Uses of Class
org.snpeff.fileIterator.VcfFileIterator
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Packages that use VcfFileIterator Package Description org.snpeff.akka.vcf org.snpeff.snpEffect org.snpeff.snpEffect.commandLine org.snpeff.vcf -
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Uses of VcfFileIterator in org.snpeff.akka.vcf
Fields in org.snpeff.akka.vcf declared as VcfFileIterator Modifier and Type Field Description protected VcfFileIterator
MasterVcf. vcfFileIterator
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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 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)
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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 reportsboolean
SnpEffCmdEff. annotateInit(VcfFileIterator vcfFile)
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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 VcfConsequenceHeader(VcfFileIterator vcf)
VcfEntry(VcfFileIterator vcfFileIterator, java.lang.String line, int lineNum, boolean parseNow)
Create a line form a file iteratorVcfEntry(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)
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