCmdGenes2Bed - Class in org.snpeff.snpEffect.commandLine
Simple test program
SnpEffCmdGenes2Bed() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
 
SnpEffCmdGsa - Class in org.snpeff.snpEffect.commandLine
Command line: Gene-Sets Analysis Perform gene set analysys
SnpEffCmdGsa() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
 
SnpEffCmdLen - Class in org.snpeff.snpEffect.commandLine
Calculate the maximum interval length by type, for all markers in a genome
SnpEffCmdLen() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdLen
 
SnpEffCmdPdb - Class in org.snpeff.snpEffect.commandLine
PDB distance analysis
SnpEffCmdPdb() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
SnpEffCmdProtein - Class in org.snpeff.snpEffect.commandLine
Command line: Read protein sequences from a file and compare them to the ones calculated from our data structures Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.
SnpEffCmdProtein() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
SnpEffCmdProtein(String, String, String) - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
SnpEffCmdProtein(Config) - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
SnpEffCmdProtein(Config, String) - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
 
SnpEffCmdSeq - Class in org.snpeff.snpEffect.commandLine
Command line program: Show a transcript or a gene
SnpEffCmdSeq() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdSeq
 
SnpEffCmdShow - Class in org.snpeff.snpEffect.commandLine
Command line program: Show a transcript or a gene
SnpEffCmdShow() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdShow
 
SnpEffCmdSpliceAnalysis - Class in org.snpeff.spliceSites
Analyze sequences from splice sites
SnpEffCmdSpliceAnalysis() - Constructor for class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
SnpEffCmdTranslocationsReport - Class in org.snpeff.snpEffect.commandLine
Create an SVG representation of a Marker
SnpEffCmdTranslocationsReport() - Constructor for class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
 
snpEffect(String, String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
Run SnpEff on VCF file
snpEffect(String, String, boolean) - Method in class org.snpeff.snpEffect.testCases.integration.CompareEffects
Read snps from a file and compare them to 'out' SnpEffect predictor.
snpEffect(String, String, String[]) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Calculate snp effect for an input VCF file
snpEffect(String, String, String[], EffFormatVersion) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Calculate snp effect for an input VCF file
snpEffect(List<Variant>, String, boolean, boolean) - Method in class org.snpeff.snpEffect.testCases.integration.CompareEffects
Calculate snp effect for a list of snps
snpEffectCancer(String, String, String, boolean, String, String, String, String) - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
Calculate snp effect for a list of snps using cancer samples
snpEffectNegate(String, String, boolean) - Method in class org.snpeff.snpEffect.testCases.integration.CompareEffects
 
snpEffectPredictor - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
snpEffectPredictor - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
snpEffectPredictor - Variable in class org.snpeff.snpEffect.testCases.unity.TestGenome
 
SnpEffectPredictor - Class in org.snpeff.snpEffect
Predicts effects of SNPs
SnpEffectPredictor(Genome) - Constructor for class org.snpeff.snpEffect.SnpEffectPredictor
 
SnpEffPredictorFactory - Class in org.snpeff.snpEffect.factory
This class creates a SnpEffectPredictor from a file (or a set of files) and a configuration
SnpEffPredictorFactory(Config, int) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
 
SnpEffPredictorFactoryEmbl - Class in org.snpeff.snpEffect.factory
This class creates a SnpEffectPredictor from an Embl file.
SnpEffPredictorFactoryEmbl(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryEmbl
 
SnpEffPredictorFactoryEmbl(Config, String) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryEmbl
 
SnpEffPredictorFactoryFeatures - Class in org.snpeff.snpEffect.factory
This class creates a SnpEffectPredictor from a 'features' file.
SnpEffPredictorFactoryFeatures(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
 
SnpEffPredictorFactoryGenBank - Class in org.snpeff.snpEffect.factory
This class creates a SnpEffectPredictor from a GenBank file.
SnpEffPredictorFactoryGenBank(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenBank
 
SnpEffPredictorFactoryGenBank(Config, String) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenBank
 
SnpEffPredictorFactoryGenesFile - Class in org.snpeff.snpEffect.factory
This class creates a SnpEffectPredictor from a file (or a set of files) and a configuration The files used are: - genes.txt : Biomart query from Ensembl (see scripts/genes_dataset.xml) - Fasta files: One per chromosome (as described in the config file)
SnpEffPredictorFactoryGenesFile(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenesFile
 
SnpEffPredictorFactoryGff - Class in org.snpeff.snpEffect.factory
This class creates a SnpEffectPredictor from a GFF file.
SnpEffPredictorFactoryGff(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
 
SnpEffPredictorFactoryGff2 - Class in org.snpeff.snpEffect.factory
This class creates a SnpEffectPredictor from a GFF2 file.
SnpEffPredictorFactoryGff2(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff2
 
SnpEffPredictorFactoryGff3 - Class in org.snpeff.snpEffect.factory
This class creates a SnpEffectPredictor from a GFF3 file References: - http://www.sequenceontology.org/gff3.shtml - http://gmod.org/wiki/GFF3 - http://www.eu-sol.net/science/bioinformatics/standards-documents/gff3-format-description
SnpEffPredictorFactoryGff3(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff3
 
SnpEffPredictorFactoryGtf22 - Class in org.snpeff.snpEffect.factory
This class creates a SnpEffectPredictor from a GTF 2.2 file References: http://mblab.wustl.edu/GTF22.html
SnpEffPredictorFactoryGtf22(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22
 
SnpEffPredictorFactoryKnownGene - Class in org.snpeff.snpEffect.factory
This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser Fields in this table Field Example SQL type Info Description ----- ------- -------- ---- ----------- name uc001aaa.3 varchar(255) values Name of gene chrom chr1 varchar(255) values Reference sequence chromosome or scaffold strand + char(1) values + or - for strand txStart 11873 int(10) unsigned range Transcription start position txEnd 14409 int(10) unsigned range Transcription end position cdsStart 11873 int(10) unsigned range Coding region start cdsEnd 11873 int(10) unsigned range Coding region end exonCount 3 int(10) unsigned range Number of exons exonStarts 11873,12612,13220, longblob Exon start positions exonEnds 12227,12721,14409, longblob Exon end positions proteinID varchar(40) values UniProt display ID for Known Genes, UniProt accession or RefSeq protein ID for UCSC Genes alignID uc001aaa.3 varchar(255) values Unique identifier for each (known gene, alignment position) pair
SnpEffPredictorFactoryKnownGene(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
 
SnpEffPredictorFactoryRand - Class in org.snpeff.snpEffect.factory
This class creates a random set of chromosomes, genes, transcripts and exons
SnpEffPredictorFactoryRand(Config, Random, int, int, int) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
 
SnpEffPredictorFactoryRefSeq - Class in org.snpeff.snpEffect.factory
This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser RefSeq table schema: http://genome.ucsc.edu/cgi-bin/hgTables field example SQL type info description bin 585 smallint(5) range Indexing field to speed chromosome range queries.
SnpEffPredictorFactoryRefSeq(Config) - Constructor for class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRefSeq
 
snpOrMnp() - Method in class org.snpeff.snpEffect.HgvsProtein
SNP or MNP changes
snRNA - Enum constant in enum class org.snpeff.interval.BioType
 
SOFTWARE_NAME - Static variable in class org.snpeff.SnpEff
 
sort() - Method in class org.snpeff.interval.Markers
Sort intervals
sort() - Method in class org.snpeff.reactome.Monitor
 
sort() - Method in class org.snpeff.snpEffect.VariantEffects
 
sort(boolean, boolean) - Method in class org.snpeff.interval.Markers
Sort intervals
sortCds() - Method in class org.snpeff.interval.Transcript
 
sorted() - Method in class org.snpeff.interval.Genes
 
sorted() - Method in class org.snpeff.interval.IntervalAndSubIntervals
Return a collection of sub intervals sorted by natural order
sortedStrand() - Method in class org.snpeff.interval.IntervalAndSubIntervals
Return a collection of sub intervals sorted by start position (if strand is >= 0) or by reverse end position (if strand < 0)
SOURCE - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
SPLICE_REGION_EXON_SIZE - Static variable in class org.snpeff.interval.SpliceSite
 
SPLICE_REGION_INTRON_MAX - Static variable in class org.snpeff.interval.SpliceSite
 
SPLICE_REGION_INTRON_MIN - Static variable in class org.snpeff.interval.SpliceSite
 
SPLICE_SITE_ACCEPTOR - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
SPLICE_SITE_BRANCH - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
SPLICE_SITE_BRANCH_U12 - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
SPLICE_SITE_DONOR - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
SPLICE_SITE_REGION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
spliceRegionExonSize - Variable in class org.snpeff.SnpEff
 
spliceRegionExonSize - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
spliceRegionIntronMax - Variable in class org.snpeff.SnpEff
 
spliceRegionIntronMax - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
spliceRegionIntronMin - Variable in class org.snpeff.SnpEff
 
spliceRegionIntronMin - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
SpliceSite - Class in org.snpeff.interval
Interval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes.
SpliceSite() - Constructor for class org.snpeff.interval.SpliceSite
 
SpliceSite(Exon, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSite
 
SpliceSite(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSite
 
SpliceSiteAcceptor - Class in org.snpeff.interval
Interval for a splice site acceptor Note: Splice sites donnor are defined as the last 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicing
SpliceSiteAcceptor() - Constructor for class org.snpeff.interval.SpliceSiteAcceptor
 
SpliceSiteAcceptor(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteAcceptor
 
SpliceSiteBranch - Class in org.snpeff.interval
A (putative) branch site.
SpliceSiteBranch() - Constructor for class org.snpeff.interval.SpliceSiteBranch
 
SpliceSiteBranch(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteBranch
 
SpliceSiteBranchU12 - Class in org.snpeff.interval
A (putative) U12 branch site.
SpliceSiteBranchU12() - Constructor for class org.snpeff.interval.SpliceSiteBranchU12
 
SpliceSiteBranchU12(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteBranchU12
 
SpliceSiteDonor - Class in org.snpeff.interval
Interval for a splice site donnor Note: Splice sites donnor are defined as the first 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicing
SpliceSiteDonor() - Constructor for class org.snpeff.interval.SpliceSiteDonor
 
SpliceSiteDonor(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteDonor
 
SpliceSiteRegion - Class in org.snpeff.interval
Interval for a splice site acceptor From Sequence Ontology: A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
SpliceSiteRegion() - Constructor for class org.snpeff.interval.SpliceSiteRegion
 
SpliceSiteRegion(Exon, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteRegion
 
SpliceSiteRegion(Intron, int, int, boolean, String) - Constructor for class org.snpeff.interval.SpliceSiteRegion
 
spliceSites() - Method in class org.snpeff.interval.Transcript
 
spliceSiteSize - Variable in class org.snpeff.SnpEff
 
SpliceTypes - Class in org.snpeff.spliceSites
Analyze sequences from splice sites
SpliceTypes(Config) - Constructor for class org.snpeff.spliceSites.SpliceTypes
 
split(String) - Method in class org.snpeff.vcf.VcfEffect
Split a 'effect' string to an array of strings
split(String, char) - Static method in class org.snpeff.util.Gpr
Splits a separated string into an array of String tokens.
splitFile(RegulationFileIterator, String) - Method in class org.snpeff.RegulationFileSplitBytType
Read a regulation file and split into one file for each "regulation type"
sRNA - Enum constant in enum class org.snpeff.interval.BioType
 
sseqid - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
sstart - Variable in class org.snpeff.fileIterator.BlastResultEntry
 
stab(int) - Method in class org.snpeff.interval.tree.IntervalTree
Perform a stabbing query, returning the interval objects
stab(int) - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
stab(int) - Method in class org.snpeff.interval.tree.IntervalTreeOri
Perform a stabbing query, returning the interval objects
stab(int) - Method in interface org.snpeff.interval.tree.Itree
Perform a stabbing query, returning the interval objects
stab(int, int, Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
stab(Integer) - Method in class org.snpeff.interval.tree.IntervalNode
Perform a stabbing query on the node
stab(Integer) - Method in class org.snpeff.interval.tree.IntervalNodeOri
Perform a stabbing query on the node
stab(String, int) - Method in class org.snpeff.interval.tree.IntervalForest
Obtain all intervals that intersect with 'point'
stab(Marker) - Method in class org.snpeff.interval.tree.IntervalForest
Obtain all intervals that intersect with 'marker.start'
stabIntersects(int, int, Markers) - Method in class org.snpeff.interval.tree.IntervalTreeArray
Stab entries intersecting 'point' at node 'idx'
STANDARD_TABLE - Static variable in class org.snpeff.codons.CodonTables
 
STANDARD_TABLE_NAME - Static variable in class org.snpeff.codons.CodonTables
 
start - Variable in class org.snpeff.binseq.indexer.OverlapRessult
 
start - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
start - Variable in class org.snpeff.genBank.FeatureCoordinates
 
start - Variable in class org.snpeff.interval.Interval
 
start() - Method in class org.snpeff.util.Timer
 
START_CODON - Enum constant in enum class org.snpeff.interval.GffType
 
START_GAINED - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
START_LOST - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
startElement(String, String, String, Attributes) - Method in class org.snpeff.nextProt.NextProtHandler
Parse XML's element start
startSection(Marker) - Method in class org.snpeff.outputFormatter.BedOutputFormatter
 
startSection(Marker) - Method in class org.snpeff.outputFormatter.OutputFormatter
Starts a new section
startSection(Marker) - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
 
stats() - Method in class org.snpeff.stats.MineMarkerIntervals
 
stats() - Method in class org.snpeff.stats.MineTwoMarkerIntervals
 
STOP_CODON - Enum constant in enum class org.snpeff.interval.GffType
 
STOP_GAINED - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
STOP_LOST - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
stopCriteria(Result) - Method in class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
Stop criteria
stopCriteria(Result) - Method in class org.snpeff.geneSets.algorithm.RankSumPValueGreedyAlgorithm
Stop criteria
strand - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
strandMinus - Variable in class org.snpeff.interval.Interval
 
strandMinus - Variable in class org.snpeff.snpEffect.Hgvs
 
strandMinus - Variable in class org.snpeff.snpEffect.testCases.unity.TestGenome
 
strandPlus - Variable in class org.snpeff.snpEffect.Hgvs
 
StreamGobbler - Class in org.snpeff.osCmd
Read the contents of a stream in a separate thread This class is used when executing OS commands in order to read STDOUT / STDERR and prevent process blocking It can alert an AlertListener when a given string is in the stream
strict - Variable in class org.snpeff.SnpEff
 
String - Enum constant in enum class org.snpeff.vcf.VcfInfoType
 
string2fasta(String, String) - Static method in class org.snpeff.util.GprSeq
Transform into a FASTA formatted string
sub(double) - Method in class org.snpeff.stats.CounterDouble
 
sub(long) - Method in class org.snpeff.stats.Counter
 
sub(long) - Method in class org.snpeff.stats.CounterDouble
 
SUB_FIELD_SEP - Static variable in class org.snpeff.vcf.VcfEntry
 
subIntervals() - Method in class org.snpeff.interval.IntervalAndSubIntervals
Return a collection of sub intervals
subsample(int, boolean) - Method in class org.snpeff.stats.plot.GooglePlotInt
Re sample data so it has at most 'numberOfPoints'
SubsequenceComparator<T extends BinarySequence> - Class in org.snpeff.binseq.comparator
Compare two subsequences (actually it compares two sequences from different starting points)
SubsequenceComparator() - Constructor for class org.snpeff.binseq.comparator.SubsequenceComparator
 
SuffixIndexerNmer<T extends BinarySequence> - Class in org.snpeff.binseq.indexer
Index all suffixes of all the sequences (it indexes using Nmers).
SuffixIndexerNmer(SubsequenceComparator<T>, int) - Constructor for class org.snpeff.binseq.indexer.SuffixIndexerNmer
 
sum() - Method in class org.snpeff.gsa.ScoreList
Get sum of scores
sum() - Method in class org.snpeff.stats.CountByType
Sum all counts.
SUM - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
 
SUMMARY_CSV_TEMPLATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
SUMMARY_GENES_TEMPLATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
SUMMARY_TEMPLATE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
suppressOutput - Variable in class org.snpeff.SnpEff
 
Svg - Class in org.snpeff.svg
Create an SVG representation of a Marker
Svg() - Constructor for class org.snpeff.svg.Svg
 
Svg(Marker, Svg) - Constructor for class org.snpeff.svg.Svg
 
SvgBnd - Class in org.snpeff.svg
Create an SVG representation of a BND (translocation) variant In a VCF file, there are four possible translocations (BND) entries: REF ALT Meaning type 1: s t[p[ piece extending to the right of p is joined after t type 2: s t]p] reverse comp piece extending left of p is joined after t type 3: s ]p]t piece extending to the left of p is joined before t type 4: s [p[t reverse comp piece extending right of p is joined before t
SvgBnd(VariantBnd, Svg, Svg) - Constructor for class org.snpeff.svg.SvgBnd
 
SvgCds - Class in org.snpeff.svg
Create an SVG representation of a Marker
SvgCds(Cds, Svg) - Constructor for class org.snpeff.svg.SvgCds
 
SvgExon - Class in org.snpeff.svg
Create an SVG representation of a Marker
SvgExon(Exon, Svg) - Constructor for class org.snpeff.svg.SvgExon
 
SvgGene - Class in org.snpeff.svg
Create an SVG representation of a Marker
SvgGene(Gene, Svg) - Constructor for class org.snpeff.svg.SvgGene
 
SvgIntron - Class in org.snpeff.svg
Create an SVG representation of a Marker
SvgIntron(Intron, Svg) - Constructor for class org.snpeff.svg.SvgIntron
 
SvgNextProt - Class in org.snpeff.svg
Create an SVG representation of a NextProt annotation tracks
SvgNextProt(Transcript, Svg, Markers) - Constructor for class org.snpeff.svg.SvgNextProt
 
SvgScale - Class in org.snpeff.svg
Create an SVG representation of a "Scale and Chromsome labels
SvgScale(Marker, Svg) - Constructor for class org.snpeff.svg.SvgScale
 
SvgSpacer - Class in org.snpeff.svg
Leave an empty vertical space
SvgSpacer(Marker, Svg) - Constructor for class org.snpeff.svg.SvgSpacer
 
SvgTranscript - Class in org.snpeff.svg
Create an SVG representation of a transcript
SvgTranscript(Transcript, Svg) - Constructor for class org.snpeff.svg.SvgTranscript
 
SvgTranslocation - Class in org.snpeff.svg
Create an SVG representation of a BND (translocation) variant In a VCF file, there are four possible translocations (BND) entries: REF ALT Meaning type 1: s t[p[ piece extending to the right of p is joined after t type 2: s t]p] reverse comp piece extending left of p is joined after t type 3: s ]p]t piece extending to the left of p is joined before t type 4: s [p[t reverse comp piece extending right of p is joined before t
SvgTranslocation(Transcript, Transcript, VariantBnd, SnpEffectPredictor) - Constructor for class org.snpeff.svg.SvgTranslocation
 
SYNONYMOUS_CODING - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
SYNONYMOUS_START - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
SYNONYMOUS_STOP - Enum constant in enum class org.snpeff.snpEffect.EffectType
 

T

T - Static variable in class org.snpeff.fastq.FastqSplit
 
T2D_GENES - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
 
TableFile - Class in org.snpeff.fileIterator
Load a table from a file.
TableFile(int) - Constructor for class org.snpeff.fileIterator.TableFile
 
TableFile(String) - Constructor for class org.snpeff.fileIterator.TableFile
 
TableFile(String, String) - Constructor for class org.snpeff.fileIterator.TableFile
 
tabs(int) - Static method in class org.snpeff.util.Gpr
 
tail(Object) - Static method in class org.snpeff.util.Gpr
 
TANH - Enum constant in enum class org.snpeff.reactome.Entity.TransferFunction
 
TB - Static variable in class org.snpeff.util.Gpr
 
TEC - Enum constant in enum class org.snpeff.interval.BioType
 
TEMPLATES_DIR - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
 
TERMINATION_CODON - Static variable in class org.snpeff.codons.CodonTable
 
TERMINATION_CODON_1 - Static variable in class org.snpeff.codons.CodonTable
 
terminology - Variable in class org.snpeff.nextProt.CvTerm
 
test(int[], int[], double[]) - Method in class org.snpeff.probablility.CochranArmitageTest
Calculate CochranArmitageTest using the following contingency table B=1 B=2 ...
test_0() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest
 
test_0() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric
 
test_00() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
 
test_00() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader
 
test_00() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Check that the size is correct (at least for SNPs)
test_00_decomposeVariant_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose
Variant before exon
test_00_decomposeVariant_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose
 
test_00_long_file() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test getting random lines from a file
test_00_short_file() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test getting random lines from a file
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBuildPdb
Interaction within protein using PDB entry '1A12'
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
Test Somatic vs Germline
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCanonical
Test canonical transcripts
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCodingTag
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCovid19
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCutsomIntervals
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
Test output order
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationExonFrame
Test database: Build, check and annotate
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationFilterTranscripts
Filter transcripts from a file
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGenomicSequences
Check that we can recover sequences from all exons using GneomicSequence class
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsMnps
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLargeDeletion
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLof
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMarkerSeq
Test markerSeq.getSequence(marker) method Compare to trivial implementation
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMissenseSilentRatio
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMnp
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNmd
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNoChange
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationProtein
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationRefSeq
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationRegulation
Create and load a regulation track
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEff
 
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSpliceRegion
Splice region not found in some cases when there is an insertion
test_01() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscriptError
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesAlign
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBinomial
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable
Degeneracy test References: http://en.wikipedia.org/wiki/Genetic_code#Degeneracy
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDel
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDels
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFasta
Bug: Fasta file iterator should not crash if first line is empty
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Find beginning of a chromosome
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
Combined p-value : MIN
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences
Create many small chromosomes, check that they are saved in only one sequences.bin file Test that we can recover the exact sequences
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvs
Test case: Use 1-letter AA change
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup
Test case: p.Gly4_Gln6dup in the sequence MKMGHQQQCC denotes a duplication of amino acids Glycine-4 (Gly, G) to Glutamine-6 (Gln, Q) (i.e.
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIns
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Read file
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
Test small intervals
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntStats
Calculate statistics, compare results with other programs' results
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIubString
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesJaspar
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesMnps
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesReactome
Reaction with two molecules
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader
Basic parsing
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
Sequence comparison test
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSnps
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite
 
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
Shift by one position
test_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Basic parsing
test_01_ann() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
 
test_01_Annotation_Stop() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesAnn
 
test_01_build() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNextProt
 
test_01_canonical() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
Test output order: Canonical first
test_01_chromoNamesDoNotMatch_Gff() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBuild
 
test_01_coding() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon
 
test_01_ConfigOverride() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationConfig
Check that config file can be overriden by command line options
test_01_del_repeated_effects() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationDelEtc
A deletion having multiple splice_region effects (should show only one)
test_01_dup() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationDup
 
test_01_dup() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsDnaDup
 
test_01_DUP_fusion() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationStructural
Duplication creates a gene fusion
test_01_ENST00000369219() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEnsembl
 
test_01_ENST00000369368() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEnsembl
 
test_01_ENST00000415551() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEnsembl
 
test_01_ENST00000434489() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEnsembl
 
test_01_ERROR_CHROMOSOME_NOT_FOUND() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationErrors
 
test_01_Exon_SNPs() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
Test 'apply' on exons (test sequence changes) Only using SNPs variants
test_01_hgvs_deletions_chr11() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsDel
This frameshift caused an exception while processing HGVS protein notation
test_01_hgvs_frameshift() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsFrameShift
Test HGVS.P in a synonymous frame shift
test_01_hgvs_upstream() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsUpDownStream
Test for HGVS.C notation on upstream variants
test_01_hyper() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric
 
test_01_InsOffByOne() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationInsEtc
Insertion on minus strand
test_01_intron() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron
 
test_01_MixedVep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
Make sure we can read VCF and parse variants without producing any exception
test_01_mRnaSequence() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscript
 
test_01_multi_thread() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEffMultiThread
 
test_01_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_01_short() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
 
test_01_short() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_01_short_getBase() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
 
test_01_short_getBase() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_01_short_getBases() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
 
test_01_short_getBases() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_01_short_replaceBase() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
 
test_01_short_replaceBase() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_01_split_codon_base() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction
Get protein interaction loci when a codon is split by an intron
test_01_vcf_bed_filter() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVcfs
 
test_01_VcfRawAlt() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesAnn
Check that RAW alt fields are kept in 'Allele/Genotype'
test_01_Vep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSequenceOntology
 
test_01_within_protein_interactions() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationProteinInteraction
Annotate within protein interaction
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBuildPdb
Interaction between two proteins PDB entry 4OVU should have an interaction between chains 'A' and 'B' (Min distance :2.45 Angstrom) AA.pos AA chr:pos transcript 22 E 3:178916679 NM_006218.2 533 R 5:67591006 NM_181523.2
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
Test Somatic vs Germline (using TXT file)
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCanonical
Test Somatic vs Germline
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
Test GATK option: At most one effect per VCF entry
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationExonFrame
Build genome (no exceptions should be thrown)
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationFilterTranscripts
Filter transcripts from a file
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGenomicSequences
Check that we can recover sequences from all exons using GenomicSequences class, WITHOUT loading sequence form databases
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
 
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsMnps
Test MNP simplification
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLargeDeletion
 
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLof
We should be able to annotate a BED file
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
 
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNoChange
 
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationRefSeq
Test improved exon frame correction in UCSC references
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEnsembl
 
test_02() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscriptError
 
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesAlign
 
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBinomial
 
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage
 
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable
Setting genome-wide codon tables
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDel
 
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse
 
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Find a line
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
Combined p-value : AVG
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences
Create many small chromosomes and a few large ones.
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector
 
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvs
Test case: Use transcript ID
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
 
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative
 
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup
Reference: http://www.hgvs.org/mutnomen/recs-prot.html#dup duplicating insertions in single amino acid stretches (or short tandem repeats) are described as a duplication, e.g.
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Sort test
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
Test large intervals
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIubString
 
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesJaspar
 
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesReactome
Reaction with a catalyst
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
Sequence ordering test
test_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
No shift
test_02_ann() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
 
test_02_ann() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNextProt
 
test_02_Annotating_LOF_Spaces() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVcfs
Annotating LOF / NMD using a geneName that contains spaces triggers an Exception (it shouldn't happen)
test_02_Annotation_SpliceRegion() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesAnn
 
test_02_chromoNamesDoNotMatch_GffFasta() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBuild
 
test_02_del_repeated_effects_gatk() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationDelEtc
Insertion on minus strand
test_02_eff() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNextProt
 
test_02_ERROR_CHROMOSOME_NOT_FOUND() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationErrors
 
test_02_Exon_INS() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
Test 'apply' on exons (test sequence changes) Only using insertion variants
test_02_hgvs_downstream() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsUpDownStream
Test for HGVS.C notation on downstream variants
test_02_hgvs_frameshift() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsFrameShift
Test HGVS.P in a synonymous frame shift
test_02_hgvs_insertions_chr1() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsIns
Insertion / duplication issues
test_02_hyper() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric
 
test_02_INV_fusion() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationStructural
Duplication creates a gene fusion
test_02_long() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
 
test_02_long() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_02_long_getBase() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
 
test_02_long_getBase() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_02_long_getBases() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
 
test_02_long_getBases() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_02_long_replaceBase() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
 
test_02_long_replaceBase() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_02_mapping_mRna_Cds() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscript
 
test_02_MixedVep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
 
test_02_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_02_protein_protein_interactions() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationProteinInteraction
Annotate protein-protein interactions
test_02_split_codon_base() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction
Get protein interaction loci when a codon is split by an intron
test_02_Start_NonSyn() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnp
Change of start codon to an alternative start codon
test_02_StopGained_HighImpact() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnp
Stop gained should have 'HIGH' impact
test_02_Vep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSequenceOntology
 
test_03() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
 
test_03() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLargeDeletion
 
test_03() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
 
test_03() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEnsembl
 
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesBinomial
 
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage
 
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse
 
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Find a chr:pos
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
Combined p-value : AVG10
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvs
Test case: Use old HGVS.C nomenclature E.g.
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
Test case from http://www.hgvs.org/mutnomen/recs-DNA.html g.5dupT (or g.5dup, not g.5_6insT) denotes a duplication ("insertion") of the T nucleotide at position 5 in the genomic reference sequence changing ACTCTGTGCC to ACTCTTGTGCC
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative
Dup on the reverse strand: More than one base
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Sort (by end) test
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIubString
 
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesReactome
Reaction with positive regulation
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
Sequence indexer test (add sequences)
test_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
Shift by one position
test_03_ann() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
 
test_03_ann() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNextProt
 
test_03_Annotation_NonSyn() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesAnn
 
test_03_baseNumberCds2Codon() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscript
 
test_03_cancer_concurrent_modification() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
Concurrent modification issue on cancer samples (Intron.apply problem)
test_03_DEL_fusion() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationStructural
Deletion creates a gene fusion
test_03_do_not_annotate_non_variants() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVcfs
Non-variant VCF entries should be skipped (i.e.
test_03_eff() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNextProt
 
test_03_EmptyVcf() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
Make sure that empty VCF does not trigger an exception when creating the summary
test_03_Exon_DEL() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
Test 'apply' on exons (test sequence changes) Only using deletions variants
test_03_fisher() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest
 
test_03_hgvs_frameshift() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsFrameShift
Test HGVS.P in a synonymous frame shift
test_03_hgvs_insertions_chr3() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsIns
Insertion / duplication issues
test_03_hgvs_upstream_del() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsUpDownStream
Test that CSV summary does not throw any error
test_03_InsVep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationInsVep
 
test_03_MixedVep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
 
test_03_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_03_Nmers() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNmers
 
test_03_protein_protein_interactions_hgvs() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationProteinInteraction
Annotate protein-structural interaction Make sure that the HGVS notation positions (DNA and Protein) are consistent.
test_03_Start_Loss() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnp
Change of start codon to an alternative start codon
test_03_Vep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSequenceOntology
 
test_04() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
Test Somatic vs Germline: Check HGVS notation "c."
test_04() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
Test that CSV summary does not throw any error
test_04() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
 
test_04() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLargeDeletion
Show transcripts deleted when there is a gene-fusion due to deletion
test_04() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
MNP outside Motif: Should not throw any exception
test_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage
 
test_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse
 
test_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Find a chr:pos
test_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
Complementary CDF for Chi^2 distribution
test_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
Test case from http://www.hgvs.org/mutnomen/recs-DNA.html g.7dupT (or g.7dup, not g.5dupT, not g.7_8insT) denotes a duplication ("insertion") of the T nucleotide at position 7 in the genomic reference sequence changing AGACTTTGTGCC to AGACTTTTGTGCC
test_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative
Dup on the reverse strand: More than one base
test_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Merge intervals
test_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIubString
 
test_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesReactome
Reaction with negative regulation
test_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
Sequence indexer test (overlap sequences)
test_04_Annotation_Intergenic() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesAnn
 
test_04_codonNumber2Pos() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscript
 
test_04_del() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Deletions
test_04_Exon_MNP() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
Test 'apply' on exons (test sequence changes) Only using deletions variants
test_04_fisher() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest
 
test_04_fusion() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationStructural
Deletion creates a gene fusion
test_04_hgvs_frameshift() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsFrameShift
Test HGVS.P in a synonymous frame shift
test_04_hgvs_insertions_chr4() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsIns
Insertion / duplication issues
test_04_hgvs_upstream_negative_strand() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsUpDownStream
Test HGVS.C upstream of a variant affecting a transcript on the negative strand
test_04_InsVep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationInsVep
 
test_04_Intron() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
Shift by one position in an intron
test_04_MixedVep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
 
test_04_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_04_parse() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNextProt
 
test_04_Pe() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_04_Vep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSequenceOntology
 
test_05() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
Cancer mutation is reversion to the REF base
test_05() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
GATK mode should not have SPLICE_REGION (it is currently not supported)
test_05() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
 
test_05() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
Motif has 9 bases but ENSEMBL file marks it as a 10 base interval SNP affect last base (as marked by ENSEMBL), since there is no sequence for that base position, an exception is thrown.
test_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage
 
test_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse
 
test_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Find a chr:pos that does not exists
test_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
Combined p-value : FISHER_CHI_SQUARE
test_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
Test case from http://www.hgvs.org/mutnomen/recs-DNA.html g.7_8dup (or g.7_8dupTG, not g.5_6dup, not g.8_9insTG) denotes a TG duplication in the TG-tandem repeat sequence changing ACTTTGTGCC to ACTTTGTGTGCC
test_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Adding intervals
test_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesReactome
Reaction with requirement
test_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
Sequence indexer test (trivial assembly)
test_05_ann_disulphide_bond() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNextProt
 
test_05_Annotation_EndOfChromosome() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesAnn
 
test_05_choking_on_dot_slash_dot() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Problems parsing
test_05_codonNumber_aaNumber() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscript
 
test_05_fastqReader() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_05_fisher() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest
 
test_05_fusion() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationStructural
Deletion creates a gene fusion
test_05_hgvs_downstream_negative_strand() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsUpDownStream
Test HGVS.C upstream of a variant affecting a transcript on the negative strand
test_05_hgvs_frameshift() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsFrameShift
Test HGVS.P in a synonymous frame shift
test_05_hgvs_insertions_chr19() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsIns
Insertion / duplication issues
test_05_MixedVep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
 
test_05_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_05_quality_short() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_05_savant() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
Test case from Savant's poster http://www.well.ox.ac.uk/savant (Marton Munz, Elise Ruark, Nazneen Rahman, Gerton Lunter)
test_05_savant_opposite() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
 
test_05_Vep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSequenceOntology
 
test_06() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
Cancer mutation is reversion to the REF base
test_06() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
test_06() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
 
test_06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Find a chr:pos that does not exists
test_06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
Combined p-value : Z_SCORES
test_06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
 
test_06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Intersect of 2 intervals We have 2 implementation (brute force and interval trees), so we can compare them.
test_06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA' bug Sequences with nmers '0' were not being indexed
test_06_ann_disulphide_bond() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNextProt
 
test_06_fisher_vs_chi2() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest
Compare Fisher exact test to Chi^2 approximation
test_06_fusion() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationStructural
Annotate intron rank in gene_fusion
test_06_hgvs_frameshift() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsFrameShift
Test HGVS frameshift at CDS end
test_06_hgvs_insertions_chr7() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsIns
Insertion / duplication issues
test_06_hgvs_upstream_negative_strand() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsUpDownStream
Test HGVS upstream of a variant affecting a transcript on the negative strand
test_06_mixed_change() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Problems creating variants
test_06_MixedVep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
 
test_06_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_06_phased() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
Cancer mutation is reversion to the REF base (pahsed VCF genotypes)
test_06_quality_long() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
test_06_savant() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
Same as test Savant's test case, but using variant and GenomicSequences
test_06_Vep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSequenceOntology
 
test_07() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
Cancer mutation is reversion to the REF base
test_07() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
test_07() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNextProt
 
test_07() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Find a chr:pos that does not exists
test_07() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
Combined p-value : FDR
test_07() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
Duplication with variant shifted towards 3-prime
test_07() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
Sequence length = Nmer size (bug) Sequences with same length as nmers were not being indexed properly
test_07_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Minus operation for intervals
test_07_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Minus operation for intervals
test_07_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Minus operation for intervals
test_07_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Minus operation for intervals
test_07_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Minus operation for intervals
test_07_hgvs_downstream_negative_strand() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsUpDownStream
 
test_07_hgvs_insertions1() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsIns
This frameshift caused an exception while processing HGVS protein notation
test_07_long_lines() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Extremely weird long lines in a VCF file (thousands of bases long)
test_07_MixedVep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
 
test_07_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_07_overlap() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_07_phase() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
Cancer mutation is reversion to the REF base
test_07_savant() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
Another test case fmor Savant's poster
test_08() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
CDS test (CDS = CoDing Sequences) Build CDS form exon sequences
test_08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
Test quantile
test_08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
Duplication with variant shifted towards 3-prime
test_08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Test distance (in bases) from a list of markers
test_08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaac"
test_08_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Test distance (in bases) from a list of markers
test_08_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
Test distance (in bases) from a list of markers
test_08_alt_del() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Test for "" in ALT field
test_08_gatk_missing_annotations() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
Fixing bug: GATK does not annotate all VCF entries
test_08_hgvs_downstream_negative_strand() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsUpDownStream
 
test_08_MixedVep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
 
test_08_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_08_overlap() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_08_reallyLongRealign() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
This test should trigger progressive realignment.
test_09() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor for a transcript
test_09() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
Test CDF (cumulative distribution function)
test_09() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
Dup in intron
test_09() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "caaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa"
test_09_chrOrder() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
 
test_09_empty_ALT() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Empty ALT: Not a variant
test_09_MixedVep() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
 
test_09_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_09_overlap() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_09_reallyLongRealign() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
This test should trigger (AND fail) to make a progressive realignment.
test_1() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare
 
test_10() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
 
test_10() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
Dup in exon-intron boundary
test_10() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "caaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaag"
test_10_chrOrder() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
 
test_10_empty_QUAL() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Empty Quality: Not a variant
test_10_MixedVep_HGVS() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
 
test_10_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_10_overlap() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_11() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor: Test UTR distances, Up/Downstream distances
test_11() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Find a chr:pos that does not exists
test_11() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
Dup in intron-exon boundary
test_11_empty() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Empty fields should show '.' when printed
test_11_ExonRank() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
 
test_11_Hg19Hgvs() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
 
test_11_Hg19Hgvs_noShift() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
 
test_11_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_11_overlap() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_12() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor: Test Splice sites
test_12_2() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor: Test Splice sites (make sure they are only 2 bases long)
test_12_BRCA_Splice_15_Hgvs() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
Using non-standard splice size (15 instead of 2) may cause some HGVS annotations issues
test_12_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_12_overlap() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_12_readHeader() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_12_readHeader_NL() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Header should NOT have a trailing '\n'
test_13_chrOri() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_13_large_Del_Hgvs() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsLarge
Using non-standard splice size (15 instead of 2) may cause some HGVS annotations issues
test_13_nextprotFactory() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_13_overlap() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_13_reverseWc() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
 
test_14() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_14_splice_region_Hgvs() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
Using non-standard splice size (15 instead of 2) may cause some HGVS annotations issues
test_14_VcfInfoKey() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_14_VcfInfoValue() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_15() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_15_DnaCoder_copy_1() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_15_Eff_format_version_guess() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_15_hgvs_INS_intergenic() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
Using non-standard splice size (15 instead of 2) may cause some HGVS annotations issues
test_16() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_16_DnaCoder_copy_2() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_16_indels() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_17() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_17_overlap_rand() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_18() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_18_DnaCoder_score_rand() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_18_vcf_tabix() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_19() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor: Test start codon gained
test_19() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
test_19_score_threshold_rand() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
test_20() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor: Test start codon gained (reverse strand)
test_20() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Find a chr:pos that does not exists
test_20_Nmers_read_write() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesNmers
 
test_21() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor for a transcript (Insertions)
test_21() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Find a chr:pos that does not exists
test_21_2() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor for a transcript (Insertions)
test_21_3() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor for a transcript (Insertions)
test_22() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Read file test: Should throw an exception (chromosome not found)
test_22() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Find a chr:pos that does not exists
test_22_huge_headers() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_23() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Dump small portions of a file
test_23_MNP_on_exon_edge() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor for a transcript (Insertions)
test_23_VcfUnsorted() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_24() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
Test : Dump large portions of a file
test_24_delete_exon_utr() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor for a transcript (Insertions)
test_24_VcfEffect_parse_SO() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Parsing effect that created an exception (going from SO -> Classic)
test_25_exon_bases() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
 
test_25_Genomic_VCF() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Parsing Genomic VCFs http://www.broadinstitute.org/gatk/guide/article?id=4017
test_26_chr15_78909452() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test SNP effect predictor for a transcript (Insertions)
test_26_vcfInfoHeaderAdd() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Add a new INFO and the respective header
test_27_vcfInfoHeaderReplace() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Add and replace an INFO header
test_28_Splice_mm37_ENSMUSG00000005763() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Splice site: Bug reported by Wang, Xusheng
test_28_vcfInfoReplace() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Add and replace an INFO header
test_29() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Test old effect separator '+' instead of '&'
test_29_Intergenic_in_Gene() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test effect when hits a gene, but not any transcript within a gene.
test_30_gVCF_NON_REF() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
Non-variant gVCF entries (i.e.
test_30_RareAa() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Rare Amino acid
test_31_CodonTable() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
MT chromo Effectusing an alternative codon table: Codon change : atA / atG Standard codon table : Ile / Met => NON_SYNONYMOUS Mithocondria codon table: Met / Met => SYNONYMOUS
test_31_MISSING_REF() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_32_StartGained() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Start gained
test_32_VcfInfoKeyNames() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_33_StartGained_NOT() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Not start gained
test_33_translocations() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_34_StartGained() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Start gained
test_34_vcfInfoEncoding() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_35_StartGained_NOT() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Not start gained
test_35_translocations_parsing() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_36_cleanupUnderscores() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
test_36_EffectImpact() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Make sure all variant effects have appropriate impacts
test_38_NON_SYNONYMOUS_START() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test
test_apply_05_delete_whole_exon() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
Exon completely removed by a deletion.
test_apply_06_delete_upstream() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
Upstream region is completely removed by a deletion.
test_apply_07_delete_upstream() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
Upstream region is completely removed by a deletion.
test_apply_variant_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant before exon
test_apply_variant_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant before exon
test_apply_variant_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant before exon
test_apply_variant_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp
Variant before exon
test_apply_variant_01_longer() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant before exon
test_apply_variant_01_shorter() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant before exon
test_apply_variant_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant right before exon start
test_apply_variant_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant before exon
test_apply_variant_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant right before exon start
test_apply_variant_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp
Variant ending right before exon start
test_apply_variant_02_longer() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant before exon
test_apply_variant_02_shorter() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant before exon
test_apply_variant_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant overlapping exon start
test_apply_variant_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant overlapping exon start
test_apply_variant_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant overlapping exon start
test_apply_variant_03_longer() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant overlapping exon start
test_apply_variant_03_shorter() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant overlapping exon start
test_apply_variant_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant at exon start
test_apply_variant_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant at exon start
test_apply_variant_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant at exon start
test_apply_variant_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp
Variant at exon start
test_apply_variant_04_longer() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant at exon start
test_apply_variant_04_shorter() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant at exon start
test_apply_variant_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant in exon
test_apply_variant_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant in exon
test_apply_variant_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant in exon
test_apply_variant_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp
Variant in exon
test_apply_variant_05_longer() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant in exon
test_apply_variant_05_shorter() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant in exon
test_apply_variant_06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant right before exon end
test_apply_variant_06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant in exon
test_apply_variant_06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant right before exon end
test_apply_variant_06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp
Variant right before exon end
test_apply_variant_06_longer() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant in exon
test_apply_variant_06_shorter() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant in exon
test_apply_variant_07() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant overlapping exon end
test_apply_variant_07() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant overlapping exon end
test_apply_variant_07() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant overlapping exon end
test_apply_variant_07_longer() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant overlapping exon end
test_apply_variant_07_shorter() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant overlapping exon end
test_apply_variant_08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant right after exon end
test_apply_variant_08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant right after exon end
test_apply_variant_08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant right after exon end
test_apply_variant_08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp
Variant right after exon end
test_apply_variant_08_longer() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant right after exon end
test_apply_variant_08_shorter() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant right after exon end
test_apply_variant_09() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant after exon end
test_apply_variant_09() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant after exon end
test_apply_variant_09() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant after exon end
test_apply_variant_09() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp
Variant after exon end
test_apply_variant_09_longer() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant after exon end
test_apply_variant_09_shorter() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
Variant after exon end
test_apply_variant_10() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant over exon: variant is larger than exon, starts before exon and overlaps the whole exon
test_apply_variant_10() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant over exon: variant is larger than exon, starts before exon and overlaps the whole exon
test_apply_variant_10() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant over exon: variant is larger than exon, starts before exon and overlaps the whole exon
test_apply_variant_11() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant over exon: variant is larger than exon and starts right at exons start and ends after exon end
test_apply_variant_11() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant over exon: variant is larger than exon and starts right at exons start and ends after exon end
test_apply_variant_11() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant over exon: variant is larger than exon and starts right at exons start and ends after exon end
test_apply_variant_12() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant over exon: variant is larger than exon, starts before exon start and end right at exon end
test_apply_variant_12() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant over exon: variant is larger than exon, starts before exon start and end right at exon end
test_apply_variant_12() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant over exon: variant is larger than exon, starts before exon start and end right at exon end
test_apply_variant_13() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Variant over exon: variant is on the same coordiantes as exon
test_apply_variant_13() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
Variant over exon: variant is on the same coordiantes as exon
test_apply_variant_13() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
Variant over exon: variant is on the same coordiantes as exon
test_binSeq_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_07() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_09() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_10() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_11() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_12() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_binSeq_13() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
test_CdsPos() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCds
 
test_cdsStartEnd_1() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCds
Simple CDS start & CSD end case
test_cdsStartEnd_2() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCds
CDS start & CSD end case where transcript is ALL UTR (nothing codes, presumably because of a database annotation error)
test_circular_01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCircular
 
test_circular_02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCircular
 
test_circular_03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCircular
 
test_circular_04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCircular
 
test_collapseZeroGap() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils
Test for collapsing markers with zero gaps
test_EffectType() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse
Make sure all effect_tpyes have appropriate impacts, regions, etc.
test_hgvs_dup() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsHard
Test some 'dup' form chr17
test_hgvs_md_chr17() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsHard
 
test_hgvs_walk_and_roll_1() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsHard
 
test_hgvs_walk_and_roll_2() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsHard
 
test_hgvs_walk_and_roll_3() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsHard
 
test_HgvsP_deleteion_length() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsHard
HGVS (protein) was reporting a wrong deletion length
test_HgvsP_deleteion_length_2() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsHard
Some difficult HGVS test case
test_old_SO() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse
 
test_old_SO_vcf() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse
 
test_start_codon_translate() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationProtein
 
test01() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands
Test that we can load cytobands
test01_0() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction (both genes in positive strand)
test01_0_nonFs() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction (both genes in positive strand)
test01_1() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in opposite directions
test01_2() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in opposite directions
test01_3() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction (both genes in negative strand)
test01_3_noFs() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction (both genes in negative strand)
test01_delGene() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
Deletion Whole gene / whole transcript
test01_delTr() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
Deletion Whole gene / whole transcript
test01_dupGene() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Duplication Whole gene
test01_dupTr() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Duplication whole transcript
test01_invGene() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
Inversion: Whole gene
test01_invTr() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
Inversion: whole transcript
test02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands
Query cytobands
test02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
Deletion One coding exon
test02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Duplication One coding exon
test02() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
Inversion: One coding exon
test02_0() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in opposite directions (both genes in positive strand)
test02_1() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction
test02_1_nonFs() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction
test02_2() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction
test02_2_nonFs() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction
test02_3() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the opposite directions
test03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
Deletion two coding exons (within the same gene)
test03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Duplication two coding exons (within the same gene)
test03() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
Inversion: Two coding exons
test03_0() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in opposite directions
test03_1() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction
test03_1_nonFs() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction
test03_2() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction
test03_2_nonFs() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction
test03_3() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the opposite directions
test04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
Deletion Part of one coding exon
test04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Duplication Part of one coding exon
test04() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
Inversion: Part of one coding exon
test04_0() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction (both genes in positive strand)
test04_0_nonFs() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction (both genes in positive strand)
test04_1() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in opposite directions
test04_2() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in opposite directions
test04_3() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction
test04_3_nonFs() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation in the same direction
test05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
Deletion Part of two coding exons (within the same gene)
test05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Duplication Part of two coding exons (within the same gene)
test05() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
Inversion: Part of two coding exon
test05_1_one_gene() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation affecting a gene and an intergenic region
test05_2_one_gene() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation affecting a gene and an intergenic region
test06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
Deletion one genes and part of another gene
test06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Duplication Two genes
test06() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
Inversion: Two genes
test06_no_gene() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
Translocation not affecting any gene (intergenic regions)
test07() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
Deletion after gene's coding region (LOW impact)
test07() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Duplication After gene's coding region (LOW impact)
test07() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
Inversion: Part of two genes (fusions) cutting on introns
test08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
Deletion Part of two genes cutting on introns
test08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Duplication Part of two genes cutting on introns
test08() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
Inversion: Part of two genes (fusions) cutting exons
test09() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
Deletion Part of two genes cutting exons
test09() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Duplication Part of two genes cutting exons
test09() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
Inversion: Intron
test10() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
Deletion Intron
test10() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Duplication Intron
test10() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
Inversion creating a fusion between two pairs (i.e.
testCase_01_CircularGenome() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCircularGenome
 
testCase_01_Exon_Simple() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
testCase_02_CircularGenome() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCircularGenome
 
testCase_02_CircularGenome_end() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCircularGenome
 
testCase_02_ExonIn() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
testCase_03_CircularGenome() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCircularGenome
 
testCase_03_ExonOut() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
testCase_04_AthalianaTair10_AT5G66790() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
testCase_04_CircularGenome() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCircularGenome
 
testCase_05_CircularGenome_ExonsOrder() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCircularGenome
 
testCase_05_PaeruPA14muccA() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
testCase_06_CircularGenome_ExonsOrder() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCircularGenome
 
testCase_06_Ppersica() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
testCase_07_Rice5() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
testCase_08_Vibrio() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
testCase_09() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
testCase_09_AP() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
testCase_10_MaizeZmB73() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
Exon.frameCorrection: Exon too short (size: 1), cannot correct frame!
testCase_11_mita() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
Test for bug: Infinite loop when looking up "Parent ID" in some GFF3 files
testCase_Exon_Simple() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEmbl
 
testCase_multiple_CDS() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGenBank
 
testCase_tfbs_ablation() - Method in class org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse
Make sure there are no exceptions thrown when parsing TFBS_abalation SO term
testCaseHg37_61_ENST00000250838() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGtf22
 
testCaseHg37_61_ENST00000331397() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGtf22
 
testCaseMm37_61_ENSMUSG00000051951() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGtf22
 
testCaseMm37_61_ENSMUST00000070533() - Method in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGtf22
 
TestCasesAlign - Class in org.snpeff.snpEffect.testCases.unity
test cases for Sequence alignment
TestCasesAlign() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesAlign
 
TestCasesAnn - Class in org.snpeff.snpEffect.testCases.integration
Test case
TestCasesAnn() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesAnn
 
TestCasesAnnParse - Class in org.snpeff.snpEffect.testCases.unity
Test case for parsing ANN fields
TestCasesAnnParse() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse
 
TestCasesApplyDel - Class in org.snpeff.snpEffect.testCases.unity
Test cases: apply a variant (DEL) to a transcript
TestCasesApplyDel() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
 
TestCasesApplyIns - Class in org.snpeff.snpEffect.testCases.unity
Test cases: apply a variant (INS) to a transcript
TestCasesApplyIns() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
 
TestCasesApplyMixed - Class in org.snpeff.snpEffect.testCases.unity
Test cases: apply a variant (MIXED) to a transcript
TestCasesApplyMixed() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
 
TestCasesApplyMnp - Class in org.snpeff.snpEffect.testCases.unity
Test cases: apply a variant (MNP) to a transcript
TestCasesApplyMnp() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
 
TestCasesApplySnp - Class in org.snpeff.snpEffect.testCases.unity
Test cases: apply a variant (SNP) to a transcript
TestCasesApplySnp() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp
 
TestCasesBase - Class in org.snpeff.snpEffect.testCases.unity
Base class for some test cases
TestCasesBase() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
TestCasesBaseApply - Class in org.snpeff.snpEffect.testCases.unity
Test case
TestCasesBaseApply() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesBaseApply
 
TestCasesBinomial - Class in org.snpeff.snpEffect.testCases.unity
Test for Binomial distribution
TestCasesBinomial() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesBinomial
 
TestCasesBuild - Class in org.snpeff.snpEffect.testCases.unity
Test case
TestCasesBuild() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesBuild
 
TestCasesCds - Class in org.snpeff.snpEffect.testCases.unity
Test random SNP changes
TestCasesCds() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesCds
 
TestCasesChiSquare - Class in org.snpeff.snpEffect.testCases.unity
Test for Hypergeometric distribution and Fisher exact test
TestCasesChiSquare() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare
 
TestCasesCircular - Class in org.snpeff.snpEffect.testCases.unity
Test cases for circular genomes
TestCasesCircular() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesCircular
 
TestCasesCochranArmitage - Class in org.snpeff.snpEffect.testCases.unity
Cochran-Armitage test statistic test case
TestCasesCochranArmitage() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage
 
TestCasesCodonTable - Class in org.snpeff.snpEffect.testCases.unity
Codon tables
TestCasesCodonTable() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable
 
TestCasesCytoBands - Class in org.snpeff.snpEffect.testCases.unity
Test case for cytobands
TestCasesCytoBands() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands
 
TestCasesDel - Class in org.snpeff.snpEffect.testCases.unity
Test random DEL changes
TestCasesDel() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesDel
 
TestCasesDels - Class in org.snpeff.snpEffect.testCases.unity
Test random DEL changes
TestCasesDels() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesDels
 
TestCasesDnaNSequence - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesDnaNSequence() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
 
TestCasesDnaOverlap - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesDnaOverlap() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
TestCasesDnaSequence - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesDnaSequence() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
 
TestCasesDnaSequenceByte - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesDnaSequenceByte() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte
 
TestCasesEffectCollapse - Class in org.snpeff.snpEffect.testCases.unity
Test Splice sites variants
TestCasesEffectCollapse() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse
 
TestCasesEffectCollapse2 - Class in org.snpeff.snpEffect.testCases.unity
Test case
TestCasesEffectCollapse2() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2
 
TestCasesFasta - Class in org.snpeff.snpEffect.testCases.unity
Test case for FASTA file parsing
TestCasesFasta() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesFasta
 
TestCasesFileIndexChrPos - Class in org.snpeff.snpEffect.testCases.unity
Test cases for file index (chr:pos index on files)
TestCasesFileIndexChrPos() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
 
TestCasesFisherExactTest - Class in org.snpeff.snpEffect.testCases.unity
Test for Hypergeometric distribution and Fisher exact test
TestCasesFisherExactTest() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest
 
TestCasesGenePvalueList - Class in org.snpeff.snpEffect.testCases.unity
GenePvalueList statistics test case
TestCasesGenePvalueList() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
 
TestCasesGenomicSequences - Class in org.snpeff.snpEffect.testCases.unity
Test case
TestCasesGenomicSequences() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences
 
TestCasesGenotypeVector - Class in org.snpeff.snpEffect.testCases.unity
Test cases for GenotypeVector class
TestCasesGenotypeVector() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector
 
TestCasesHgvs - Class in org.snpeff.snpEffect.testCases.unity
Test case for basic HGV annotations
TestCasesHgvs() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesHgvs
 
TestCasesHgvsBase - Class in org.snpeff.snpEffect.testCases.integration
Test random SNP changes
TestCasesHgvsBase() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
TestCasesHgvsDnaDup - Class in org.snpeff.snpEffect.testCases.unity
Test case
TestCasesHgvsDnaDup() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
 
TestCasesHgvsDnaDupNegative - Class in org.snpeff.snpEffect.testCases.unity
Test cases for HGVS's 'dup' on the negative strand
TestCasesHgvsDnaDupNegative() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative
 
TestCasesHgvsExon - Class in org.snpeff.snpEffect.testCases.unity
Test random SNP changes
TestCasesHgvsExon() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon
 
TestCasesHgvsIntron - Class in org.snpeff.snpEffect.testCases.unity
Test random SNP changes
TestCasesHgvsIntron() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron
 
TestCasesHgvsProtDup - Class in org.snpeff.snpEffect.testCases.unity
Test case
TestCasesHgvsProtDup() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup
 
TestCasesHypergeometric - Class in org.snpeff.snpEffect.testCases.unity
Test for Hypergeometric distribution and Fisher exact test
TestCasesHypergeometric() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric
 
TestCasesIns - Class in org.snpeff.snpEffect.testCases.unity
Test random SNP changes
TestCasesIns() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesIns
 
TestCasesIntegrationAlphaFold - Class in org.snpeff.snpEffect.testCases.integration
Test case
TestCasesIntegrationAlphaFold() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationAlphaFold
 
TestCasesIntegrationApply - Class in org.snpeff.snpEffect.testCases.integration
Test 'apply' method (apply variant to marker)
TestCasesIntegrationApply() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
 
TestCasesIntegrationBase - Class in org.snpeff.snpEffect.testCases.integration
Base class: Provides common methods used for testing
TestCasesIntegrationBase() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
TestCasesIntegrationBuildPdb - Class in org.snpeff.snpEffect.testCases.integration
Test cases for annotation of protein interaction loci
TestCasesIntegrationBuildPdb() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBuildPdb
 
TestCasesIntegrationCancer - Class in org.snpeff.snpEffect.testCases.integration
Test cases for cancer effect (difference betwee somatic an germline tissue)
TestCasesIntegrationCancer() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
 
TestCasesIntegrationCanonical - Class in org.snpeff.snpEffect.testCases.integration
Test cases for canonical transcript selection
TestCasesIntegrationCanonical() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCanonical
 
TestCasesIntegrationCircularGenome - Class in org.snpeff.snpEffect.testCases.integration
Test case
TestCasesIntegrationCircularGenome() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCircularGenome
 
TestCasesIntegrationCodingTag - Class in org.snpeff.snpEffect.testCases.integration
Test case: Make sure VCF entries have some 'coding' (transcript biotype), even when biotype info is not available (e.g.
TestCasesIntegrationCodingTag() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCodingTag
 
TestCasesIntegrationConfig - Class in org.snpeff.snpEffect.testCases.integration
Test case
TestCasesIntegrationConfig() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationConfig
 
TestCasesIntegrationCovid19 - Class in org.snpeff.snpEffect.testCases.integration
Test COVID19 build
TestCasesIntegrationCovid19() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCovid19
 
TestCasesIntegrationCutsomIntervals - Class in org.snpeff.snpEffect.testCases.integration
Test Loss of Function prediction
TestCasesIntegrationCutsomIntervals() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCutsomIntervals
 
TestCasesIntegrationDelEtc - Class in org.snpeff.snpEffect.testCases.integration
Test cases on deletions
TestCasesIntegrationDelEtc() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationDelEtc
 
TestCasesIntegrationDup - Class in org.snpeff.snpEffect.testCases.integration
Test case
TestCasesIntegrationDup() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationDup
 
TestCasesIntegrationEff - Class in org.snpeff.snpEffect.testCases.integration
Test cases for other 'effect' issues
TestCasesIntegrationEff() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
 
TestCasesIntegrationEmbl - Class in org.snpeff.snpEffect.testCases.integration
Test case for EMBL file parsing (database creation)
TestCasesIntegrationEmbl() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEmbl
 
TestCasesIntegrationErrors - Class in org.snpeff.snpEffect.testCases.integration
Test cases for error reporting
TestCasesIntegrationErrors() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationErrors
 
TestCasesIntegrationExonFrame - Class in org.snpeff.snpEffect.testCases.integration
Test case for exon frames
TestCasesIntegrationExonFrame() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationExonFrame
 
TestCasesIntegrationFilterTranscripts - Class in org.snpeff.snpEffect.testCases.integration
Filter transcripts
TestCasesIntegrationFilterTranscripts() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationFilterTranscripts
 
TestCasesIntegrationGenBank - Class in org.snpeff.snpEffect.testCases.integration
Test case for EMBL file parsing (database creation)
TestCasesIntegrationGenBank() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGenBank
 
TestCasesIntegrationGenomicSequences - Class in org.snpeff.snpEffect.testCases.integration
Test case for genomic sequences
TestCasesIntegrationGenomicSequences() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGenomicSequences
 
TestCasesIntegrationGff3 - Class in org.snpeff.snpEffect.testCases.integration
Test case for GFF3 file parsing
TestCasesIntegrationGff3() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
 
TestCasesIntegrationGtf22 - Class in org.snpeff.snpEffect.testCases.integration
Test case for GTF22 file parsing
TestCasesIntegrationGtf22() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGtf22
 
TestCasesIntegrationHgvs - Class in org.snpeff.snpEffect.testCases.integration
Test random SNP changes
TestCasesIntegrationHgvs() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
 
TestCasesIntegrationHgvsDel - Class in org.snpeff.snpEffect.testCases.integration
Test cases for HGVS notation on insertions
TestCasesIntegrationHgvsDel() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsDel
 
TestCasesIntegrationHgvsDnaDup - Class in org.snpeff.snpEffect.testCases.integration
Test case
TestCasesIntegrationHgvsDnaDup() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsDnaDup
 
TestCasesIntegrationHgvsFrameShift - Class in org.snpeff.snpEffect.testCases.integration
Test case
TestCasesIntegrationHgvsFrameShift() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsFrameShift
 
TestCasesIntegrationHgvsHard - Class in org.snpeff.snpEffect.testCases.integration
Test case HGSV: Hard cases
TestCasesIntegrationHgvsHard() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsHard
 
TestCasesIntegrationHgvsIns - Class in org.snpeff.snpEffect.testCases.integration
Test cases for HGVS notation on insertions
TestCasesIntegrationHgvsIns() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsIns
 
TestCasesIntegrationHgvsLarge - Class in org.snpeff.snpEffect.testCases.integration
Test random SNP changes
TestCasesIntegrationHgvsLarge() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsLarge
 
TestCasesIntegrationHgvsMnps - Class in org.snpeff.snpEffect.testCases.integration
Test case HGSV for MNPs
TestCasesIntegrationHgvsMnps() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsMnps
 
TestCasesIntegrationHgvsUpDownStream - Class in org.snpeff.snpEffect.testCases.integration
Test cases for HGVS notation
TestCasesIntegrationHgvsUpDownStream() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsUpDownStream
 
TestCasesIntegrationInsEtc - Class in org.snpeff.snpEffect.testCases.integration
Test random SNP changes
TestCasesIntegrationInsEtc() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationInsEtc
 
TestCasesIntegrationInsVep - Class in org.snpeff.snpEffect.testCases.integration
Test random SNP changes
TestCasesIntegrationInsVep() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationInsVep
 
TestCasesIntegrationLargeDeletion - Class in org.snpeff.snpEffect.testCases.integration
Test case where VCF entries are huge (e.g.
TestCasesIntegrationLargeDeletion() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLargeDeletion
 
TestCasesIntegrationLof - Class in org.snpeff.snpEffect.testCases.integration
Test Loss of Function prediction
TestCasesIntegrationLof() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLof
 
TestCasesIntegrationMarkerSeq - Class in org.snpeff.snpEffect.testCases.integration
Test case
TestCasesIntegrationMarkerSeq() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMarkerSeq
 
TestCasesIntegrationMissenseSilentRatio - Class in org.snpeff.snpEffect.testCases.integration
Calculate missense over silent ratio
TestCasesIntegrationMissenseSilentRatio() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMissenseSilentRatio
 
TestCasesIntegrationMixedVariants - Class in org.snpeff.snpEffect.testCases.integration
Test mixed variants
TestCasesIntegrationMixedVariants() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
 
TestCasesIntegrationMnp - Class in org.snpeff.snpEffect.testCases.integration
Test random SNP changes
TestCasesIntegrationMnp() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMnp
 
TestCasesIntegrationMotif - Class in org.snpeff.snpEffect.testCases.integration
Test Motif databases
TestCasesIntegrationMotif() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
 
TestCasesIntegrationNextProt - Class in org.snpeff.snpEffect.testCases.integration
Test NextProt databases
TestCasesIntegrationNextProt() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNextProt
 
TestCasesIntegrationNmd - Class in org.snpeff.snpEffect.testCases.integration
Test Nonsense mediated decay prediction
TestCasesIntegrationNmd() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNmd
 
TestCasesIntegrationNoChange - Class in org.snpeff.snpEffect.testCases.integration
Test case where VCF entries has no sequence change (either REF=ALT or ALT=".")
TestCasesIntegrationNoChange() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNoChange
 
TestCasesIntegrationProtein - Class in org.snpeff.snpEffect.testCases.integration
Protein translation test case
TestCasesIntegrationProtein() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationProtein
 
TestCasesIntegrationProteinInteraction - Class in org.snpeff.snpEffect.testCases.integration
Test cases for annotation of protein interaction loci
TestCasesIntegrationProteinInteraction() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationProteinInteraction
 
TestCasesIntegrationRefSeq - Class in org.snpeff.snpEffect.testCases.integration
Test case for GTF22 file parsing
TestCasesIntegrationRefSeq() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationRefSeq
 
TestCasesIntegrationRegulation - Class in org.snpeff.snpEffect.testCases.integration
Test case
TestCasesIntegrationRegulation() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationRegulation
 
TestCasesIntegrationSequenceOntology - Class in org.snpeff.snpEffect.testCases.integration
Test case for sequence ontology
TestCasesIntegrationSequenceOntology() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSequenceOntology
 
TestCasesIntegrationSnp - Class in org.snpeff.snpEffect.testCases.integration
Test SNP variants
TestCasesIntegrationSnp() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnp
 
TestCasesIntegrationSnpEff - Class in org.snpeff.snpEffect.testCases.integration
Invoke all integration test cases
TestCasesIntegrationSnpEff() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEff
 
TestCasesIntegrationSnpEffMultiThread - Class in org.snpeff.snpEffect.testCases.integration
Invoke multi thread integration test
TestCasesIntegrationSnpEffMultiThread() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEffMultiThread
 
TestCasesIntegrationSnpEnsembl - Class in org.snpeff.snpEffect.testCases.integration
Test random SNP changes
TestCasesIntegrationSnpEnsembl() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEnsembl
 
TestCasesIntegrationSpliceRegion - Class in org.snpeff.snpEffect.testCases.integration
Test cases for variants
TestCasesIntegrationSpliceRegion() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSpliceRegion
 
TestCasesIntegrationStructural - Class in org.snpeff.snpEffect.testCases.integration
Test SNP variants
TestCasesIntegrationStructural() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationStructural
 
TestCasesIntegrationTranscript - Class in org.snpeff.snpEffect.testCases.integration
Test random SNP changes
TestCasesIntegrationTranscript() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscript
 
TestCasesIntegrationTranscriptError - Class in org.snpeff.snpEffect.testCases.integration
Test case where VCF entries hit a transcript that has errors
TestCasesIntegrationTranscriptError() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscriptError
 
TestCasesIntegrationVariant - Class in org.snpeff.snpEffect.testCases.integration
Test cases for variants
TestCasesIntegrationVariant() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
 
TestCasesIntegrationVcfs - Class in org.snpeff.snpEffect.testCases.integration
VCF annotations test cases
TestCasesIntegrationVcfs() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVcfs
 
TestCasesIntegrationZzz - Class in org.snpeff.snpEffect.testCases.integration
Test case
TestCasesIntegrationZzz() - Constructor for class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationZzz
 
TestCasesIntergenic - Class in org.snpeff.snpEffect.testCases.unity
Test intergenic markers
TestCasesIntergenic() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic
 
TestCasesIntervals - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesIntervals() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
 
TestCasesIntervalTree - Class in org.snpeff.snpEffect.testCases.unity
Test case for interval tree structure
TestCasesIntervalTree() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
TestCasesIntervalTreeArray - Class in org.snpeff.snpEffect.testCases.unity
Test case for interval tree structure
TestCasesIntervalTreeArray() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray
 
TestCasesIntervalTreeOri - Class in org.snpeff.snpEffect.testCases.unity
Test case for interval tree structure
TestCasesIntervalTreeOri() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri
 
TestCasesIntervalVariant - Class in org.snpeff.snpEffect.testCases.unity
Test random Interval Variants (e.g.
TestCasesIntervalVariant() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant
 
TestCasesIntStats - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesIntStats() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesIntStats
 
TestCasesIubString - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesIubString() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesIubString
 
TestCasesJaspar - Class in org.snpeff.snpEffect.testCases.unity
Test case for Jaspar parsing
TestCasesJaspar() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesJaspar
 
TestCasesMarkerUtils - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesMarkerUtils() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils
 
TestCasesMnps - Class in org.snpeff.snpEffect.testCases.unity
Test random SNP changes
TestCasesMnps() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesMnps
 
TestCasesNextProt - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesNextProt() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
TestCasesNmers - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesNmers() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesNmers
 
TestCasesOverlap - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesOverlap() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
 
TestCasesProteinInteraction - Class in org.snpeff.snpEffect.testCases.unity
Test cases for protein interaction
TestCasesProteinInteraction() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction
 
TestCasesReactome - Class in org.snpeff.snpEffect.testCases.unity
Test Reactome circuits
TestCasesReactome() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesReactome
 
TestCasesSeekableReader - Class in org.snpeff.snpEffect.testCases.unity
Seekable file reader test case
TestCasesSeekableReader() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader
 
TestCasesSequenceIndexer - Class in org.snpeff.snpEffect.testCases.unity
 
TestCasesSequenceIndexer() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
 
TestCasesSnps - Class in org.snpeff.snpEffect.testCases.unity
Test random SNP changes
TestCasesSnps() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesSnps
 
TestCasesSpliceRegion - Class in org.snpeff.snpEffect.testCases.unity
Test Splice sites variants
TestCasesSpliceRegion() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion
 
TestCasesSpliceSite - Class in org.snpeff.snpEffect.testCases.unity
Test Splice sites variants
TestCasesSpliceSite() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite
 
TestCasesStructuralDel - Class in org.snpeff.snpEffect.testCases.unity
Test case Gene: geneId1 1:957-1157, strand: +, id:transcript_0, Protein Exons: 1:957-988 'exon_0_0', rank: 1, frame: ., sequence: gttgcttgaatactgtatagccttgccattgt 1:1045-1057 'exon_0_1', rank: 2, frame: ., sequence: tgtgttgctaact 1:1148-1157 'exon_0_2', rank: 3, frame: ., sequence: agacatggac CDS : gttgcttgaatactgtatagccttgccattgttgtgttgctaactagacatggac Protein : VA*ILYSLAIVVLLTRHG?
TestCasesStructuralDel() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
 
TestCasesStructuralDup - Class in org.snpeff.snpEffect.testCases.unity
Test case for structural variants: Duplications
TestCasesStructuralDup() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
 
TestCasesStructuralInv - Class in org.snpeff.snpEffect.testCases.unity
Test cases for structural variants: Inversions
TestCasesStructuralInv() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
 
TestCasesStructuralTranslocations - Class in org.snpeff.snpEffect.testCases.unity
Test case for structural variants: Translocation (fusions)
TestCasesStructuralTranslocations() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
 
TestCasesVariantDecompose - Class in org.snpeff.snpEffect.testCases.unity
Test cases: apply a variant (MIXED) to a transcript
TestCasesVariantDecompose() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose
 
TestCasesVariantRealignment - Class in org.snpeff.snpEffect.testCases.unity
Test cases for variant realignment
TestCasesVariantRealignment() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
 
TestCasesVcf - Class in org.snpeff.snpEffect.testCases.unity
VCF parsing test cases
TestCasesVcf() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesVcf
 
TestCasesZzz - Class in org.snpeff.snpEffect.testCases.unity
Test playground
TestCasesZzz() - Constructor for class org.snpeff.snpEffect.testCases.unity.TestCasesZzz
 
TestGenome - Class in org.snpeff.snpEffect.testCases.unity
Creates a simple "genome" for testing:
TestGenome(boolean) - Constructor for class org.snpeff.snpEffect.testCases.unity.TestGenome
 
testsDir - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
TestSuiteIntegration - Class in org.snpeff.snpEffect.testCases
Invoke all integration test cases
TestSuiteIntegration() - Constructor for class org.snpeff.snpEffect.testCases.TestSuiteIntegration
 
TestSuiteUnity - Class in org.snpeff.snpEffect.testCases
Invoke all Unit test cases for SnpEff
TestSuiteUnity() - Constructor for class org.snpeff.snpEffect.testCases.TestSuiteUnity
 
testType - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
testType - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
text(double, double, String) - Method in class org.snpeff.svg.Svg
 
TEXT_SIZE - Static variable in class org.snpeff.svg.Svg
 
TEXT_STYLE - Static variable in class org.snpeff.svg.Svg
 
TfamEntry - Class in org.snpeff.ped
An entry in a TFAM table.
TfamEntry(String) - Constructor for class org.snpeff.ped.TfamEntry
 
TfamEntry(String, String, String, String, Sex, double) - Constructor for class org.snpeff.ped.TfamEntry
 
THRESHOLD_BRANCH_U12_PERCENTILE - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
THRESHOLD_COUNT - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
THRESHOLD_COUNT - Static variable in class org.snpeff.spliceSites.SpliceTypes
 
THRESHOLD_ENTROPY - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
THRESHOLD_ENTROPY - Static variable in class org.snpeff.spliceSites.SpliceTypes
 
THRESHOLD_P - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
THRESHOLD_P - Static variable in class org.snpeff.spliceSites.SpliceTypes
 
THRESHOLD_U12_OBSERVED_EXPECTED - Static variable in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
Timer - Class in org.snpeff.util
 
Timer() - Constructor for class org.snpeff.util.Timer
 
title() - Method in class org.snpeff.geneSets.GeneStats
 
TO_BASE - Static variable in class org.snpeff.binseq.coder.DnaCoder
 
toArray() - Method in class org.snpeff.interval.Markers
 
toArray(T[]) - Method in class org.snpeff.interval.Markers
 
toBase(int) - Method in class org.snpeff.binseq.coder.Coder
Decode a base using a binary representation
toBase(int) - Method in class org.snpeff.binseq.coder.DnaCoder
Decode a base using 2 bits
toBase(int) - Method in class org.snpeff.binseq.coder.DnaQualityCoder
Decode a base using 2 bits
toBase(long, int) - Method in class org.snpeff.binseq.coder.Coder
Decode a base from a given position in a word
toBase(long, int) - Method in class org.snpeff.binseq.coder.DnaCoder
 
toByteSize(long) - Static method in class org.snpeff.util.Gpr
 
toFile(String, Object) - Static method in class org.snpeff.util.Gpr
Write an object to a file
toFile(String, Object, boolean) - Static method in class org.snpeff.util.Gpr
Write an object to a file
toFileGz(String, Object) - Static method in class org.snpeff.util.Gpr
Write an object to a file (as a string) Note: The file is compressed using GZIP
toFileSerialize(String, Object) - Static method in class org.snpeff.util.Gpr
Write an object to a file by invoking Serialization methods
toFileSerializeGz(String, Object) - Static method in class org.snpeff.util.Gpr
Write an object to a file by invoking Serialization methods Note: The file is compressed using GZIP
toggle() - Method in class org.snpeff.stats.BooleanMutable
 
toQuality(int) - Method in class org.snpeff.binseq.coder.Coder
Decode a quality
toQuality(int) - Method in class org.snpeff.binseq.coder.DnaQualityCoder
 
toR(double, int, int) - Method in class org.snpeff.probablility.Binomial
Convert values to 'R' command
toR(int, int, int, int) - Method in class org.snpeff.probablility.Hypergeometric
Convert values to 'R' command
toR(int, int, int, int, boolean) - Method in class org.snpeff.probablility.FisherExactTest
Convert values to Fisher's 'R' command
toSequenceOntology(EffFormatVersion, Variant) - Method in enum class org.snpeff.snpEffect.EffectType
 
toStr() - Method in class org.snpeff.interval.Interval
To string as a simple "chr:start-end" format
toStr() - Method in class org.snpeff.snpEffect.VariantEffect
 
toStr() - Method in class org.snpeff.vcf.VcfEntry
To string as a simple "CHR:START_REF/ALTs" format
toString() - Method in class org.snpeff.align.NeedlemanWunsch
 
toString() - Method in class org.snpeff.align.NeedlemanWunschOverlap
 
toString() - Method in class org.snpeff.align.VariantRealign
 
toString() - Method in class org.snpeff.binseq.DnaAndQualitySequence
 
toString() - Method in class org.snpeff.binseq.DnaNSequence
 
toString() - Method in class org.snpeff.binseq.DnaSequence
 
toString() - Method in class org.snpeff.binseq.DnaSequenceByte
 
toString() - Method in class org.snpeff.binseq.DnaSequenceId
 
toString() - Method in class org.snpeff.binseq.DnaSequencePe
 
toString() - Method in class org.snpeff.binseq.GenomicSequences
 
toString() - Method in class org.snpeff.binseq.indexer.OverlapRessult
 
toString() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
 
toString() - Method in class org.snpeff.codons.CodonTable
 
toString() - Method in class org.snpeff.codons.FindRareAaIntervals
 
toString() - Method in class org.snpeff.collections.HashLongLongArray
 
toString() - Method in class org.snpeff.coverage.CountFragments
 
toString() - Method in class org.snpeff.coverage.CountReadsOnMarkers
Print table to STDOUT
toString() - Method in class org.snpeff.coverage.Coverage
 
toString() - Method in class org.snpeff.coverage.CoverageChr
 
toString() - Method in class org.snpeff.fileIterator.BlastResultEntry
 
toString() - Method in class org.snpeff.fileIterator.FileIterator
 
toString() - Method in class org.snpeff.fileIterator.GuessTableTypes
 
toString() - Method in class org.snpeff.fileIterator.MatrixEntry
 
toString() - Method in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
toString() - Method in class org.snpeff.fileIterator.SeekableBufferedReader
 
toString() - Method in class org.snpeff.genBank.Feature
 
toString() - Method in class org.snpeff.genBank.FeatureCoordinates
 
toString() - Method in class org.snpeff.genBank.Features
 
toString() - Method in class org.snpeff.geneOntology.GoTerm
 
toString() - Method in class org.snpeff.geneOntology.GoTerms
 
toString() - Method in class org.snpeff.geneSets.GeneSet
 
toString() - Method in class org.snpeff.geneSets.GeneSets
 
toString() - Method in class org.snpeff.geneSets.GeneStats
 
toString() - Method in class org.snpeff.geneSets.Result
 
toString() - Method in class org.snpeff.gsa.ChrPosScoreList
 
toString() - Method in class org.snpeff.gsa.ScoreList
 
toString() - Method in class org.snpeff.gtex.Gtex
 
toString() - Method in class org.snpeff.gtex.GtexExperiment
 
toString() - Method in class org.snpeff.interval.Cds
 
toString() - Method in class org.snpeff.interval.Chromosome
 
toString() - Method in class org.snpeff.interval.CircularCorrection
 
toString() - Method in class org.snpeff.interval.codonChange.CodonChange
 
toString() - Method in class org.snpeff.interval.Custom
 
toString() - Method in class org.snpeff.interval.CytoBands
 
toString() - Method in class org.snpeff.interval.Exon
 
toString() - Method in class org.snpeff.interval.Gene
 
toString() - Method in class org.snpeff.interval.Genes
 
toString() - Method in class org.snpeff.interval.Genome
Show number of genes, transcripts & exons
toString() - Method in class org.snpeff.interval.GffMarker
 
toString() - Method in class org.snpeff.interval.Interval
 
toString() - Method in class org.snpeff.interval.IntervalSetIterator
 
toString() - Method in class org.snpeff.interval.Marker
 
toString() - Method in class org.snpeff.interval.Markers
 
toString() - Method in class org.snpeff.interval.MarkerSeq
 
toString() - Method in class org.snpeff.interval.Regulation
 
toString() - Method in class org.snpeff.interval.Transcript
 
toString() - Method in class org.snpeff.interval.tree.IntervalForest
 
toString() - Method in class org.snpeff.interval.tree.IntervalNode
 
toString() - Method in class org.snpeff.interval.tree.IntervalNodeOri
 
toString() - Method in class org.snpeff.interval.tree.IntervalTree
 
toString() - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
toString() - Method in class org.snpeff.interval.tree.IntervalTreeOri
 
toString() - Method in class org.snpeff.interval.Variant
 
toString() - Method in class org.snpeff.interval.VariantBnd
 
toString() - Method in class org.snpeff.interval.VariantNonRef
 
toString() - Method in class org.snpeff.motif.Pwm
 
toString() - Method in class org.snpeff.motif.PwmAndSeqs
 
toString() - Method in class org.snpeff.nextProt.CvTerm
 
toString() - Method in class org.snpeff.nextProt.Location
 
toString() - Method in class org.snpeff.nextProt.LocationTargetIsoform
 
toString() - Method in class org.snpeff.nextProt.LocationTargetIsoformInteraction
 
toString() - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
toString() - Method in class org.snpeff.nextProt.NextProtXmlEntry
 
toString() - Method in class org.snpeff.nextProt.NextProtXmlIsoform
 
toString() - Method in class org.snpeff.nmer.Nmer
 
toString() - Method in class org.snpeff.nmer.NmerCount
 
toString() - Method in class org.snpeff.osCmd.ExecuteOsCommand
 
toString() - Method in class org.snpeff.osCmd.OsCmdQueue
 
toString() - Method in class org.snpeff.osCmd.OsCmdRunner
 
toString() - Method in class org.snpeff.outputFormatter.BedAnnotationOutputFormatter
Show all effects
toString() - Method in class org.snpeff.outputFormatter.BedOutputFormatter
Show all effects
toString() - Method in class org.snpeff.outputFormatter.OutputFormatter
 
toString() - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
 
toString() - Method in class org.snpeff.pdb.DistanceResult
 
toString() - Method in class org.snpeff.pdb.IdMapper
 
toString() - Method in class org.snpeff.pdb.IdMapperEntry
 
toString() - Method in class org.snpeff.ped.PedEntry
 
toString() - Method in class org.snpeff.ped.PedGenotype
 
toString() - Method in class org.snpeff.ped.PedPedigree
 
toString() - Method in class org.snpeff.ped.TfamEntry
 
toString() - Method in class org.snpeff.probablility.bootstrap.ReSampleInt
 
toString() - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
toString() - Method in class org.snpeff.reactome.Entity
 
toString() - Method in class org.snpeff.reactome.events.Pathway
 
toString() - Method in class org.snpeff.reactome.events.Reaction
 
toString() - Method in class org.snpeff.reactome.Monitor
 
toString() - Method in class org.snpeff.reactome.Reactome
 
toString() - Method in class org.snpeff.sam.SamEntry
 
toString() - Method in class org.snpeff.sam.SamHeaderRecordSq
 
toString() - Method in class org.snpeff.snpEffect.Config
 
toString() - Method in class org.snpeff.snpEffect.HgvsDna
 
toString() - Method in class org.snpeff.snpEffect.HgvsProtein
 
toString() - Method in class org.snpeff.snpEffect.LossOfFunction
 
toString() - Method in class org.snpeff.snpEffect.SnpEffectPredictor
 
toString() - Method in class org.snpeff.snpEffect.testCases.integration.CompareToVep
 
toString() - Method in class org.snpeff.snpEffect.VariantEffect
 
toString() - Method in class org.snpeff.snpEffect.VariantEffectFusion
 
toString() - Method in class org.snpeff.snpEffect.VariantEffects
 
toString() - Method in class org.snpeff.snpEffect.VariantEffectStructural
 
toString() - Method in class org.snpeff.spliceSites.AcgtTree
 
toString() - Method in class org.snpeff.stats.AlleleCountStats
Show results to stdout
toString() - Method in class org.snpeff.stats.Average
 
toString() - Method in class org.snpeff.stats.AverageInt
 
toString() - Method in class org.snpeff.stats.ChrPosStats
 
toString() - Method in class org.snpeff.stats.CountByKey
 
toString() - Method in class org.snpeff.stats.CountByType
 
toString() - Method in class org.snpeff.stats.Counter
 
toString() - Method in class org.snpeff.stats.CounterDouble
 
toString() - Method in class org.snpeff.stats.FloatStats
 
toString() - Method in class org.snpeff.stats.GenotypeStats
Show results to stdout
toString() - Method in class org.snpeff.stats.HomHetStats
Show results to stdout
toString() - Method in class org.snpeff.stats.IntStats
 
toString() - Method in class org.snpeff.stats.ReadsOnMarkersModel
 
toString() - Method in class org.snpeff.stats.TsTvStats
Show results to stdout
toString() - Method in class org.snpeff.stats.VariantTypeStats
Show results to stdout
toString() - Method in class org.snpeff.svg.Svg
 
toString() - Method in class org.snpeff.svg.SvgBnd
 
toString() - Method in class org.snpeff.svg.SvgCds
 
toString() - Method in class org.snpeff.svg.SvgExon
 
toString() - Method in class org.snpeff.svg.SvgGene
 
toString() - Method in class org.snpeff.svg.SvgIntron
 
toString() - Method in class org.snpeff.svg.SvgNextProt
 
toString() - Method in class org.snpeff.svg.SvgScale
 
toString() - Method in class org.snpeff.svg.SvgSpacer
 
toString() - Method in class org.snpeff.svg.SvgTranscript
 
toString() - Method in class org.snpeff.svg.SvgTranslocation
Create transcript and variant Svgs
toString() - Method in class org.snpeff.util.CombinatorialIterator
 
toString() - Method in class org.snpeff.util.Diff
 
toString() - Method in class org.snpeff.util.KeyValue
 
toString() - Method in class org.snpeff.util.Timer
 
toString() - Method in class org.snpeff.util.Tuple
 
toString() - Method in class org.snpeff.vcf.FileIndexChrPos.FileRegion
 
toString() - Method in class org.snpeff.vcf.FileIndexChrPos.LineAndPos
 
toString() - Method in class org.snpeff.vcf.FileIndexChrPos
 
toString() - Method in class org.snpeff.vcf.LineChrPos
 
toString() - Method in class org.snpeff.vcf.PedigreeEntry
 
toString() - Method in class org.snpeff.vcf.VariantVcfEntry
 
toString() - Method in class org.snpeff.vcf.VcfConsequence
 
toString() - Method in class org.snpeff.vcf.VcfConsequenceHeader
 
toString() - Method in class org.snpeff.vcf.VcfEffect
 
toString() - Method in class org.snpeff.vcf.VcfEntry
 
toString() - Method in class org.snpeff.vcf.VcfGenotype
 
toString() - Method in class org.snpeff.vcf.VcfHeader
Get header information
toString() - Method in class org.snpeff.vcf.VcfHeaderEntry
 
toString() - Method in class org.snpeff.vcf.VcfHeaderFormat
 
toString() - Method in class org.snpeff.vcf.VcfHeaderInfo
 
toString() - Method in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
 
toString() - Method in class org.snpeff.vcf.VcfLof
 
toString(boolean) - Method in class org.snpeff.interval.Gene
 
toString(boolean) - Method in class org.snpeff.interval.Transcript
 
toString(boolean) - Method in class org.snpeff.ped.PedGenotype
 
toString(boolean) - Method in class org.snpeff.stats.CountByType
 
toString(boolean) - Method in class org.snpeff.stats.FloatStats
 
toString(boolean[]) - Static method in class org.snpeff.util.Gpr
 
toString(boolean, boolean) - Method in class org.snpeff.snpEffect.VariantEffect
 
toString(double) - Static method in class org.snpeff.util.Gpr
 
toString(double[]) - Static method in class org.snpeff.util.Gpr
 
toString(double[][]) - Static method in class org.snpeff.util.Gpr
 
toString(int) - Method in class org.snpeff.fileIterator.TableFile
Return line number 'index' as a string
toString(int) - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
toString(int[]) - Static method in class org.snpeff.util.Gpr
 
toString(int, HashSet<Entity>) - Method in class org.snpeff.reactome.Entity
 
toString(int, HashSet<Entity>) - Method in class org.snpeff.reactome.events.Complex
 
toString(int, HashSet<Entity>) - Method in class org.snpeff.reactome.events.Pathway
 
toString(int, HashSet<Entity>) - Method in class org.snpeff.reactome.events.Reaction
 
toString(long, boolean) - Static method in class org.snpeff.util.Timer
 
toString(String) - Method in class org.snpeff.nextProt.NextProtXmlAnnotation
 
toString(String) - Method in class org.snpeff.stats.CountByType
 
toString(StringBuilder) - Method in class org.snpeff.interval.Genome
Show number of genes, transcripts & exons Arr all errors to buffer
toString(String, double, double, int) - Method in class org.snpeff.spliceSites.AcgtTree
 
toStringAll() - Method in class org.snpeff.geneOntology.GoTerm
 
toStringAll() - Method in class org.snpeff.geneSets.GeneSet
 
toStringAll() - Method in class org.snpeff.gtex.GtexExperiment
 
toStringAll() - Method in class org.snpeff.interval.tree.IntervalTreeArray
 
toStringAll() - Method in class org.snpeff.nmer.NmerCount
 
toStringAll(boolean) - Method in class org.snpeff.geneOntology.GoTerm
 
toStringAll(int) - Method in class org.snpeff.nmer.NmerCount
 
toStringAsciiArt(boolean) - Method in class org.snpeff.interval.Transcript
Show a transcript as an ASCII Art
toStringAsciiArt(int) - Method in class org.snpeff.interval.Interval
Show it as an ASCII art
toStringAsciiArt(int) - Method in class org.snpeff.interval.Markers
Show all intervals as an ASCII art
toStringCache() - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Some cache statistics
toStringCounts() - Method in class org.snpeff.stats.IntStats
Show a histogram as a list of numbers
toStringDetails() - Method in class org.snpeff.reactome.Reactome
Show details
toStringEnsembl() - Method in class org.snpeff.interval.Variant
Show variant in ENSEMBL's VEP format
toStringHead(double[]) - Static method in class org.snpeff.util.Gpr
 
toStringHeader() - Method in class org.snpeff.outputFormatter.BedAnnotationOutputFormatter
Show header
toStringHeader() - Method in class org.snpeff.outputFormatter.BedOutputFormatter
Show header
toStringHeader() - Method in class org.snpeff.outputFormatter.OutputFormatter
Show header
toStringHeader() - Method in class org.snpeff.outputFormatter.VcfOutputFormatter
Show header
toStringHex() - Method in class org.snpeff.binseq.DnaSequenceByte
 
toStringHisto() - Method in class org.snpeff.stats.IntStats
Show a histogram as a list of numbers
toStringHistoPlot(String, String, String) - Method in class org.snpeff.stats.ChrPosStats
Create a histogram plot using Google charts
toStringHtml(int, int, EffectType) - Method in class org.snpeff.motif.MotifLogo
Return an HTML string that represents the motif.
toStringHtmlBody() - Method in class org.snpeff.stats.plot.GoogleGeneRegionChart
 
toStringHtmlBody() - Method in class org.snpeff.stats.plot.GoogleLineChart
 
toStringHtmlHeader() - Method in class org.snpeff.stats.plot.GoogleBarChart
 
toStringHtmlHeader() - Method in class org.snpeff.stats.plot.GoogleGeneRegionChart
 
toStringHtmlHeader() - Method in class org.snpeff.stats.plot.GoogleLineChart
 
toStringLine() - Method in class org.snpeff.stats.CountByType
 
toStringNoGt() - Method in class org.snpeff.vcf.VcfEntry
Show only first eight fields (no genotype entries)
toStringOld() - Method in class org.snpeff.interval.Variant
Old format, used for some test cases
toStringPlot(String, String, boolean) - Method in class org.snpeff.stats.IntStats
Create a histogram plot using Google charts
toStringPos() - Method in class org.snpeff.pdb.DistanceResult
Show genomic positions only
toStringSequences() - Method in class org.snpeff.binseq.indexer.SuffixIndexerNmer
 
toStringSimple() - Method in class org.snpeff.reactome.Entity
 
toStringSimple(boolean) - Method in class org.snpeff.snpEffect.VariantEffect
Get the simplest string describing the effect (this is mostly used for testcases)
toStringSort() - Method in class org.snpeff.stats.CountByType
 
toStringTab() - Method in class org.snpeff.stats.IntStats
 
toStringTabTitle() - Static method in class org.snpeff.stats.IntStats
 
toStringTop(int) - Method in class org.snpeff.stats.CountByType
 
toStringTxt() - Method in class org.snpeff.interval.Markers
 
toStringValues() - Method in class org.snpeff.stats.IntStats
Histogram values
toStringVcfLof() - Method in class org.snpeff.snpEffect.LossOfFunction
Get LOF value for VCF info field
toStringVcfNmd() - Method in class org.snpeff.snpEffect.LossOfFunction
Get NMD value for VCF info field
ToStringVersion - Static variable in class org.snpeff.interval.Exon
 
toStrPos() - Method in class org.snpeff.interval.Interval
To string as a simple "chr:start-end" format
total() - Method in class org.snpeff.nmer.NmerCount
Total number of nmers
TOTAL_TYPE - Static variable in class org.snpeff.stats.CountByType
 
toURLString() - Method in class org.snpeff.stats.plot.GoogleChartVenn
Create a histogram plot using Google charts
toURLString() - Method in class org.snpeff.stats.plot.GoogleGenePercentBar
Create a histogram plot using Google charts
toURLString() - Method in class org.snpeff.stats.plot.GoogleHistogram
Create a histogram plot using Google charts
toURLString() - Method in class org.snpeff.stats.plot.GooglePlot
Create a histogram plot using Google charts
toURLString() - Method in class org.snpeff.stats.plot.GooglePlotInt
Create a histogram plot using Google charts
tr - Variable in class org.snpeff.snpEffect.Hgvs
 
tr - Variable in class org.snpeff.snpEffect.testCases.unity.TestGenome
 
TR_C_gene - Enum constant in enum class org.snpeff.interval.BioType
 
TR_D_gene - Enum constant in enum class org.snpeff.interval.BioType
 
TR_J_gene - Enum constant in enum class org.snpeff.interval.BioType
 
TR_J_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
TR_V_gene - Enum constant in enum class org.snpeff.interval.BioType
 
TR_V_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
trAaLen - Variable in class org.snpeff.pdb.IdMapperEntry
 
transcribed_processed_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
transcribed_unitary_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
transcribed_unprocessed_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
transcript - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
transcript - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
Transcript - Class in org.snpeff.interval
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
Transcript() - Constructor for class org.snpeff.interval.Transcript
 
Transcript(Gene, int, int, boolean, String) - Constructor for class org.snpeff.interval.Transcript
 
TRANSCRIPT - Enum constant in enum class org.snpeff.interval.GffType
 
TRANSCRIPT - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
TRANSCRIPT_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
TRANSCRIPT_DUPLICATION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
TRANSCRIPT_ID_SEPARATORS - Static variable in class org.snpeff.fileIterator.FastaFileIterator
 
TRANSCRIPT_ID_SEPARATORS_REGEX - Static variable in class org.snpeff.fileIterator.FastaFileIterator
 
TRANSCRIPT_INVERSION - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
transcriptId - Variable in class org.snpeff.fileIterator.microCosm.MicroCosmEntry
 
transcriptIdNoVersion(String) - Static method in class org.snpeff.pdb.IdMapper
Remove version form transcript ID
transcriptIds(List<IdMapperEntry>) - Static method in class org.snpeff.pdb.IdMapper
 
TranscriptSet - Class in org.snpeff.spliceSites
A set of transcripts
TranscriptSet(Genome) - Constructor for class org.snpeff.spliceSites.TranscriptSet
 
TranscriptSupportLevel - Enum Class in org.snpeff.interval
Transcript level support Reference: http://useast.ensembl.org/Help/Glossary?id=492;redirect=no
TRANSFER_FUNCTION - Static variable in class org.snpeff.reactome.Entity
 
transferFunction(double) - Method in class org.snpeff.reactome.Entity
Transfer function
transferFunction(double, double, double, double, double) - Method in class org.snpeff.reactome.events.Reaction
Transfer function
translated_unprocessed_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
translocation() - Method in class org.snpeff.snpEffect.HgvsProtein
Translocation nomenclature.
TranslocationReport - Class in org.snpeff.stats
Pojo for translocation reports
TranslocationReport(VariantBnd, VcfEffect, Transcript, Transcript) - Constructor for class org.snpeff.stats.TranslocationReport
 
treatAllAsProteinCoding - Variable in class org.snpeff.SnpEff
 
trId - Variable in class org.snpeff.pdb.IdMapperEntry
 
trId1 - Variable in class org.snpeff.pdb.DistanceResult
 
trId2 - Variable in class org.snpeff.pdb.DistanceResult
 
trim(Fastq) - Method in class org.snpeff.fastq.FastqTrimmer
Create a new fastq sequence by trimming the given sequence
trimTrailingZeros() - Method in class org.snpeff.collections.OpenBitSet
Lowers numWords, the number of words in use, by checking for trailing zero words.
TRNA - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
tsl(TranscriptSupportLevel) - Static method in enum class org.snpeff.interval.TranscriptSupportLevel
Return TSL level (-1 if not available / invalid)
TSL_1 - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
 
TSL_2 - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
 
TSL_3 - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
 
TSL_4 - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
 
TSL_5 - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
 
TSL_NA - Enum constant in enum class org.snpeff.interval.TranscriptSupportLevel
The transcript was not analyzed for one of the following reasons: pseudo-gene annotation, including transcribed pseudo-genes human leukocyte antigen (HLA) transcript immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version)
TSL_NULL_VALUE - Static variable in enum class org.snpeff.interval.TranscriptSupportLevel
 
TsTvStats - Class in org.snpeff.stats
Calculate Ts/Tv rations per sample (transitions vs transversions)
TsTvStats() - Constructor for class org.snpeff.stats.TsTvStats
 
Tuple<A,B> - Class in org.snpeff.util
Tuple: A pair of objects
Tuple(A, B) - Constructor for class org.snpeff.util.Tuple
 
TXT - Enum constant in enum class org.snpeff.snpEffect.commandLine.SnpEffCmdDump.DumpFormat
 
TxtSerializable - Interface in org.snpeff.serializer
 
type - Variable in class org.snpeff.interval.Marker
 
type - Variable in class org.snpeff.nextProt.Location
 
typeOfReference() - Method in class org.snpeff.snpEffect.HgvsDna
Prefix for coding or non-coding sequences
typeOfReference() - Method in class org.snpeff.snpEffect.HgvsProtein
Return "p." string with/without transcript ID, according to user command line options.
types - Variable in class org.snpeff.stats.plot.GoogleGeneRegionChart
 

U

UCSC - Enum constant in enum class org.snpeff.interval.FrameType
 
uncompressGenotypes() - Method in class org.snpeff.vcf.VcfEntry
Uncompress VCF entry having genotypes in "HO,HE,NA" fields
union() - Method in class org.snpeff.interval.Markers
Perform the union of all overlapping intervals
union(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
this = this OR other
union(GoTerm) - Method in class org.snpeff.geneOntology.GoTerm
Union this term with 'goTerm' (union for 'symbolIdSet' and 'interestingSymbolIdSet').
union(GeneSet) - Method in class org.snpeff.geneSets.GeneSet
Union this term with 'geneSet' (union for 'geneSet' and 'interestingGeneSet').
union(Marker) - Method in class org.snpeff.interval.Marker
Union of two markers
union(Marker) - Method in class org.snpeff.interval.MarkerSeq
Union of two markers
unionCount(OpenBitSet, OpenBitSet) - Static method in class org.snpeff.collections.OpenBitSet
Returns the popcount or cardinality of the union of the two sets.
UNIPROT_DATABASE - Static variable in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
 
unique() - Method in class org.snpeff.interval.Markers
Remove duplicated markers
unitary_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
Unknown - Enum constant in enum class org.snpeff.ped.Sex
 
UNKNOWN - Enum constant in enum class org.snpeff.interval.FrameType
 
UNKNOWN - Enum constant in enum class org.snpeff.interval.Gene.GeneType
 
UNKNOWN - Enum constant in enum class org.snpeff.interval.GffType
 
UNKNOWN - Enum constant in enum class org.snpeff.vcf.VcfInfoType
 
UNLIMITED - Enum constant in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
 
unprocessed_pseudogene - Enum constant in enum class org.snpeff.interval.BioType
 
unzip(String, String, String) - Method in class org.snpeff.util.Download
UnZIP all files
updateCounts(String) - Method in class org.snpeff.motif.Pwm
 
updateCounts(String, int) - Method in class org.snpeff.motif.Pwm
Update counts matrix.
updateCounts(String, int, long) - Method in class org.snpeff.motif.PwmAndSeqs
Update counts matrix.
upDownStreamLength - Variable in class org.snpeff.SnpEff
 
Upstream - Class in org.snpeff.interval
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
Upstream() - Constructor for class org.snpeff.interval.Upstream
 
Upstream(Transcript, int, int, boolean, String) - Constructor for class org.snpeff.interval.Upstream
 
UPSTREAM - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
urlBaseName(String) - Static method in class org.snpeff.util.Download
File name from URL (i.e.
usage(String) - Method in class org.snpeff.fastq.FastqSplit
Usage message
usage(String) - Method in class org.snpeff.SnpEff
Show 'usage' message and exit with an error code '-1'
usage(String) - Method in interface org.snpeff.snpEffect.commandLine.CommandLine
Show 'usage' message and exit with an error code '-1'
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
Show usage and exit
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
Show 'usage;' message and exit with an error code '-1'
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdBuildNextProt
 
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCds
Show usage and exit
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
Show usage and exit
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdCount
 
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
 
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDownload
Show 'usage;' message and exit with an error code '-1'
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdDump
Show 'usage;' message and exit with an error code '-1'
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdEff
Show 'usage;' message and exit with an error code '-1'
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
 
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
Show usage and exit
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdLen
Show usage and exit
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
Show 'usage;' message and exit with an error code '-1'
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
Show usage and exit
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdSeq
Show 'usage' message and exit with an error code '-1'
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdShow
Show 'usage;' message and exit with an error code '-1'
usage(String) - Method in class org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
Show 'usage;' message and exit with an error code '-1'
usage(String) - Method in class org.snpeff.snpEffect.VcfAnnotatorChain
 
usage(String) - Method in class org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
 
usageDb() - Method in class org.snpeff.SnpEff
Show database load and build options
usageGeneric() - Method in class org.snpeff.SnpEff
Show generic options
usageGenericAndDb() - Method in class org.snpeff.SnpEff
 
Utr - Class in org.snpeff.interval
Interval for a UTR (5 prime UTR and 3 prime UTR
Utr() - Constructor for class org.snpeff.interval.Utr
 
Utr(Exon, int, int, boolean, String) - Constructor for class org.snpeff.interval.Utr
 
UTR_3 - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
UTR_3_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
UTR_3_PRIME - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
UTR_5 - Enum constant in enum class org.snpeff.genBank.Feature.Type
 
UTR_5_DELETED - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
UTR_5_PRIME - Enum constant in enum class org.snpeff.snpEffect.EffectType
 
UTR3 - Enum constant in enum class org.snpeff.interval.GffType
 
Utr3prime - Class in org.snpeff.interval
Interval for a UTR (5 prime UTR and 3 prime UTR
Utr3prime() - Constructor for class org.snpeff.interval.Utr3prime
 
Utr3prime(Exon, int, int, boolean, String) - Constructor for class org.snpeff.interval.Utr3prime
 
UTR5 - Enum constant in enum class org.snpeff.interval.GffType
 
Utr5prime - Class in org.snpeff.interval
Interval for a UTR (5 prime UTR and 3 prime UTR
Utr5prime() - Constructor for class org.snpeff.interval.Utr5prime
 
Utr5prime(Exon, int, int, boolean, String) - Constructor for class org.snpeff.interval.Utr5prime
 
utrFromCds(boolean) - Method in class org.snpeff.interval.Transcript
Calculate UTR regions from CDSs

V

value - Variable in class org.snpeff.stats.BooleanMutable
 
value - Variable in class org.snpeff.util.KeyValue
 
valueOf(String) - Static method in enum class org.snpeff.genBank.Feature.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.gsa.ScoreList.ScoreSummary
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.interval.BioType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.interval.Exon.ExonSpliceType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.interval.FrameType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.interval.Gene.GeneType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.interval.GffType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.interval.TranscriptSupportLevel
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.interval.Variant.VariantType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.logStatsServer.LogStats.RequestResult
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.ped.Sex
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.reactome.Entity.TransferFunction
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.reactome.events.Reaction.RegulationType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.SnpEff.GeneDatabaseFormat
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.SnpEff.InputFormat
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.SnpEff.OutputFormat
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.snpEffect.commandLine.SnpEffCmdDump.DumpFormat
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.snpEffect.EffectType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.snpEffect.ErrorWarningType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.snpEffect.VariantEffect.Coding
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.util.Log.FatalErrorBehabiour
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.vcf.EffFormatVersion
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.vcf.VcfEntry.AlleleFrequencyType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpeff.vcf.VcfInfoType
Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.snpeff.genBank.Feature.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Method in class org.snpeff.geneOntology.GoTerms
 
values() - Static method in enum class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Method in class org.snpeff.geneSets.GeneSets
 
values() - Static method in enum class org.snpeff.gsa.ScoreList.ScoreSummary
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.interval.BioType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.interval.Exon.ExonSpliceType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.interval.FrameType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.interval.Gene.GeneType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Method in class org.snpeff.interval.Genes
 
values() - Static method in enum class org.snpeff.interval.GffType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.interval.TranscriptSupportLevel
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.interval.Variant.VariantType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.logStatsServer.LogStats.RequestResult
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Method in class org.snpeff.ped.PedPedigree
 
values() - Static method in enum class org.snpeff.ped.Sex
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.reactome.Entity.TransferFunction
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.reactome.events.Reaction.RegulationType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.SnpEff.GeneDatabaseFormat
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.SnpEff.InputFormat
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.SnpEff.OutputFormat
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.snpEffect.commandLine.SnpEffCmdDump.DumpFormat
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.snpEffect.EffectType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.snpEffect.ErrorWarningType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.snpEffect.VariantEffect.Coding
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.snpEffect.VariantEffect.EffectImpact
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.snpEffect.VariantEffect.FunctionalClass
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.util.Log.FatalErrorBehabiour
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.vcf.EffFormatVersion
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.vcf.VcfEntry.AlleleFrequencyType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpeff.vcf.VcfInfoType
Returns an array containing the constants of this enum class, in the order they are declared.
variance(int) - Method in class org.snpeff.probablility.RankSumNoReplacementSimulate
 
variance(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Variance for a given N and N_T
variance(int, int) - Static method in class org.snpeff.probablility.RankSumPdf
Variance for a given N and N_T
variance(int, int, int, int) - Method in class org.snpeff.probablility.FisherExactTest
Calculate the variance References: http://en.wikipedia.org/wiki/Hypergeometric_distribution
varianceSlow(int, int) - Method in class org.snpeff.probablility.RankSumNoReplacementPdf
Variance for a given N and N_T (slow method, only used for debugging)
variant - Variable in class org.snpeff.snpEffect.Hgvs
 
variant - Variable in class org.snpeff.snpEffect.VariantEffect
 
Variant - Class in org.snpeff.interval
A variant represents a change in a reference sequence
Variant() - Constructor for class org.snpeff.interval.Variant
 
Variant(Marker, int, int, String) - Constructor for class org.snpeff.interval.Variant
This constructor is used when we only have interval data (e.g.
Variant(Marker, int, String, String) - Constructor for class org.snpeff.interval.Variant
 
Variant(Marker, int, String, String, String) - Constructor for class org.snpeff.interval.Variant
 
Variant.VariantType - Enum Class in org.snpeff.interval
 
VariantBnd - Class in org.snpeff.interval
A 'BND' variant (i.e.
VariantBnd() - Constructor for class org.snpeff.interval.VariantBnd
 
VariantBnd(Marker, int, String, String, Chromosome, int, boolean, boolean) - Constructor for class org.snpeff.interval.VariantBnd
 
variantEffect - Variable in class org.snpeff.snpEffect.Hgvs
 
variantEffect(Variant) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Predict the effect of a variant
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Custom
 
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Downstream
 
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Exon
Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' class
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Gene
Get some details about the effect on this gene
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Intron
 
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Marker
Calculate the effect of this variant
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.MicroRnaBindingSite
 
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Motif
Calculate the effect of this variant
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.NextProt
 
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.ProteinInteractionLocus
Calculate the effect of this variant
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.ProteinProteinInteractionLocus
Calculate the effect of this variant
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Regulation
Calculate the effect of this variant
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.SpliceSite
 
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Transcript
Get some details about the effect on this transcript
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Upstream
 
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Utr3prime
 
variantEffect(Variant, VariantEffects) - Method in class org.snpeff.interval.Utr5prime
 
variantEffect(Variant, VariantEffects, Markers) - Method in class org.snpeff.snpEffect.SnpEffectPredictor
Calculate variant effect for each marker in 'intersect'
VariantEffect - Class in org.snpeff.snpEffect
Effect of a variant.
VariantEffect(Variant) - Constructor for class org.snpeff.snpEffect.VariantEffect
 
VariantEffect(Variant, Marker, EffectType, VariantEffect.EffectImpact, String, String, int, int, int) - Constructor for class org.snpeff.snpEffect.VariantEffect
 
VariantEffect.Coding - Enum Class in org.snpeff.snpEffect
 
VariantEffect.EffectImpact - Enum Class in org.snpeff.snpEffect
 
VariantEffect.FunctionalClass - Enum Class in org.snpeff.snpEffect
This class is only getFused for SNPs
VariantEffectFilter - Class in org.snpeff.filter
A Generic ChangeEffect filter
VariantEffectFilter() - Constructor for class org.snpeff.filter.VariantEffectFilter
 
VariantEffectFusion - Class in org.snpeff.snpEffect
Effect of a structural variant (fusion) affecting two genes
VariantEffectFusion(Variant, Marker, Marker) - Constructor for class org.snpeff.snpEffect.VariantEffectFusion
 
variantEffectGene(Variant, VariantEffects) - Method in class org.snpeff.interval.Gene
Add gene-specific annotations
variantEffectNonRef(Variant, VariantEffects) - Method in class org.snpeff.interval.Marker
Calculate the effect of this variant
VariantEffects - Class in org.snpeff.snpEffect
A sorted collection of variant effects
VariantEffects() - Constructor for class org.snpeff.snpEffect.VariantEffects
 
VariantEffectStats - Class in org.snpeff.stats
Variants effect statistics
VariantEffectStats(Genome) - Constructor for class org.snpeff.stats.VariantEffectStats
 
VariantEffectStructural - Class in org.snpeff.snpEffect
Effect of a structural variant affecting multiple genes
VariantEffectStructural(Variant) - Constructor for class org.snpeff.snpEffect.VariantEffectStructural
 
VariantEffectStructural(Variant, Markers) - Constructor for class org.snpeff.snpEffect.VariantEffectStructural
 
VariantFileIterator - Class in org.snpeff.fileIterator
Opens a sequence change file and iterates over all sequence changes
VariantFileIterator(String) - Constructor for class org.snpeff.fileIterator.VariantFileIterator
 
VariantFileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.VariantFileIterator
 
VariantNonRef - Class in org.snpeff.interval
A variant respect to non-reference (e.g.
VariantNonRef() - Constructor for class org.snpeff.interval.VariantNonRef
 
VariantNonRef(Variant, Variant) - Constructor for class org.snpeff.interval.VariantNonRef
 
VariantRealign - Class in org.snpeff.align
Re-align a variant towards the leftmost (rightmost) position Note: We perform a 'progressive' realignment, asking for more reference sequence as we need it
VariantRealign() - Constructor for class org.snpeff.align.VariantRealign
 
VariantRealign(Variant) - Constructor for class org.snpeff.align.VariantRealign
 
variants - Variable in class org.snpeff.vcf.VcfEntry
 
variants() - Method in class org.snpeff.vcf.VcfEntry
Create a list of variants from this VcfEntry
VariantStats - Class in org.snpeff.stats
Variants statistics
VariantStats(Genome) - Constructor for class org.snpeff.stats.VariantStats
 
VariantTxtFileIterator - Class in org.snpeff.fileIterator
Opens a sequence change file and iterates over all sequence changes TXT Format: Tab-separated format, containing five columns that correspond to: chr \t position \t refSeq \t newSeq \t strand \t quality \t coverage \t id \n Fields strand, quality, coverage and id are optional E.g.
VariantTxtFileIterator(String) - Constructor for class org.snpeff.fileIterator.VariantTxtFileIterator
 
VariantTxtFileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.VariantTxtFileIterator
 
variantType - Variable in class org.snpeff.interval.Variant
 
VariantTypeStats - Class in org.snpeff.stats
Count variant types (SNP, MNP, INS, DEL)
VariantTypeStats() - Constructor for class org.snpeff.stats.VariantTypeStats
 
VariantVcfEntry - Class in org.snpeff.vcf
Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.
VariantVcfEntry(Variant, VcfEntry) - Constructor for class org.snpeff.vcf.VariantVcfEntry
 
VariantWithScore - Class in org.snpeff.interval
A variant that has a numeric score.
VariantWithScore() - Constructor for class org.snpeff.interval.VariantWithScore
 
VariantWithScore(Marker, int, int, String, double) - Constructor for class org.snpeff.interval.VariantWithScore
 
vaultRNA - Enum constant in enum class org.snpeff.interval.BioType
 
VCF - Enum constant in enum class org.snpeff.SnpEff.InputFormat
 
VCF - Enum constant in enum class org.snpeff.SnpEff.OutputFormat
 
VCF_ALT_MISSING_REF - Static variable in class org.snpeff.vcf.VcfEntry
 
VCF_ALT_MISSING_REF_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
 
VCF_ALT_NON_REF - Static variable in class org.snpeff.vcf.VcfEntry
 
VCF_ALT_NON_REF_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
 
VCF_ALT_NON_REF_gVCF - Static variable in class org.snpeff.vcf.VcfEntry
 
VCF_ALT_NON_REF_gVCF_ARRAY - Static variable in class org.snpeff.vcf.VcfEntry
 
VCF_INFO_ANN_NAME - Static variable in enum class org.snpeff.vcf.EffFormatVersion
 
VCF_INFO_ANN_NAMES - Static variable in enum class org.snpeff.vcf.EffFormatVersion
 
VCF_INFO_CSQ_NAME - Static variable in class org.snpeff.vcf.VcfConsequence
 
VCF_INFO_EFF_NAME - Static variable in enum class org.snpeff.vcf.EffFormatVersion
 
VCF_INFO_END - Static variable in class org.snpeff.vcf.VcfEntry
 
VCF_INFO_HETS - Static variable in class org.snpeff.vcf.VcfEntry
 
VCF_INFO_HOMS - Static variable in class org.snpeff.vcf.VcfEntry
 
VCF_INFO_LOF_NAME - Static variable in class org.snpeff.snpEffect.LossOfFunction
 
VCF_INFO_NAS - Static variable in class org.snpeff.vcf.VcfEntry
 
VCF_INFO_NMD_NAME - Static variable in class org.snpeff.snpEffect.LossOfFunction
 
VCF_INFO_OICR_NAME - Static variable in class org.snpeff.outputFormatter.VcfOutputFormatter
 
VCF_INFO_PRIVATE - Static variable in class org.snpeff.vcf.VcfEntry
 
VcfAnnotator - Interface in org.snpeff.snpEffect
Annotate a VCF file: E.g.
VcfAnnotatorChain - Class in org.snpeff.snpEffect
Maintains a list of VcfAnnotators and applies them one by one in the specified order
VcfAnnotatorChain() - Constructor for class org.snpeff.snpEffect.VcfAnnotatorChain
 
VcfConsequence - Class in org.snpeff.vcf
An 'CSQ' entry in a vcf line ('Consequence' from ENSEMBL's VEP) Format: ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP.
VcfConsequence(VcfConsequenceHeader, String) - Constructor for class org.snpeff.vcf.VcfConsequence
 
VcfConsequenceHeader - Class in org.snpeff.vcf
An 'CSQ' entry in a vcf header line
VcfConsequenceHeader(VcfFileIterator) - Constructor for class org.snpeff.vcf.VcfConsequenceHeader
 
VcfEffect - Class in org.snpeff.vcf
An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *
VcfEffect(String) - Constructor for class org.snpeff.vcf.VcfEffect
Constructor: Guess format version
VcfEffect(String, EffFormatVersion) - Constructor for class org.snpeff.vcf.VcfEffect
Constructor: Force format version
VcfEffect(VariantEffect, EffFormatVersion) - Constructor for class org.snpeff.vcf.VcfEffect
 
VcfEffect(VariantEffect, EffFormatVersion, boolean, boolean) - Constructor for class org.snpeff.vcf.VcfEffect
 
vcfEffects - Variable in class org.snpeff.vcf.VcfEntry
 
vcfEntry - Variable in class org.snpeff.vcf.VariantVcfEntry
 
VcfEntry - Class in org.snpeff.vcf
A VCF entry (a line) in a VCF file
VcfEntry(VcfFileIterator, String, int, boolean) - Constructor for class org.snpeff.vcf.VcfEntry
Create a line form a file iterator
VcfEntry(VcfFileIterator, Marker, String, int, String, String, String, double, String, String, String) - Constructor for class org.snpeff.vcf.VcfEntry
 
VcfEntry.AlleleFrequencyType - Enum Class in org.snpeff.vcf
 
vcfFileIterator - Variable in class org.snpeff.vcf.VcfEntry
 
VcfFileIterator - Class in org.snpeff.fileIterator
Opens a VCF file and iterates over all entries Format: VCF 4.1 Reference: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 Old 4.0 format: http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0 1.
VcfFileIterator() - Constructor for class org.snpeff.fileIterator.VcfFileIterator
 
VcfFileIterator(BufferedReader) - Constructor for class org.snpeff.fileIterator.VcfFileIterator
 
VcfFileIterator(String) - Constructor for class org.snpeff.fileIterator.VcfFileIterator
 
VcfFileIterator(String, Genome) - Constructor for class org.snpeff.fileIterator.VcfFileIterator
 
VcfGenotype - Class in org.snpeff.vcf
A VCF genotype field There is one genotype per sample in each VCF entry
VcfGenotype(VcfEntry, String, String) - Constructor for class org.snpeff.vcf.VcfGenotype
 
vcfGenotypes - Variable in class org.snpeff.vcf.VcfEntry
 
VcfHapMapFileIterator - Class in org.snpeff.fileIterator
Opens a Hapmap phased file and iterates over all entries, returning VcfEntries for each line Note: Each HapMap file has one chromosome.
VcfHapMapFileIterator(String, String, Genome) - Constructor for class org.snpeff.fileIterator.VcfHapMapFileIterator
 
vcfHeader() - Method in enum class org.snpeff.vcf.EffFormatVersion
VCF header for each format type
VcfHeader - Class in org.snpeff.vcf
Represents the header of a vcf file.
VcfHeader() - Constructor for class org.snpeff.vcf.VcfHeader
 
VcfHeaderEntry - Class in org.snpeff.vcf
Represents a info elements in a VCF file's header References: https://samtools.github.io/hts-specs/VCFv4.3.pdf http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
VcfHeaderEntry(String) - Constructor for class org.snpeff.vcf.VcfHeaderEntry
Constructor
VcfHeaderFormat - Class in org.snpeff.vcf
 
VcfHeaderFormat(String) - Constructor for class org.snpeff.vcf.VcfHeaderFormat
Constructor using a "##FORMAT" line from a VCF file
VcfHeaderFormat(String, VcfInfoType, String, String) - Constructor for class org.snpeff.vcf.VcfHeaderFormat
 
VcfHeaderInfo - Class in org.snpeff.vcf
Represents a info elements in a VCF file References: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 INFO fields should be described as follows (all keys are required): ##INFO=<ID=ID,Number=number,Type=type,Description=description> Possible Types for INFO fields are: Integer, Float, Flag, Character, and String.
VcfHeaderInfo(String) - Constructor for class org.snpeff.vcf.VcfHeaderInfo
Constructor using a "##INFO" line from a VCF file
VcfHeaderInfo(String, VcfInfoType, String, String) - Constructor for class org.snpeff.vcf.VcfHeaderInfo
 
VcfHeaderInfo(VcfHeaderInfo) - Constructor for class org.snpeff.vcf.VcfHeaderInfo
 
VcfHeaderInfo.VcfInfoNumber - Enum Class in org.snpeff.vcf
Number of values in an INFO field.
vcfInfoDecode(String) - Static method in class org.snpeff.vcf.VcfEntry
Decode INFO value
vcfInfoEncode(String) - Static method in class org.snpeff.vcf.VcfEntry
Encode a string to be used in an 'INFO' field value From the VCF 4.3 specification Characters with special meaning (such as field delimiters ';' in INFO or ':' FORMAT fields) must be represented using the capitalized percent encoding: %3A : (colon) %3B ; (semicolon) %3D = (equal sign) %25 % (percent sign) %2C , (comma) %0D CR %0A LF %09 TAB
vcfInfoKeySafe(String) - Static method in class org.snpeff.vcf.VcfEntry
Return a string safe to be used in an 'INFO' field key
vcfInfoNames - Static variable in enum class org.snpeff.vcf.EffFormatVersion
 
vcfInfoNumber - Variable in class org.snpeff.vcf.VcfHeaderInfo
 
vcfInfoType - Variable in class org.snpeff.vcf.VcfHeaderInfo
 
VcfInfoType - Enum Class in org.snpeff.vcf
 
vcfInfoValueSafe(String) - Static method in class org.snpeff.vcf.VcfEntry
Return a string safe to be used in an 'INFO' field value
VcfLof - Class in org.snpeff.vcf
An 'LOF' entry in a vcf line
VcfLof(String) - Constructor for class org.snpeff.vcf.VcfLof
 
VcfLof(String, String, int, double) - Constructor for class org.snpeff.vcf.VcfLof
 
VcfLof(Gene, double) - Constructor for class org.snpeff.vcf.VcfLof
 
VcfLof(VcfEntry, String) - Constructor for class org.snpeff.vcf.VcfLof
 
VcfNmd - Class in org.snpeff.vcf
An 'NMD' entry in a vcf line
VcfNmd(String) - Constructor for class org.snpeff.vcf.VcfNmd
 
VcfNmd(String, String, int, double) - Constructor for class org.snpeff.vcf.VcfNmd
 
VcfNmd(Gene, double) - Constructor for class org.snpeff.vcf.VcfNmd
 
VcfNmd(VcfEntry, String) - Constructor for class org.snpeff.vcf.VcfNmd
 
VcfOutputFormatter - Class in org.snpeff.outputFormatter
Formats output as VCF
VcfOutputFormatter() - Constructor for class org.snpeff.outputFormatter.VcfOutputFormatter
 
VcfOutputFormatter(List<VcfEntry>) - Constructor for class org.snpeff.outputFormatter.VcfOutputFormatter
Add all vcf entries to a list (used only for debugging and test-cases)
VcfRefAltAlign - Class in org.snpeff.align
Needleman-Wunsch (global sequence alignment) algorithm for sequence alignment Only used for short strings (algorithm is not optimized)
VcfRefAltAlign(String, String) - Constructor for class org.snpeff.align.VcfRefAltAlign
 
VcfStats - Class in org.snpeff.stats
VCF statistics: This are usually multi-sample statistics
VcfStats() - Constructor for class org.snpeff.stats.VcfStats
 
verbose - Variable in class org.snpeff.fileIterator.FileIterator
 
verbose - Variable in class org.snpeff.fileIterator.TableFile
 
verbose - Static variable in class org.snpeff.geneOntology.GoTerms
 
verbose - Variable in class org.snpeff.interval.tree.IntervalTreeArray
 
verbose - Variable in class org.snpeff.logStatsServer.LogStats
 
verbose - Variable in class org.snpeff.SnpEff
 
verbose - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
 
verbose - Variable in class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
 
verbose - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesBase
 
verbose - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
 
verbose - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
 
verbose - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte
 
verbose - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
 
verbose - Variable in class org.snpeff.snpEffect.testCases.unity.TestCasesIubString
 
verbose - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
 
verbose - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesNmers
 
verbose - Static variable in class org.snpeff.snpEffect.testCases.unity.TestCasesReactome
 
verbose - Variable in class org.snpeff.snpEffect.testCases.unity.TestGenome
 
version(String, String, String, boolean) - Static method in class org.snpeff.logStatsServer.VersionCheck
Get version data
VERSION - Static variable in class org.snpeff.SnpEff
 
VERSION_AUTHOR - Static variable in class org.snpeff.SnpEff
 
VERSION_BUILD - Static variable in class org.snpeff.SnpEff
 
VERSION_MAJOR - Static variable in class org.snpeff.SnpEff
 
VERSION_SHORT - Static variable in class org.snpeff.SnpEff
 
VersionCheck - Class in org.snpeff.logStatsServer
Check is a new version is available
VersionCheck(String, String, String) - Constructor for class org.snpeff.logStatsServer.VersionCheck
 

W

warnCDF - Static variable in class org.snpeff.probablility.RankSumNoReplacementPdf
 
warnCount - Static variable in class org.snpeff.util.Log
 
warning - Variable in class org.snpeff.snpEffect.VariantEffect
 
warning(String) - Static method in class org.snpeff.util.Log
 
warning(ErrorWarningType, String) - Static method in class org.snpeff.util.Log
Show a warning message (up to MAX_ERRORS times)
WARNING_CANNOT_ADD_UTR - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_CDS_TOO_SHORT - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_CHROMOSOME_CIRCULAR - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_CHROMOSOME_LENGTH - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_CHROMOSOME_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_DUPLICATE_PRIMARY_KEY - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_EXON_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_EXON_SEQUENCE_LENGTH - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_EXON_TOO_SHORT - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_FILE_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_FRAMES_ZERO - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_GENE_COORDINATES - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_GENE_ID_DUPLICATE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_GENE_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_INVALID_INFO_KEY - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_INVALID_INFO_VALUE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_RARE_AA_POSSITION_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_REF_DOES_NOT_MATCH_GENOME - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_SEQUENCE_NOT_AVAILABLE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_TRANSCRIPT_ID_DUPLICATE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_TRANSCRIPT_INCOMPLETE - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_TRANSCRIPT_NO_START_CODON - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_TRANSCRIPT_NO_STOP_CODON - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
WARNING_TRANSCRIPT_NOT_FOUND - Enum constant in enum class org.snpeff.snpEffect.ErrorWarningType
 
warningln(String) - Static method in class org.snpeff.util.Log
 
wc() - Method in class org.snpeff.nmer.Nmer
Watson-Cricks complement of this nmer Since {A, C, G, T} is translated into binary {00, 01, 10, 11}.
wc(char) - Static method in class org.snpeff.util.GprSeq
Watson-Cricks complement
wc(String) - Static method in class org.snpeff.util.GprSeq
Watson-Cricks complement
weight - Variable in class org.snpeff.reactome.Entity
 
WEIGHT_DOMINANT - Static variable in class org.snpeff.probablility.CochranArmitageTest
 
WEIGHT_RECESSIVE - Static variable in class org.snpeff.probablility.CochranArmitageTest
 
WEIGHT_TREND - Static variable in class org.snpeff.probablility.CochranArmitageTest
 
WITHIN_FIELD_SEP - Static variable in class org.snpeff.vcf.VcfEntry
 
wlen - Variable in class org.snpeff.collections.OpenBitSet
 
write(DataOutputStream) - Method in class org.snpeff.binseq.BinarySequence
Write to a binary stream
write(DataOutputStream) - Method in class org.snpeff.binseq.DnaAndQualitySequence
Write data in binary format
write(DataOutputStream) - Method in class org.snpeff.binseq.DnaAndQualitySequenceWithId
Write data in binary format
write(DataOutputStream) - Method in class org.snpeff.binseq.DnaNSequence
Write data in binary format
write(DataOutputStream) - Method in class org.snpeff.binseq.DnaSequence
Write data in binary format
write(DataOutputStream) - Method in class org.snpeff.binseq.DnaSequenceId
Write data in binary format
write(DataOutputStream) - Method in class org.snpeff.binseq.DnaSequencePe
Write data in binary format
write(OutputStream) - Method in class org.snpeff.nmer.Nmer
 

X

xor(OpenBitSet) - Method in class org.snpeff.collections.OpenBitSet
this = this XOR other
xorCount(OpenBitSet, OpenBitSet) - Static method in class org.snpeff.collections.OpenBitSet
Returns the popcount or cardinality of the exclusive-or of the two sets.

Z

Z_SCORES - Enum constant in enum class org.snpeff.gsa.ScoreList.ScoreSummary
 
Zzz - Class in org.snpeff
 
Zzz(String, String) - Constructor for class org.snpeff.Zzz
 
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