Uses of Class
org.snpeff.interval.Chromosome
Packages that use Chromosome
Package
Description
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Uses of Chromosome in org.snpeff.codons
Methods in org.snpeff.codons with parameters of type ChromosomeModifier and TypeMethodDescriptionvoid
CodonTables.set
(Genome genome, Chromosome chr, CodonTable codonTable) Set a codon table for a given genome & chromosome -
Uses of Chromosome in org.snpeff.fileIterator
Methods in org.snpeff.fileIterator that return ChromosomeModifier and TypeMethodDescriptionMarkerFileIterator.getChromosome
(String chromoName) Find chromosome 'chromoName'.Methods in org.snpeff.fileIterator with parameters of type ChromosomeModifier and TypeMethodDescriptionvoid
MarkerFileIterator.sanityCheckChromo
(String chromoName, Chromosome chromo) Sanity check -
Uses of Chromosome in org.snpeff.gsa
Methods in org.snpeff.gsa that return ChromosomeMethods in org.snpeff.gsa with parameters of type ChromosomeModifier and TypeMethodDescriptionvoid
ChrPosScoreList.add
(Chromosome chr, int start, int end, double score) -
Uses of Chromosome in org.snpeff.interval
Methods in org.snpeff.interval that return ChromosomeModifier and TypeMethodDescriptionChromosome.cloneShallow()
Genome.getChromosome
(String chromoName) Find chromosome 'chromoName'Interval.getChromosome()
Genome.getOrCreateChromosome
(String chromoName) Get or create a chromosomeMethods in org.snpeff.interval that return types with arguments of type ChromosomeModifier and TypeMethodDescriptionGenome.getChromosomes()
Genome.getChromosomesSortedSize()
Return chromosomes sorted by size (largest chromosomes first)Genome.iterator()
Methods in org.snpeff.interval with parameters of type ChromosomeModifier and TypeMethodDescriptionvoid
Genome.add
(Chromosome chromo) Add a chromosomeVariant.factory
(Chromosome chromo, int start, String ref, String altStr, String id, boolean expand) Create variants from ALT (which can be multiple values)void
Genome.remove
(Chromosome chromo) Remove a chromosome WARINIG: Doesn't check any dependencies!Constructors in org.snpeff.interval with parameters of type ChromosomeModifierConstructorDescriptionIntergenic
(Chromosome parent, int start, int end, boolean strandMinus, String id, String name) IntergenicConserved
(Chromosome parent, int start, int end, boolean strandMinus, String id) VariantBnd
(Marker parent, int start, String ref, String alt, Chromosome chrTr, int startTr, boolean left, boolean before) -
Uses of Chromosome in org.snpeff.snpEffect.factory
Methods in org.snpeff.snpEffect.factory that return ChromosomeModifier and TypeMethodDescriptionSnpEffPredictorFactoryRand.getChromo()
protected Chromosome
SnpEffPredictorFactory.getOrCreateChromosome
(String chromoName) Get a chromosome.Methods in org.snpeff.snpEffect.factory with parameters of type ChromosomeModifier and TypeMethodDescriptionprotected void
SnpEffPredictorFactory.add
(Chromosome chromo) void
SnpEffPredictorFactoryRand.setChromo
(Chromosome chromo) -
Uses of Chromosome in org.snpeff.snpEffect.testCases.integration
Fields in org.snpeff.snpEffect.testCases.integration declared as Chromosome -
Uses of Chromosome in org.snpeff.snpEffect.testCases.unity
Fields in org.snpeff.snpEffect.testCases.unity declared as ChromosomeModifier and TypeFieldDescriptionprotected Chromosome
TestCasesVariantDecompose.chr
TestGenome.chr
protected Chromosome
TestCasesBase.chromosome
protected Chromosome
TestCasesIntervalTree.chromosome
Methods in org.snpeff.snpEffect.testCases.unity with parameters of type ChromosomeModifier and TypeMethodDescriptionprotected Markers
TestCasesIntervalTree.createRandomLargeMarkers
(Chromosome chr, int num) protected Markers
TestCasesIntervalTree.createRandomSmallMarkers
(Chromosome chr, int num)