Uses of Class
org.snpeff.fileIterator.VcfFileIterator

Packages that use VcfFileIterator

Package	Description
org.snpeff.snpEffect
org.snpeff.snpEffect.commandLine
org.snpeff.vcf

Uses of VcfFileIterator in org.snpeff.snpEffect

Methods in org.snpeff.snpEffect with parameters of type VcfFileIterator

Modifier and Type	Method	Description
boolean	VcfAnnotator.addHeaders(VcfFileIterator vcfFile)	Add annotation headers to VCF file
boolean	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 VcfFileIterator

Modifier and Type	Method	Description
boolean	SnpEffCmdEff.addHeaders(VcfFileIterator vcfFile)
boolean	SnpEffCmdEff.annotateFinish(VcfFileIterator vcfFile)	Finish annotations and create reports
boolean	SnpEffCmdEff.annotateInit(VcfFileIterator vcfFile)

Uses of VcfFileIterator in org.snpeff.vcf

Fields in org.snpeff.vcf declared as VcfFileIterator

Modifier and Type	Field	Description
protected VcfFileIterator	VcfEntry.vcfFileIterator

Methods in org.snpeff.vcf that return VcfFileIterator

Modifier and Type	Method	Description
VcfFileIterator	VcfEntry.getVcfFileIterator()

Constructors in org.snpeff.vcf with parameters of type VcfFileIterator

Constructor	Description
Pedigree(VcfFileIterator vcfFile)
Pedigree(VcfFileIterator vcfFile, java.lang.String cancerSamples)
VcfConsequenceHeader(VcfFileIterator vcf)
VcfEntry(VcfFileIterator vcfFileIterator, java.lang.String line, int lineNum, boolean parseNow)	Create a line form a file iterator
VcfEntry(VcfFileIterator vcfFileIterator, Marker parent, java.lang.String chromosomeName, int start, java.lang.String id, java.lang.String ref, java.lang.String altsStr, double quality, java.lang.String filterPass, java.lang.String infoStr, java.lang.String format)