Uses of Class
org.snpeff.fileIterator.VcfFileIterator
Packages that use VcfFileIterator
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Uses of VcfFileIterator in org.snpeff.snpEffect
Methods in org.snpeff.snpEffect with parameters of type VcfFileIteratorModifier and TypeMethodDescriptionboolean
VcfAnnotator.addHeaders
(VcfFileIterator vcfFile) Add annotation headers to VCF fileboolean
VcfAnnotatorChain.addHeaders
(VcfFileIterator vcfFile) boolean
VcfAnnotator.annotateFinish
(VcfFileIterator vcfFile) This method is called after all annotations have been performed.boolean
VcfAnnotatorChain.annotateFinish
(VcfFileIterator vcf) boolean
VcfAnnotator.annotateInit
(VcfFileIterator vcfFile) Initialize annotator: This method is called after vcfFile is opened, but before the header is output.boolean
VcfAnnotatorChain.annotateInit
(VcfFileIterator vcfFile) -
Uses of VcfFileIterator in org.snpeff.snpEffect.commandLine
Methods in org.snpeff.snpEffect.commandLine with parameters of type VcfFileIteratorModifier and TypeMethodDescriptionboolean
SnpEffCmdEff.addHeaders
(VcfFileIterator vcfFile) boolean
SnpEffCmdEff.annotateFinish
(VcfFileIterator vcfFile) Finish annotations and create reportsboolean
SnpEffCmdEff.annotateInit
(VcfFileIterator vcfFile) -
Uses of VcfFileIterator in org.snpeff.vcf
Fields in org.snpeff.vcf declared as VcfFileIteratorMethods in org.snpeff.vcf that return VcfFileIteratorConstructors in org.snpeff.vcf with parameters of type VcfFileIteratorModifierConstructorDescriptionPedigree
(VcfFileIterator vcfFile) Pedigree
(VcfFileIterator vcfFile, String cancerSamples) VcfEntry
(VcfFileIterator vcfFileIterator, String line, int lineNum, boolean parseNow) Create a line form a file iteratorVcfEntry
(VcfFileIterator vcfFileIterator, Marker parent, String chromosomeName, int start, String id, String ref, String altsStr, double quality, String filterPass, String infoStr, String format)