Uses of Class
org.snpeff.vcf.VcfEntry
Packages that use VcfEntry
Package
Description
-
Uses of VcfEntry in org.snpeff.fileIterator
Methods in org.snpeff.fileIterator that return VcfEntryModifier and TypeMethodDescriptionVcfFileIterator.parseVcfLine
(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 -
Uses of VcfEntry in org.snpeff.outputFormatter
Methods in org.snpeff.outputFormatter with parameters of type VcfEntryModifier and TypeMethodDescriptionprotected void
Add effects to INFO fieldConstructor parameters in org.snpeff.outputFormatter with type arguments of type VcfEntryModifierConstructorDescriptionVcfOutputFormatter
(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 -
Uses of VcfEntry in org.snpeff.snpEffect.commandLine
Methods in org.snpeff.snpEffect.commandLine that return types with arguments of type VcfEntryModifier and TypeMethodDescriptionSnpEffCmdEff.run
(boolean createList) Run according to command line optionsMethods in org.snpeff.snpEffect.commandLine with parameters of type VcfEntry -
Uses of VcfEntry in org.snpeff.stats
Methods in org.snpeff.stats with parameters of type VcfEntryModifier and TypeMethodDescriptionvoid
Update MAC countersvoid
Update countersvoid
Update Hom/Het countersvoid
Update Ts and Tv counters Only for SNPsvoid
Update MAC countersvoid
-
Uses of VcfEntry in org.snpeff.vcf
Fields in org.snpeff.vcf declared as VcfEntryMethods in org.snpeff.vcf that return VcfEntryModifier and TypeMethodDescriptionVariantVcfEntry.getVcfEntry()
VcfGenotype.getVcfEntry()
VcfLof.getVcfEntry()
VcfEntry.uncompressGenotypes()
Uncompress VCF entry having genotypes in "HO,HE,NA" fieldsMethods in org.snpeff.vcf with parameters of type VcfEntryModifier and TypeMethodDescriptionboolean
Pedigree.anyBackToRef
(VcfEntry vcfEntry) Are there any "back to reference" cancer variantPedigree.compareCancerGenotypes
(VcfEntry vcfEntry) Analyze which comparisons to make in cancer genomesstatic Collection
<VariantVcfEntry> Create a collection of all invalid input: '<'Variant, VcfEntry>static List
<VcfConsequence> VcfConsequence.parse
(VcfConsequenceHeader vcfConsequenceHeader, VcfEntry ve) Constructors in org.snpeff.vcf with parameters of type VcfEntry