Index (de.charite.compbio:jannovar-htsjdk 0.38 API)

A B C D E F G H I K L M N O P R S T V X
All Classes All Packages

A

AD - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender: Constant for autosomal dominant
addCompatibleMode(SubModeOfInheritance) - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
addHeaders(VCFHeader) - Method in class de.charite.compbio.jannovar.htsjdk.VariantEffectHeaderExtender: Add header entries.
annotateRecord(VariantContext) - Method in class de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator: Annotate VariantContext with compatibility for Mendelian inheritance
annotateRecords(List<VariantContext>) - Method in class de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator: Annotate List of VariantContext objects
annotateVariantContext(VariantContext) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator: Annotate variant vc and return annoated variant
applyAnnotations(VariantContext, List<VariantAnnotations>) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator: Write annotations from annos to vc l
applySVAnnotations(VariantContext, List<SVAnnotations>) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator
AR - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender: Constant for autosomal recessive
AR_COMP_HET - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender: Constant for autosomal recessive compound het.
AR_HOM_ALT - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender: Constant for autosomal recessive hom.

B

buildAnnotations(VariantContext) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator: Given a VariantContext, generate one VariantAnnotations for each alternative allele.
buildErrorAnnotations(GenomeVariant) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator
buildGenomeVariant(VariantContext, int) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator: Build a GenomeVariant from a VariantContext object.
buildSVAnnotations(VariantContext) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator
buildSVErrorAnnotations(SVGenomeVariant) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator
buildSVGenomeVariant(VariantContext) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

C

CannotAnnotateMendelianInheritance - Exception in de.charite.compbio.jannovar.mendel.bridge: Raised in the case of problems with annotating Mendelian inheritance
CannotAnnotateMendelianInheritance(String) - Constructor for exception de.charite.compbio.jannovar.mendel.bridge.CannotAnnotateMendelianInheritance
CannotAnnotateMendelianInheritance(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.mendel.bridge.CannotAnnotateMendelianInheritance
CannotTranslateHGVSVariant - Exception in de.charite.compbio.jannovar.hgvs.bridge: Helper class thrown on problems with translating HGVSVariant to GenomeVariant.
CannotTranslateHGVSVariant() - Constructor for exception de.charite.compbio.jannovar.hgvs.bridge.CannotTranslateHGVSVariant
CannotTranslateHGVSVariant(String) - Constructor for exception de.charite.compbio.jannovar.hgvs.bridge.CannotTranslateHGVSVariant
CannotTranslateHGVSVariant(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.hgvs.bridge.CannotTranslateHGVSVariant
close() - Method in class de.charite.compbio.jannovar.mendel.filter.ConsumerProcessor
close() - Method in class de.charite.compbio.jannovar.mendel.filter.CoordinateSortingChecker
close() - Method in class de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor
close() - Method in interface de.charite.compbio.jannovar.mendel.filter.VariantContextProcessor: Mark processing as done, no more variants will come in.
computeCompatibleInheritanceModes(List<VariantContext>) - Method in class de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator: Compute compatible modes of inheritance for a list of VariantContext objects
computeCompatibleInheritanceSubModes(List<VariantContext>) - Method in class de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator: Compute compatible modes of inheritance for a list of VariantContext objects
construct(SAMSequenceDictionary) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionListFactoryFromSAMSequenceDictionary
ConsumerProcessor - Class in de.charite.compbio.jannovar.mendel.filter: Call a function for each variant put into the pipeline step
ConsumerProcessor(Consumer<VariantContext>) - Constructor for class de.charite.compbio.jannovar.mendel.filter.ConsumerProcessor
CoordinateSortingChecker - Class in de.charite.compbio.jannovar.mendel.filter: Check that the VCF file is sorted by coordinate
CoordinateSortingChecker(VariantContextProcessor) - Constructor for class de.charite.compbio.jannovar.mendel.filter.CoordinateSortingChecker: Initialize the checker

D

de.charite.compbio.jannovar.hgvs.bridge - package de.charite.compbio.jannovar.hgvs.bridge
de.charite.compbio.jannovar.htsjdk - package de.charite.compbio.jannovar.htsjdk
de.charite.compbio.jannovar.mendel.bridge - package de.charite.compbio.jannovar.mendel.bridge
de.charite.compbio.jannovar.mendel.filter - package de.charite.compbio.jannovar.mendel.filter
de.charite.compbio.jannovar.progress - package de.charite.compbio.jannovar.progress
decrement() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
dispatchAnnotateVariantContext(VariantContext) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator: Dispatch annotation of VariantContext depending on whether it describes a sequence or a structural variant.
done() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

E

equals(Object) - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
equals(Object) - Method in class de.charite.compbio.jannovar.progress.GenomeRegion
equals(Object) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList
extendHeader(VCFHeader) - Method in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender
extendHeader(VCFHeader, String) - Method in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender
extendHeader(VCFHeader, String) - Method in class de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor: Appropriately extend VCFHeader
extendHeaderFields(VCFHeader) - Static method in class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper: Extend a VCFHeader with the given fields.

F

FILTER_EFFECT_OFF_EXOME - Static variable in class de.charite.compbio.jannovar.htsjdk.VariantEffectHeaderExtender
formatDuration(long) - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

G

GeneWiseMendelianAnnotationProcessor - Class in de.charite.compbio.jannovar.mendel.filter: Process VariantContext objects and annotate them with mendelian inheritance compatibility
GeneWiseMendelianAnnotationProcessor(Pedigree, JannovarData, Consumer<VariantContext>, boolean) - Constructor for class de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor: Construct processor with the path to the PED file to use
GenomeRegion - Class in de.charite.compbio.jannovar.progress: A region on a genome, can be a whole chromosome
GenomeRegion(String, int, int) - Constructor for class de.charite.compbio.jannovar.progress.GenomeRegion
GenomeRegionList - Class in de.charite.compbio.jannovar.progress: A list of GenomeRegion objects
GenomeRegionList(Iterable<GenomeRegion>) - Constructor for class de.charite.compbio.jannovar.progress.GenomeRegionList
GenomeRegionListFactoryFromSAMSequenceDictionary - Class in de.charite.compbio.jannovar.progress: Construct GenomeRegionList from a SAMSequenceDictionary
GenomeRegionListFactoryFromSAMSequenceDictionary() - Constructor for class de.charite.compbio.jannovar.progress.GenomeRegionListFactoryFromSAMSequenceDictionary
GenomeRegionSequenceExtractor - Class in de.charite.compbio.jannovar.htsjdk: Extract sequence for a GenomeInterval from a IndexedFastaSequenceFile.
GenomeRegionSequenceExtractor(JannovarData, IndexedFastaSequenceFile) - Constructor for class de.charite.compbio.jannovar.htsjdk.GenomeRegionSequenceExtractor
getAnnotationMessage() - Method in exception de.charite.compbio.jannovar.htsjdk.InvalidCoordinatesException
getAnnotator() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator
getBeginPos() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion
getChromosomeMap() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator
getCompatibleModes() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
getContig() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion
getCounter() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
getCurrentVC() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter
getEndPos() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion
getGenomeRegion(String) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList
getGenomeRegions() - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList
getNameToRegion() - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList
getNumProcessed() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter
getOptions() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator
getRefDict() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator
getVariantContext() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

H

hashCode() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
hashCode() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion
hashCode() - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList

I

increment() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
InvalidBreakendDescriptionException - Exception in de.charite.compbio.jannovar.htsjdk: Thrown in VariantContextAnnotator in the case of invalid breakend descriptions.
InvalidBreakendDescriptionException(String) - Constructor for exception de.charite.compbio.jannovar.htsjdk.InvalidBreakendDescriptionException
InvalidBreakendDescriptionException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.htsjdk.InvalidBreakendDescriptionException
InvalidCoordinatesException - Exception in de.charite.compbio.jannovar.htsjdk: Thrown in VariantContextAnnotator in the case of invalid positions (unknown chromsomes).
InvalidCoordinatesException(AnnotationMessage) - Constructor for exception de.charite.compbio.jannovar.htsjdk.InvalidCoordinatesException
InvalidCoordinatesException(String, AnnotationMessage) - Constructor for exception de.charite.compbio.jannovar.htsjdk.InvalidCoordinatesException
InvalidCoordinatesException(String, Throwable, AnnotationMessage) - Constructor for exception de.charite.compbio.jannovar.htsjdk.InvalidCoordinatesException
isEscapeAnnField() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options
isNt3PrimeShifting() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options
isOffTargetFilterEnabled() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options
isOffTargetFilterIntronicSpliceIsOffTarget() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options
isOffTargetFilterUtrIsOffTarget() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options
isOneAnnotationOnly() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options

K

key() - Static method in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender
key(String) - Static method in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender
keySub() - Static method in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender
keySub(String) - Static method in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender

L

length() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion
lengthUpTo(String, int) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList
load(GenomeInterval) - Method in class de.charite.compbio.jannovar.htsjdk.GenomeRegionSequenceExtractor: Load sequence from the given region from GenomeRegionSequenceExtractor.indexedFile

M

MendelVCFHeaderExtender - Class in de.charite.compbio.jannovar.mendel.bridge: Helper class for extending VCF header for mendelian inheritance annotation
MendelVCFHeaderExtender() - Constructor for class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender
MissingEndInfoField - Exception in de.charite.compbio.jannovar.htsjdk: Thrown in VariantContextAnnotator in the case missing END in the INFO field.
MissingEndInfoField(String) - Constructor for exception de.charite.compbio.jannovar.htsjdk.MissingEndInfoField
MissingEndInfoField(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.htsjdk.MissingEndInfoField
MissingSVTypeInfoField - Exception in de.charite.compbio.jannovar.htsjdk: Thrown in VariantContextAnnotator in the case missing SVTYPE in the INFO field.
MissingSVTypeInfoField(String) - Constructor for exception de.charite.compbio.jannovar.htsjdk.MissingSVTypeInfoField
MissingSVTypeInfoField(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.htsjdk.MissingSVTypeInfoField
MixingSmallAndSVAlleles - Exception in de.charite.compbio.jannovar.htsjdk: Thrown in VariantContextAnnotator in the case of mixing small and SV alleles.
MixingSmallAndSVAlleles(String) - Constructor for exception de.charite.compbio.jannovar.htsjdk.MixingSmallAndSVAlleles
MixingSmallAndSVAlleles(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.htsjdk.MixingSmallAndSVAlleles
MT - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender: Constant for mitochondrial
MultipleSVAlleles - Exception in de.charite.compbio.jannovar.htsjdk: Thrown in VariantContextAnnotator in the case of having more than one SV allele in a variant.
MultipleSVAlleles(String) - Constructor for exception de.charite.compbio.jannovar.htsjdk.MultipleSVAlleles
MultipleSVAlleles(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.htsjdk.MultipleSVAlleles

N

NucleotideChangeToGenomeVariantTranslationImplBase - Class in de.charite.compbio.jannovar.hgvs.bridge
NucleotideChangeToGenomeVariantTranslationImplBase(GenomeRegionSequenceExtractor) - Constructor for class de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslationImplBase
NucleotideChangeToGenomeVariantTranslator - Class in de.charite.compbio.jannovar.hgvs.bridge: Helper for converting a NucleotideChange to a GenomeVariant.
NucleotideChangeToGenomeVariantTranslator(JannovarData, IndexedFastaSequenceFile) - Constructor for class de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslator
NucleotideLocationConverter - Class in de.charite.compbio.jannovar.hgvs.bridge: Helper class for converting NucleotidePointLocations and NucleotideRanges to GenomePositions and GenomeIntervals.
NucleotideLocationConverter() - Constructor for class de.charite.compbio.jannovar.hgvs.bridge.NucleotideLocationConverter

O

openVariantContextWriter(VCFHeader, OutputStream, Collection<VCFHeaderLine>) - Static method in class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper: Return a new VariantContextWriter that uses the header from reader but has the header extended header through VariantContextWriterConstructionHelper.extendHeaderFields(htsjdk.variant.vcf.VCFHeader).
openVariantContextWriter(VCFHeader, String) - Static method in class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper: Forward to #openVariantContextWriter(VCFHeader, String, InfoFields, Collection).
openVariantContextWriter(VCFHeader, String, Collection<VCFHeaderLine>) - Static method in class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper: Return a new VariantContextWriter that uses the header from reader but has the header extended header through VariantContextWriterConstructionHelper.extendHeaderFields(htsjdk.variant.vcf.VCFHeader).
openVariantContextWriter(VCFHeader, String, Collection<VCFHeaderLine>, boolean) - Static method in class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper: Return a new VariantContextWriter that uses the header from reader but has the header extended header through VariantContextWriterConstructionHelper.extendHeaderFields(htsjdk.variant.vcf.VCFHeader).
Options() - Constructor for class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options: Constructor
Options(boolean, AminoAcidCode, boolean, boolean, boolean, boolean, boolean) - Constructor for class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options: constructor using fields

P

print() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter
printHeader() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter
ProgressReporter - Class in de.charite.compbio.jannovar.progress: Helper for displaying progress
ProgressReporter(GenomeRegionList, int) - Constructor for class de.charite.compbio.jannovar.progress.ProgressReporter
put(VariantContext) - Method in class de.charite.compbio.jannovar.mendel.filter.ConsumerProcessor
put(VariantContext) - Method in class de.charite.compbio.jannovar.mendel.filter.CoordinateSortingChecker
put(VariantContext) - Method in class de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor
put(VariantContext) - Method in interface de.charite.compbio.jannovar.mendel.filter.VariantContextProcessor: Put a Variant Context into the filter.
putErrorAnnotation(VariantContext, Set<AnnotationMessage>) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator: Put error annotation messages to a VariantContext into the ANN field in the INFO column.

R

run() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

S

setCompatibleModes(TreeSet<SubModeOfInheritance>) - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
setCounter(int) - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
setCurrentVC(VariantContext) - Method in class de.charite.compbio.jannovar.progress.ProgressReporter
setGenomeRegions(ImmutableList<GenomeRegion>) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList
setNameToRegion(ImmutableMap<String, GenomeRegion>) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList
setVariantContext(VariantContext) - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
start() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

T

toString() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
toString() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion
toString() - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList
totalLength() - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList
translateNucleotidePointLocation(TranscriptModel, NucleotidePointLocation, SequenceType) - Method in class de.charite.compbio.jannovar.hgvs.bridge.NucleotideLocationConverter: Convert NucleotidePointLocation on a TranscriptModel to a GenomePosition
translateNucleotideRange(TranscriptModel, NucleotideRange, SequenceType) - Method in class de.charite.compbio.jannovar.hgvs.bridge.NucleotideLocationConverter: Convert NucleotideRange on a TranscriptModel to a GenomePosition
translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant) - Method in class de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslator: Shortcut to NucleotideChangeToGenomeVariantTranslator.translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant, boolean) with using true for the second parameter.
translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant, boolean) - Method in class de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslator: Translate single-change SingleAlleleNucleotideVariant into a GenomeVariant

V

VariantContextAnnotator - Class in de.charite.compbio.jannovar.htsjdk: Helper class for generating VariantAnnotations objects from VariantContexts.
VariantContextAnnotator(ReferenceDictionary, ImmutableMap<Integer, Chromosome>) - Constructor for class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator: Construct annotator with default options.
VariantContextAnnotator(ReferenceDictionary, ImmutableMap<Integer, Chromosome>, VariantContextAnnotator.Options) - Constructor for class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator: Construct Annotator.
VariantContextAnnotator.Options - Class in de.charite.compbio.jannovar.htsjdk: Options class for VariantContextAnnotator.
VariantContextCounter - Class in de.charite.compbio.jannovar.mendel.filter: A VariantContext with an integer counter and set of compatible modes
VariantContextCounter(VariantContext) - Constructor for class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
VariantContextCounter(VariantContext, int) - Constructor for class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
VariantContextFilterException - Exception in de.charite.compbio.jannovar.mendel.filter: Thrown on problems during the filtration.
VariantContextFilterException(String) - Constructor for exception de.charite.compbio.jannovar.mendel.filter.VariantContextFilterException
VariantContextFilterException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.mendel.filter.VariantContextFilterException
VariantContextMendelianAnnotator - Class in de.charite.compbio.jannovar.mendel.bridge: Helper class for annotating one VariantContext or a Collection thereof for compatibility with Mendelian inheritance
VariantContextMendelianAnnotator(Pedigree, boolean, boolean) - Constructor for class de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator
VariantContextProcessor - Interface in de.charite.compbio.jannovar.mendel.filter: Step in a VariantContext processing pipeline, designed as a sink
VariantContextWriterConstructionHelper - Class in de.charite.compbio.jannovar.htsjdk: Helper for creating a VariantContextWriter from a OutputStream.
VariantContextWriterConstructionHelper() - Constructor for class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper
VariantEffectHeaderExtender - Class in de.charite.compbio.jannovar.htsjdk: Code for adding headers for variant effect to VCF files
VariantEffectHeaderExtender() - Constructor for class de.charite.compbio.jannovar.htsjdk.VariantEffectHeaderExtender

X

XD - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender: Constant for X dominant
XR - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender: Constant for X recessive
XR_COMP_HET - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender: Constant for X recessive compound het.
XR_HOM_ALT - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender: Constant for X recessive hom.

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