Uses of Class
org.snpeff.vcf.VcfEntry

Packages that use VcfEntry

Package	Description
org.snpeff.fileIterator
org.snpeff.outputFormatter
org.snpeff.snpEffect
org.snpeff.snpEffect.commandLine
org.snpeff.snpEffect.testCases.integration
org.snpeff.stats
org.snpeff.vcf

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 file
protected 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)

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 field

Constructor 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 entry
boolean	VcfAnnotatorChain.annotate(VcfEntry vcfEntry)

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 options

Methods 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.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 file
java.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 counters
void	GenotypeStats.sample(VcfEntry vcfEntry)	Update counters
void	HomHetStats.sample(VcfEntry vcfEntry)	Update Hom/Het counters
void	TsTvStats.sample(VcfEntry vcfEntry)	Update Ts and Tv counters Only for SNPs
void	VariantTypeStats.sample(VcfEntry vcfEntry)	Update MAC counters
void	VcfStats.sample(VcfEntry vcfEntry)

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" fields

Methods in org.snpeff.vcf with parameters of type VcfEntry

Modifier and Type	Method	Description
boolean	Pedigree.anyBackToRef(VcfEntry vcfEntry)	Are there any "back to reference" cancer variant
java.util.Set<Tuple<java.lang.Integer,java.lang.Integer>>	Pedigree.compareCancerGenotypes(VcfEntry vcfEntry)	Analyze which comparisons to make in cancer genomes
static java.util.Collection<VariantVcfEntry>	VariantVcfEntry.factory(VcfEntry vcfEntry)	Create a collection of all
static 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)