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 TypeMethodDescriptionbooleanVcfAnnotator.addHeaders(VcfFileIterator vcfFile) Add annotation headers to VCF filebooleanVcfAnnotatorChain.addHeaders(VcfFileIterator vcfFile) booleanVcfAnnotator.annotateFinish(VcfFileIterator vcfFile) This method is called after all annotations have been performed.booleanVcfAnnotatorChain.annotateFinish(VcfFileIterator vcf) booleanVcfAnnotator.annotateInit(VcfFileIterator vcfFile) Initialize annotator: This method is called after vcfFile is opened, but before the header is output.booleanVcfAnnotatorChain.annotateInit(VcfFileIterator vcfFile) -
Uses of VcfFileIterator in org.snpeff.snpEffect.commandLine
Methods in org.snpeff.snpEffect.commandLine with parameters of type VcfFileIteratorModifier and TypeMethodDescriptionbooleanSnpEffCmdEff.addHeaders(VcfFileIterator vcfFile) booleanSnpEffCmdEff.annotateFinish(VcfFileIterator vcfFile) Finish annotations and create reportsbooleanSnpEffCmdEff.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)