Uses of Class
org.snpeff.vcf.VcfEntry
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Uses of VcfEntry in org.snpeff.akka.vcf
Methods in org.snpeff.akka.vcf that return VcfEntry Modifier and Type Method Description VcfEntry
WorkerVcf. calculate(VcfEntry vcfEntry)
VcfEntry
MasterVcf. next()
Methods in org.snpeff.akka.vcf with parameters of type VcfEntry Modifier and Type Method Description VcfEntry
WorkerVcf. calculate(VcfEntry vcfEntry)
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Uses of VcfEntry in org.snpeff.akka.vcfStr
Methods in org.snpeff.akka.vcfStr with parameters of type VcfEntry Modifier and Type Method Description java.lang.String
WorkerVcfStr. calculate(VcfEntry vcfEntry)
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Uses of VcfEntry in org.snpeff.fileIterator
Methods in org.snpeff.fileIterator that return VcfEntry Modifier and Type Method Description VcfEntry
VcfFileIterator. parseVcfLine(java.lang.String line)
Parse a line from a VCF fileprotected VcfEntry
VcfFileIterator. readNext()
protected VcfEntry
VcfHapMapFileIterator. readNext()
Methods in org.snpeff.fileIterator that return types with arguments of type VcfEntry Modifier and Type Method Description java.util.Collection<VcfEntry>
VcfFileIterator. parse(java.lang.String str)
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Uses of VcfEntry in org.snpeff.outputFormatter
Methods in org.snpeff.outputFormatter with parameters of type VcfEntry Modifier and Type Method Description protected void
VcfOutputFormatter. addInfo(VcfEntry vcfEntry)
Add effects to INFO fieldConstructor parameters in org.snpeff.outputFormatter with type arguments of type VcfEntry Constructor Description VcfOutputFormatter(java.util.List<VcfEntry> vcfEntries)
Add all vcf entries to a list (used only for debugging and test-cases) -
Uses of VcfEntry in org.snpeff.snpEffect
Methods in org.snpeff.snpEffect with parameters of type VcfEntry Modifier and Type Method Description boolean
VcfAnnotator. annotate(VcfEntry vcfEntry)
Annotate a VCF file entryboolean
VcfAnnotatorChain. annotate(VcfEntry vcfEntry)
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Uses of VcfEntry in org.snpeff.snpEffect.commandLine
Methods in org.snpeff.snpEffect.commandLine that return types with arguments of type VcfEntry Modifier and Type Method Description java.util.List<VcfEntry>
SnpEffCmdEff. run(boolean createList)
Run according to command line optionsMethods in org.snpeff.snpEffect.commandLine with parameters of type VcfEntry Modifier and Type Method Description boolean
SnpEffCmdEff. annotate(VcfEntry vcfEntry)
Annotate a VCF entry -
Uses of VcfEntry in org.snpeff.snpEffect.commandLine.eff
Methods in org.snpeff.snpEffect.commandLine.eff with parameters of type VcfEntry Modifier and Type Method Description java.lang.String
WorkerEff. calculate(VcfEntry vcfEntry)
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Uses of VcfEntry in org.snpeff.snpEffect.testCases.integration
Methods in org.snpeff.snpEffect.testCases.integration that return types with arguments of type VcfEntry Modifier and Type Method Description java.util.List<VcfEntry>
TestCasesIntegrationBase. snpEffect(java.lang.String genome, java.lang.String vcfFile, java.lang.String[] otherArgs)
Calculate snp effect for an input VCF filejava.util.List<VcfEntry>
TestCasesIntegrationBase. snpEffect(java.lang.String genome, java.lang.String vcfFile, java.lang.String[] otherArgs, EffFormatVersion effFormatVersion)
Calculate snp effect for an input VCF file -
Uses of VcfEntry in org.snpeff.stats
Methods in org.snpeff.stats with parameters of type VcfEntry Modifier and Type Method Description void
AlleleCountStats. sample(VcfEntry vcfEntry)
Update MAC countersvoid
GenotypeStats. sample(VcfEntry vcfEntry)
Update countersvoid
HomHetStats. sample(VcfEntry vcfEntry)
Update Hom/Het countersvoid
TsTvStats. sample(VcfEntry vcfEntry)
Update Ts and Tv counters Only for SNPsvoid
VariantTypeStats. sample(VcfEntry vcfEntry)
Update MAC countersvoid
VcfStats. sample(VcfEntry vcfEntry)
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Uses of VcfEntry in org.snpeff.vcf
Fields in org.snpeff.vcf declared as VcfEntry Modifier and Type Field Description protected VcfEntry
VariantVcfEntry. vcfEntry
Methods in org.snpeff.vcf that return VcfEntry Modifier and Type Method Description VcfEntry
VariantVcfEntry. getVcfEntry()
VcfEntry
VcfGenotype. getVcfEntry()
VcfEntry
VcfLof. getVcfEntry()
VcfEntry
VcfEntry. uncompressGenotypes()
Uncompress VCF entry having genotypes in "HO,HE,NA" fieldsMethods in org.snpeff.vcf with parameters of type VcfEntry Modifier and Type Method Description static java.util.Collection<VariantVcfEntry>
VariantVcfEntry. factory(VcfEntry vcfEntry)
Create a collection of allstatic java.util.List<VcfConsequence>
VcfConsequence. parse(VcfConsequenceHeader vcfConsequenceHeader, VcfEntry ve)
Constructors in org.snpeff.vcf with parameters of type VcfEntry Constructor Description VariantVcfEntry(Variant variant, VcfEntry vcfEntry)
VcfGenotype(VcfEntry vcfEntry, java.lang.String format, java.lang.String values)
VcfLof(VcfEntry vcfEntry, java.lang.String lofStr)
VcfNmd(VcfEntry vcfEntry, java.lang.String nmdStr)
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