Uses of Class
org.snpeff.fileIterator.MarkerFileIterator
Packages that use MarkerFileIterator
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Uses of MarkerFileIterator in org.snpeff.fileIterator
Subclasses of MarkerFileIterator in org.snpeff.fileIteratorModifier and TypeClassDescriptionclass
Opens a sequence change file and iterates over all intervals in BED format.class
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 wrapperclass
Opens a file and creates generic markers (one per line)class
Opens a sequence change file and iterates over all intervals in GFF3 format.class
Opens a regulation file and create Motif elements.class
Opens a GFF3 file and create regulatory elements.class
Opens a regulation file and create Regulation elements.class
Opens a GFF3 file and create regulatory elements.class
Opens a sequence change file and iterates over all sequence changesclass
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.class
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.class
Opens a Hapmap phased file and iterates over all entries, returning VcfEntries for each line Note: Each HapMap file has one chromosome.