A B C D E F G H I K L M N O P Q R S T V W

A

accession - Variable in class org.bdgenomics.formats.avro.Dbxref

Deprecated.

accession - Variable in class org.bdgenomics.formats.avro.OntologyTerm

Deprecated.

aliases - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

Alignment - Class in org.bdgenomics.formats.avro

Alignment() - Constructor for class org.bdgenomics.formats.avro.Alignment

Default constructor.

Alignment(String, Long, Long, Long, Integer, String, String, String, String, String, Integer, Integer, Boolean, Boolean, Boolean, Boolean, Boolean, Boolean, Boolean, Boolean, Boolean, Boolean, Boolean, String, String, String, String, Long, String, Long, Integer, String) - Constructor for class org.bdgenomics.formats.avro.Alignment

All-args constructor.

Alignment.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for Alignment instances.

alignments - Variable in class org.bdgenomics.formats.avro.Fragment

Deprecated.

alleleCount - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

alleleFrequency - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

alleles - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

Alphabet - Enum in org.bdgenomics.formats.avro

alphabet - Variable in class org.bdgenomics.formats.avro.Read

Deprecated.

alphabet - Variable in class org.bdgenomics.formats.avro.Sequence

Deprecated.

alphabet - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

alternateAllele - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

alternateAllele - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

alternateReadDepth - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

ancestralAllele - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

annotation - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

assembly - Variable in class org.bdgenomics.formats.avro.Reference

Deprecated.

attributes - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

attributes - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

attributes - Variable in class org.bdgenomics.formats.avro.Read

Deprecated.

attributes - Variable in class org.bdgenomics.formats.avro.Sample

Deprecated.

attributes - Variable in class org.bdgenomics.formats.avro.Sequence

Deprecated.

attributes - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

attributes - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

attributes - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

B

baseQRankSum - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

basesTrimmedFromEnd - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

basesTrimmedFromStart - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

BDG - Interface in org.bdgenomics.formats.avro

BDG.Callback - Interface in org.bdgenomics.formats.avro

biotype - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

build() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

build() - Method in class org.bdgenomics.formats.avro.Dbxref.Builder

build() - Method in class org.bdgenomics.formats.avro.Feature.Builder

build() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

build() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

build() - Method in class org.bdgenomics.formats.avro.OntologyTerm.Builder

build() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

build() - Method in class org.bdgenomics.formats.avro.Read.Builder

build() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

build() - Method in class org.bdgenomics.formats.avro.Reference.Builder

build() - Method in class org.bdgenomics.formats.avro.Sample.Builder

build() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

build() - Method in class org.bdgenomics.formats.avro.Slice.Builder

build() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

build() - Method in class org.bdgenomics.formats.avro.Variant.Builder

build() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

build() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

C

cdnaLength - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

cdnaPosition - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

cdsLength - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

cdsPosition - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

cigar - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

cigar - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

circular - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

clearAccession() - Method in class org.bdgenomics.formats.avro.Dbxref.Builder

Clears the value of the 'accession' field.

clearAccession() - Method in class org.bdgenomics.formats.avro.OntologyTerm.Builder

Clears the value of the 'accession' field.

clearAliases() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'aliases' field.

clearAlignments() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Clears the value of the 'alignments' field.

clearAlleleCount() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'alleleCount' field.

clearAlleleFrequency() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'alleleFrequency' field.

clearAlleles() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'alleles' field.

clearAlphabet() - Method in class org.bdgenomics.formats.avro.Read.Builder

Clears the value of the 'alphabet' field.

clearAlphabet() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Clears the value of the 'alphabet' field.

clearAlphabet() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'alphabet' field.

clearAlternateAllele() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'alternateAllele' field.

clearAlternateAllele() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'alternateAllele' field.

clearAlternateReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'alternateReadDepth' field.

clearAncestralAllele() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'ancestralAllele' field.

clearAnnotation() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'annotation' field.

clearAssembly() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Clears the value of the 'assembly' field.

clearAttributes() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'attributes' field.

clearAttributes() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'attributes' field.

clearAttributes() - Method in class org.bdgenomics.formats.avro.Read.Builder

Clears the value of the 'attributes' field.

clearAttributes() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Clears the value of the 'attributes' field.

clearAttributes() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Clears the value of the 'attributes' field.

clearAttributes() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'attributes' field.

clearAttributes() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'attributes' field.

clearAttributes() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'attributes' field.

clearBaseQRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'baseQRankSum' field.

clearBasesTrimmedFromEnd() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'basesTrimmedFromEnd' field.

clearBasesTrimmedFromStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'basesTrimmedFromStart' field.

clearBiotype() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'biotype' field.

clearCdnaLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'cdnaLength' field.

clearCdnaPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'cdnaPosition' field.

clearCdsLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'cdsLength' field.

clearCdsPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'cdsPosition' field.

clearCigar() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'cigar' field.

clearCigar() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'cigar' field.

clearCircular() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'circular' field.

clearCommandLine() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Clears the value of the 'commandLine' field.

clearCulprit() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'culprit' field.

clearDb() - Method in class org.bdgenomics.formats.avro.Dbxref.Builder

Clears the value of the 'db' field.

clearDb() - Method in class org.bdgenomics.formats.avro.OntologyTerm.Builder

Clears the value of the 'db' field.

clearDbSnp() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'dbSnp' field.

clearDbxrefs() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'dbxrefs' field.

clearDerivesFrom() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'derivesFrom' field.

clearDescription() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Clears the value of the 'description' field.

clearDescription() - Method in class org.bdgenomics.formats.avro.Read.Builder

Clears the value of the 'description' field.

clearDescription() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'description' field.

clearDescription() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Clears the value of the 'description' field.

clearDescription() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'description' field.

clearDistance() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'distance' field.

clearDownsampled() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'downsampled' field.

clearDuplicateRead() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'duplicateRead' field.

clearEffects() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'effects' field.

clearEnd() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'end' field.

clearEnd() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'end' field.

clearEnd() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'end' field.

clearEnd() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'end' field.

clearEnd() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'end' field.

clearExonId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'exonId' field.

clearExpectedAlleleDosage() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'expectedAlleleDosage' field.

clearFailedVendorQualityChecks() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'failedVendorQualityChecks' field.

clearFeatureId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'featureId' field.

clearFeatureId() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'featureId' field.

clearFeatureType() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'featureType' field.

clearFeatureType() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'featureType' field.

clearFiltersApplied() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'filtersApplied' field.

clearFiltersApplied() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'filtersApplied' field.

clearFiltersFailed() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'filtersFailed' field.

clearFiltersFailed() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'filtersFailed' field.

clearFiltersPassed() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'filtersPassed' field.

clearFiltersPassed() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'filtersPassed' field.

clearFisherStrandBiasPValue() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'fisherStrandBiasPValue' field.

clearFlowOrder() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'flowOrder' field.

clearForwardReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'forwardReadDepth' field.

clearFrame() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'frame' field.

clearGap() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'gap' field.

clearGeneId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'geneId' field.

clearGeneId() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'geneId' field.

clearGeneName() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'geneName' field.

clearGenomicHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'genomicHgvs' field.

clearGenotypeLikelihoods() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'genotypeLikelihoods' field.

clearGenotypePosteriors() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'genotypePosteriors' field.

clearGenotypePriors() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'genotypePriors' field.

clearGenotypeQuality() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'genotypeQuality' field.

clearHapMap2() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'hapMap2' field.

clearHapMap3() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'hapMap3' field.

clearId() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Clears the value of the 'id' field.

clearId() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'id' field.

clearId() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Clears the value of the 'id' field.

clearIndex() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Clears the value of the 'index' field.

clearIndex() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'index' field.

clearInsertSize() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'insertSize' field.

clearInsertSize() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Clears the value of the 'insertSize' field.

clearKeySequence() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'keySequence' field.

clearLength() - Method in class org.bdgenomics.formats.avro.Read.Builder

Clears the value of the 'length' field.

clearLength() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Clears the value of the 'length' field.

clearLength() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Clears the value of the 'length' field.

clearLength() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'length' field.

clearLibrary() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'library' field.

clearMappingQuality() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'mappingQuality' field.

clearMapq0Reads() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'mapq0Reads' field.

clearMateAlignmentStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'mateAlignmentStart' field.

clearMateMapped() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'mateMapped' field.

clearMateNegativeStrand() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'mateNegativeStrand' field.

clearMateReferenceName() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'mateReferenceName' field.

clearMd5() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Clears the value of the 'md5' field.

clearMessages() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'messages' field.

clearMinReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'minReadDepth' field.

clearMismatchingPositions() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'mismatchingPositions' field.

clearMqRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'mqRankSum' field.

clearName() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'name' field.

clearName() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Clears the value of the 'name' field.

clearName() - Method in class org.bdgenomics.formats.avro.Read.Builder

Clears the value of the 'name' field.

clearName() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Clears the value of the 'name' field.

clearName() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Clears the value of the 'name' field.

clearName() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Clears the value of the 'name' field.

clearName() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'name' field.

clearNames() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'names' field.

clearNonReferenceLikelihoods() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'nonReferenceLikelihoods' field.

clearNotes() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'notes' field.

clearOntologyTerms() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'ontologyTerms' field.

clearOriginalCigar() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'originalCigar' field.

clearOriginalQualityScores() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'originalQualityScores' field.

clearOriginalStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'originalStart' field.

clearParentIds() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'parentIds' field.

clearPhase() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'phase' field.

clearPhased() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'phased' field.

clearPhaseQuality() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'phaseQuality' field.

clearPhaseSetId() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'phaseSetId' field.

clearPlatform() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'platform' field.

clearPlatformModel() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'platformModel' field.

clearPlatformUnit() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'platformUnit' field.

clearPredictedMedianInsertSize() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'predictedMedianInsertSize' field.

clearPreviousId() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Clears the value of the 'previousId' field.

clearPrimaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'primaryAlignment' field.

clearProcessingDescription() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'processingDescription' field.

clearProcessingSteps() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'processingSteps' field.

clearProcessingSteps() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Clears the value of the 'processingSteps' field.

clearProgramName() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Clears the value of the 'programName' field.

clearProperPair() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'properPair' field.

clearProteinHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'proteinHgvs' field.

clearProteinLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'proteinLength' field.

clearProteinPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'proteinPosition' field.

clearQuality() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'quality' field.

clearQualityScores() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'qualityScores' field.

clearQualityScores() - Method in class org.bdgenomics.formats.avro.Read.Builder

Clears the value of the 'qualityScores' field.

clearRank() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'rank' field.

clearReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'readDepth' field.

clearReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'readDepth' field.

clearReadGroupId() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'readGroupId' field.

clearReadGroupId() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Clears the value of the 'readGroupId' field.

clearReadGroupSampleId() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'readGroupSampleId' field.

clearReadInFragment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'readInFragment' field.

clearReadMapped() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'readMapped' field.

clearReadName() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'readName' field.

clearReadNegativeStrand() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'readNegativeStrand' field.

clearReadPaired() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'readPaired' field.

clearReadPositionRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'readPositionRankSum' field.

clearReferenceAllele() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'referenceAllele' field.

clearReferenceForwardReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'referenceForwardReadDepth' field.

clearReferenceName() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'referenceName' field.

clearReferenceName() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'referenceName' field.

clearReferenceName() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'referenceName' field.

clearReferenceName() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'referenceName' field.

clearReferenceReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'referenceReadDepth' field.

clearReferenceReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'referenceReadDepth' field.

clearReferenceReverseReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'referenceReverseReadDepth' field.

clearReverseReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'reverseReadDepth' field.

clearRmsMapQ() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'rmsMapQ' field.

clearRunDateEpoch() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'runDateEpoch' field.

clearSampleDescription() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'sampleDescription' field.

clearSampleId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'sampleId' field.

clearSampleId() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'sampleId' field.

clearSampleId() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'sampleId' field.

clearScore() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'score' field.

clearSecondaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'secondaryAlignment' field.

clearSequence() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'sequence' field.

clearSequence() - Method in class org.bdgenomics.formats.avro.Read.Builder

Clears the value of the 'sequence' field.

clearSequence() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Clears the value of the 'sequence' field.

clearSequence() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'sequence' field.

clearSequencingCenter() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Clears the value of the 'sequencingCenter' field.

clearSlices() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'slices' field.

clearSomatic() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'somatic' field.

clearSource() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'source' field.

clearSourceAccessions() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Clears the value of the 'sourceAccessions' field.

clearSourceUri() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Clears the value of the 'sourceUri' field.

clearSpecies() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Clears the value of the 'species' field.

clearSplitFromMultiAllelic() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'splitFromMultiAllelic' field.

clearSplitFromMultiAllelic() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'splitFromMultiAllelic' field.

clearStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'start' field.

clearStart() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'start' field.

clearStart() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'start' field.

clearStart() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'start' field.

clearStart() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Clears the value of the 'start' field.

clearStrand() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'strand' field.

clearStrand() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'strand' field.

clearStrandBiasComponents() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'strandBiasComponents' field.

clearSupplementaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Clears the value of the 'supplementaryAlignment' field.

clearTarget() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'target' field.

clearThousandGenomes() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'thousandGenomes' field.

clearTotal() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'total' field.

clearTotalLength() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Clears the value of the 'totalLength' field.

clearTranscriptEffects() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'transcriptEffects' field.

clearTranscriptHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Clears the value of the 'transcriptHgvs' field.

clearTranscriptId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Clears the value of the 'transcriptId' field.

clearValidated() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Clears the value of the 'validated' field.

clearVariant() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'variant' field.

clearVariantCallingAnnotations() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Clears the value of the 'variantCallingAnnotations' field.

clearVersion() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Clears the value of the 'version' field.

clearVqslod() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Clears the value of the 'vqslod' field.

commandLine - Variable in class org.bdgenomics.formats.avro.ProcessingStep

Deprecated.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.Alignment

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.Dbxref

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.Feature

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.Fragment

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.Genotype

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.OntologyTerm

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.ProcessingStep

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.Read

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.ReadGroup

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.Reference

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.Sample

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.Sequence

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.Slice

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.TranscriptEffect

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.Variant

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.VariantAnnotation

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

createDecoder(SchemaStore) - Static method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.

culprit - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

D

db - Variable in class org.bdgenomics.formats.avro.Dbxref

Deprecated.

db - Variable in class org.bdgenomics.formats.avro.OntologyTerm

Deprecated.

dbSnp - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

Dbxref - Class in org.bdgenomics.formats.avro

Dbxref() - Constructor for class org.bdgenomics.formats.avro.Dbxref

Default constructor.

Dbxref(String, String) - Constructor for class org.bdgenomics.formats.avro.Dbxref

All-args constructor.

Dbxref.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for Dbxref instances.

dbxrefs - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

derivesFrom - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

description - Variable in class org.bdgenomics.formats.avro.ProcessingStep

Deprecated.

description - Variable in class org.bdgenomics.formats.avro.Read

Deprecated.

description - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

description - Variable in class org.bdgenomics.formats.avro.Sequence

Deprecated.

description - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

distance - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

downsampled - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

duplicateRead - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

E

effects - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

end - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

end - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

end - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

end - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

end - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

exonId - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

expectedAlleleDosage - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

F

failedVendorQualityChecks - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

Feature - Class in org.bdgenomics.formats.avro

Feature() - Constructor for class org.bdgenomics.formats.avro.Feature

Default constructor.

Feature(String, String, String, String, String, String, Long, Long, Strand, Integer, Integer, Double, String, String, String, List<String>, List<String>, String, String, String, List<String>, List<Dbxref>, List<OntologyTerm>, Boolean, Map<String, String>) - Constructor for class org.bdgenomics.formats.avro.Feature

All-args constructor.

Feature.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for Feature instances.

featureId - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

featureId - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

featureType - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

featureType - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

filtersApplied - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

filtersApplied - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

filtersFailed - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

filtersFailed - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

filtersPassed - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

filtersPassed - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

fisherStrandBiasPValue - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

flowOrder - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

forwardReadDepth - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

Fragment - Class in org.bdgenomics.formats.avro

Fragment() - Constructor for class org.bdgenomics.formats.avro.Fragment

Default constructor.

Fragment(String, String, Integer, List<Alignment>) - Constructor for class org.bdgenomics.formats.avro.Fragment

All-args constructor.

Fragment.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for Fragment instances.

frame - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.Alignment

Deserializes a Alignment from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.Dbxref

Deserializes a Dbxref from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.Feature

Deserializes a Feature from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.Fragment

Deserializes a Fragment from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.Genotype

Deserializes a Genotype from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.OntologyTerm

Deserializes a OntologyTerm from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.ProcessingStep

Deserializes a ProcessingStep from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.Read

Deserializes a Read from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.ReadGroup

Deserializes a ReadGroup from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.Reference

Deserializes a Reference from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.Sample

Deserializes a Sample from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.Sequence

Deserializes a Sequence from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.Slice

Deserializes a Slice from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.TranscriptEffect

Deserializes a TranscriptEffect from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.Variant

Deserializes a Variant from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.VariantAnnotation

Deserializes a VariantAnnotation from a ByteBuffer.

fromByteBuffer(ByteBuffer) - Static method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deserializes a VariantCallingAnnotations from a ByteBuffer.

G

gap - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

geneId - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

geneId - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

geneName - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

genomicHgvs - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

Genotype - Class in org.bdgenomics.formats.avro

Genotype() - Constructor for class org.bdgenomics.formats.avro.Genotype

Default constructor.

Genotype(Variant, String, Long, Long, VariantCallingAnnotations, String, String, String, List<GenotypeAllele>, Float, Integer, Integer, Integer, Integer, Integer, List<Double>, List<Double>, List<Integer>, Boolean, Boolean, Integer, Integer) - Constructor for class org.bdgenomics.formats.avro.Genotype

All-args constructor.

Genotype.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for Genotype instances.

GenotypeAllele - Enum in org.bdgenomics.formats.avro

genotypeLikelihoods - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

genotypePosteriors - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

genotypePriors - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

genotypeQuality - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

GenotypeType - Enum in org.bdgenomics.formats.avro

get(int) - Method in class org.bdgenomics.formats.avro.Alignment

get(int) - Method in class org.bdgenomics.formats.avro.Dbxref

get(int) - Method in class org.bdgenomics.formats.avro.Feature

get(int) - Method in class org.bdgenomics.formats.avro.Fragment

get(int) - Method in class org.bdgenomics.formats.avro.Genotype

get(int) - Method in class org.bdgenomics.formats.avro.OntologyTerm

get(int) - Method in class org.bdgenomics.formats.avro.ProcessingStep

get(int) - Method in class org.bdgenomics.formats.avro.Read

get(int) - Method in class org.bdgenomics.formats.avro.ReadGroup

get(int) - Method in class org.bdgenomics.formats.avro.Reference

get(int) - Method in class org.bdgenomics.formats.avro.Sample

get(int) - Method in class org.bdgenomics.formats.avro.Sequence

get(int) - Method in class org.bdgenomics.formats.avro.Slice

get(int) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

get(int) - Method in class org.bdgenomics.formats.avro.Variant

get(int) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

get(int) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

getAccession() - Method in class org.bdgenomics.formats.avro.Dbxref.Builder

Gets the value of the 'accession' field.

getAccession() - Method in class org.bdgenomics.formats.avro.Dbxref

Gets the value of the 'accession' field.

getAccession() - Method in class org.bdgenomics.formats.avro.OntologyTerm.Builder

Gets the value of the 'accession' field.

getAccession() - Method in class org.bdgenomics.formats.avro.OntologyTerm

Gets the value of the 'accession' field.

getAliases() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'aliases' field.

getAliases() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'aliases' field.

getAlignments() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Gets the value of the 'alignments' field.

getAlignments() - Method in class org.bdgenomics.formats.avro.Fragment

Gets the value of the 'alignments' field.

getAlleleCount() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'alleleCount' field.

getAlleleCount() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'alleleCount' field.

getAlleleFrequency() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'alleleFrequency' field.

getAlleleFrequency() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'alleleFrequency' field.

getAlleles() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'alleles' field.

getAlleles() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'alleles' field.

getAlphabet() - Method in class org.bdgenomics.formats.avro.Read.Builder

Gets the value of the 'alphabet' field.

getAlphabet() - Method in class org.bdgenomics.formats.avro.Read

Gets the value of the 'alphabet' field.

getAlphabet() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Gets the value of the 'alphabet' field.

getAlphabet() - Method in class org.bdgenomics.formats.avro.Sequence

Gets the value of the 'alphabet' field.

getAlphabet() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'alphabet' field.

getAlphabet() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'alphabet' field.

getAlternateAllele() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'alternateAllele' field.

getAlternateAllele() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'alternateAllele' field.

getAlternateAllele() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'alternateAllele' field.

getAlternateAllele() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'alternateAllele' field.

getAlternateReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'alternateReadDepth' field.

getAlternateReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'alternateReadDepth' field.

getAncestralAllele() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'ancestralAllele' field.

getAncestralAllele() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'ancestralAllele' field.

getAnnotation() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'annotation' field.

getAnnotation() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'annotation' field.

getAnnotationBuilder() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the Builder instance for the 'annotation' field and creates one if it doesn't exist yet.

getAssembly() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Gets the value of the 'assembly' field.

getAssembly() - Method in class org.bdgenomics.formats.avro.Reference

Gets the value of the 'assembly' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Read.Builder

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Read

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Sample

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Sequence

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'attributes' field.

getAttributes() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'attributes' field.

getBaseQRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'baseQRankSum' field.

getBaseQRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'baseQRankSum' field.

getBasesTrimmedFromEnd() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'basesTrimmedFromEnd' field.

getBasesTrimmedFromEnd() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'basesTrimmedFromEnd' field.

getBasesTrimmedFromStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'basesTrimmedFromStart' field.

getBasesTrimmedFromStart() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'basesTrimmedFromStart' field.

getBiotype() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'biotype' field.

getBiotype() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'biotype' field.

getCdnaLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'cdnaLength' field.

getCdnaLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'cdnaLength' field.

getCdnaPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'cdnaPosition' field.

getCdnaPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'cdnaPosition' field.

getCdsLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'cdsLength' field.

getCdsLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'cdsLength' field.

getCdsPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'cdsPosition' field.

getCdsPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'cdsPosition' field.

getCigar() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'cigar' field.

getCigar() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'cigar' field.

getCigar() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'cigar' field.

getCigar() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'cigar' field.

getCircular() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'circular' field.

getCircular() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'circular' field.

getClassSchema() - Static method in class org.bdgenomics.formats.avro.Alignment

getClassSchema() - Static method in enum org.bdgenomics.formats.avro.Alphabet

getClassSchema() - Static method in class org.bdgenomics.formats.avro.Dbxref

getClassSchema() - Static method in class org.bdgenomics.formats.avro.Feature

getClassSchema() - Static method in class org.bdgenomics.formats.avro.Fragment

getClassSchema() - Static method in class org.bdgenomics.formats.avro.Genotype

getClassSchema() - Static method in enum org.bdgenomics.formats.avro.GenotypeAllele

getClassSchema() - Static method in enum org.bdgenomics.formats.avro.GenotypeType

getClassSchema() - Static method in class org.bdgenomics.formats.avro.OntologyTerm

getClassSchema() - Static method in class org.bdgenomics.formats.avro.ProcessingStep

getClassSchema() - Static method in class org.bdgenomics.formats.avro.Read

getClassSchema() - Static method in class org.bdgenomics.formats.avro.ReadGroup

getClassSchema() - Static method in class org.bdgenomics.formats.avro.Reference

getClassSchema() - Static method in class org.bdgenomics.formats.avro.Sample

getClassSchema() - Static method in class org.bdgenomics.formats.avro.Sequence

getClassSchema() - Static method in class org.bdgenomics.formats.avro.Slice

getClassSchema() - Static method in enum org.bdgenomics.formats.avro.Strand

getClassSchema() - Static method in class org.bdgenomics.formats.avro.TranscriptEffect

getClassSchema() - Static method in class org.bdgenomics.formats.avro.Variant

getClassSchema() - Static method in class org.bdgenomics.formats.avro.VariantAnnotation

getClassSchema() - Static method in enum org.bdgenomics.formats.avro.VariantAnnotationMessage

getClassSchema() - Static method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

getCommandLine() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Gets the value of the 'commandLine' field.

getCommandLine() - Method in class org.bdgenomics.formats.avro.ProcessingStep

Gets the value of the 'commandLine' field.

getCulprit() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'culprit' field.

getCulprit() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'culprit' field.

getDb() - Method in class org.bdgenomics.formats.avro.Dbxref.Builder

Gets the value of the 'db' field.

getDb() - Method in class org.bdgenomics.formats.avro.Dbxref

Gets the value of the 'db' field.

getDb() - Method in class org.bdgenomics.formats.avro.OntologyTerm.Builder

Gets the value of the 'db' field.

getDb() - Method in class org.bdgenomics.formats.avro.OntologyTerm

Gets the value of the 'db' field.

getDbSnp() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'dbSnp' field.

getDbSnp() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'dbSnp' field.

getDbxrefs() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'dbxrefs' field.

getDbxrefs() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'dbxrefs' field.

getDecoder() - Static method in class org.bdgenomics.formats.avro.Alignment

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.Dbxref

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.Feature

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.Fragment

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.Genotype

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.OntologyTerm

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.ProcessingStep

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.Read

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.ReadGroup

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.Reference

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.Sample

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.Sequence

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.Slice

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.TranscriptEffect

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.Variant

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.VariantAnnotation

Return the BinaryMessageDecoder instance used by this class.

getDecoder() - Static method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Return the BinaryMessageDecoder instance used by this class.

getDerivesFrom() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'derivesFrom' field.

getDerivesFrom() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'derivesFrom' field.

getDescription() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Gets the value of the 'description' field.

getDescription() - Method in class org.bdgenomics.formats.avro.ProcessingStep

Gets the value of the 'description' field.

getDescription() - Method in class org.bdgenomics.formats.avro.Read.Builder

Gets the value of the 'description' field.

getDescription() - Method in class org.bdgenomics.formats.avro.Read

Gets the value of the 'description' field.

getDescription() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'description' field.

getDescription() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'description' field.

getDescription() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Gets the value of the 'description' field.

getDescription() - Method in class org.bdgenomics.formats.avro.Sequence

Gets the value of the 'description' field.

getDescription() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'description' field.

getDescription() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'description' field.

getDistance() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'distance' field.

getDistance() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'distance' field.

getDownsampled() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'downsampled' field.

getDownsampled() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'downsampled' field.

getDuplicateRead() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'duplicateRead' field.

getDuplicateRead() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'duplicateRead' field.

getEffects() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'effects' field.

getEffects() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'effects' field.

getEnd() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'end' field.

getEnd() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'end' field.

getEnd() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'end' field.

getEnd() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'end' field.

getEnd() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'end' field.

getEnd() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'end' field.

getEnd() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'end' field.

getEnd() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'end' field.

getEnd() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'end' field.

getEnd() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'end' field.

getExonId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'exonId' field.

getExonId() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'exonId' field.

getExpectedAlleleDosage() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'expectedAlleleDosage' field.

getExpectedAlleleDosage() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'expectedAlleleDosage' field.

getFailedVendorQualityChecks() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'failedVendorQualityChecks' field.

getFailedVendorQualityChecks() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'failedVendorQualityChecks' field.

getFeatureId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'featureId' field.

getFeatureId() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'featureId' field.

getFeatureId() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'featureId' field.

getFeatureId() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'featureId' field.

getFeatureType() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'featureType' field.

getFeatureType() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'featureType' field.

getFeatureType() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'featureType' field.

getFeatureType() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'featureType' field.

getFiltersApplied() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'filtersApplied' field.

getFiltersApplied() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'filtersApplied' field.

getFiltersApplied() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'filtersApplied' field.

getFiltersApplied() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'filtersApplied' field.

getFiltersFailed() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'filtersFailed' field.

getFiltersFailed() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'filtersFailed' field.

getFiltersFailed() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'filtersFailed' field.

getFiltersFailed() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'filtersFailed' field.

getFiltersPassed() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'filtersPassed' field.

getFiltersPassed() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'filtersPassed' field.

getFiltersPassed() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'filtersPassed' field.

getFiltersPassed() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'filtersPassed' field.

getFisherStrandBiasPValue() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'fisherStrandBiasPValue' field.

getFisherStrandBiasPValue() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'fisherStrandBiasPValue' field.

getFlowOrder() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'flowOrder' field.

getFlowOrder() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'flowOrder' field.

getForwardReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'forwardReadDepth' field.

getForwardReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'forwardReadDepth' field.

getFrame() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'frame' field.

getFrame() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'frame' field.

getGap() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'gap' field.

getGap() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'gap' field.

getGeneId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'geneId' field.

getGeneId() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'geneId' field.

getGeneId() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'geneId' field.

getGeneId() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'geneId' field.

getGeneName() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'geneName' field.

getGeneName() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'geneName' field.

getGenomicHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'genomicHgvs' field.

getGenomicHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'genomicHgvs' field.

getGenotypeLikelihoods() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'genotypeLikelihoods' field.

getGenotypeLikelihoods() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'genotypeLikelihoods' field.

getGenotypePosteriors() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'genotypePosteriors' field.

getGenotypePosteriors() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'genotypePosteriors' field.

getGenotypePriors() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'genotypePriors' field.

getGenotypePriors() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'genotypePriors' field.

getGenotypeQuality() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'genotypeQuality' field.

getGenotypeQuality() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'genotypeQuality' field.

getHapMap2() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'hapMap2' field.

getHapMap2() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'hapMap2' field.

getHapMap3() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'hapMap3' field.

getHapMap3() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'hapMap3' field.

getId() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Gets the value of the 'id' field.

getId() - Method in class org.bdgenomics.formats.avro.ProcessingStep

Gets the value of the 'id' field.

getId() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'id' field.

getId() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'id' field.

getId() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Gets the value of the 'id' field.

getId() - Method in class org.bdgenomics.formats.avro.Sample

Gets the value of the 'id' field.

getIndex() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Gets the value of the 'index' field.

getIndex() - Method in class org.bdgenomics.formats.avro.Reference

Gets the value of the 'index' field.

getIndex() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'index' field.

getIndex() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'index' field.

getInsertSize() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'insertSize' field.

getInsertSize() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'insertSize' field.

getInsertSize() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Gets the value of the 'insertSize' field.

getInsertSize() - Method in class org.bdgenomics.formats.avro.Fragment

Gets the value of the 'insertSize' field.

getKeySequence() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'keySequence' field.

getKeySequence() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'keySequence' field.

getLength() - Method in class org.bdgenomics.formats.avro.Read.Builder

Gets the value of the 'length' field.

getLength() - Method in class org.bdgenomics.formats.avro.Read

Gets the value of the 'length' field.

getLength() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Gets the value of the 'length' field.

getLength() - Method in class org.bdgenomics.formats.avro.Reference

Gets the value of the 'length' field.

getLength() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Gets the value of the 'length' field.

getLength() - Method in class org.bdgenomics.formats.avro.Sequence

Gets the value of the 'length' field.

getLength() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'length' field.

getLength() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'length' field.

getLibrary() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'library' field.

getLibrary() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'library' field.

getMappingQuality() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'mappingQuality' field.

getMappingQuality() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'mappingQuality' field.

getMapq0Reads() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'mapq0Reads' field.

getMapq0Reads() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'mapq0Reads' field.

getMateAlignmentStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'mateAlignmentStart' field.

getMateAlignmentStart() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'mateAlignmentStart' field.

getMateMapped() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'mateMapped' field.

getMateMapped() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'mateMapped' field.

getMateNegativeStrand() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'mateNegativeStrand' field.

getMateNegativeStrand() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'mateNegativeStrand' field.

getMateReferenceName() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'mateReferenceName' field.

getMateReferenceName() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'mateReferenceName' field.

getMd5() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Gets the value of the 'md5' field.

getMd5() - Method in class org.bdgenomics.formats.avro.Reference

Gets the value of the 'md5' field.

getMessages() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'messages' field.

getMessages() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'messages' field.

getMinReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'minReadDepth' field.

getMinReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'minReadDepth' field.

getMismatchingPositions() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'mismatchingPositions' field.

getMismatchingPositions() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'mismatchingPositions' field.

getMqRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'mqRankSum' field.

getMqRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'mqRankSum' field.

getName() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Fragment

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Read.Builder

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Read

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Reference

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Sample

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Sequence

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'name' field.

getName() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'name' field.

getNames() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'names' field.

getNames() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'names' field.

getNonReferenceLikelihoods() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'nonReferenceLikelihoods' field.

getNonReferenceLikelihoods() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'nonReferenceLikelihoods' field.

getNotes() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'notes' field.

getNotes() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'notes' field.

getOntologyTerms() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'ontologyTerms' field.

getOntologyTerms() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'ontologyTerms' field.

getOriginalCigar() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'originalCigar' field.

getOriginalCigar() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'originalCigar' field.

getOriginalQualityScores() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'originalQualityScores' field.

getOriginalQualityScores() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'originalQualityScores' field.

getOriginalStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'originalStart' field.

getOriginalStart() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'originalStart' field.

getParentIds() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'parentIds' field.

getParentIds() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'parentIds' field.

getPhase() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'phase' field.

getPhase() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'phase' field.

getPhased() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'phased' field.

getPhased() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'phased' field.

getPhaseQuality() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'phaseQuality' field.

getPhaseQuality() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'phaseQuality' field.

getPhaseSetId() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'phaseSetId' field.

getPhaseSetId() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'phaseSetId' field.

getPlatform() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'platform' field.

getPlatform() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'platform' field.

getPlatformModel() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'platformModel' field.

getPlatformModel() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'platformModel' field.

getPlatformUnit() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'platformUnit' field.

getPlatformUnit() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'platformUnit' field.

getPredictedMedianInsertSize() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'predictedMedianInsertSize' field.

getPredictedMedianInsertSize() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'predictedMedianInsertSize' field.

getPreviousId() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Gets the value of the 'previousId' field.

getPreviousId() - Method in class org.bdgenomics.formats.avro.ProcessingStep

Gets the value of the 'previousId' field.

getPrimaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'primaryAlignment' field.

getPrimaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'primaryAlignment' field.

getProcessingDescription() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'processingDescription' field.

getProcessingDescription() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'processingDescription' field.

getProcessingSteps() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'processingSteps' field.

getProcessingSteps() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'processingSteps' field.

getProcessingSteps() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Gets the value of the 'processingSteps' field.

getProcessingSteps() - Method in class org.bdgenomics.formats.avro.Sample

Gets the value of the 'processingSteps' field.

getProgramName() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Gets the value of the 'programName' field.

getProgramName() - Method in class org.bdgenomics.formats.avro.ProcessingStep

Gets the value of the 'programName' field.

getProperPair() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'properPair' field.

getProperPair() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'properPair' field.

getProteinHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'proteinHgvs' field.

getProteinHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'proteinHgvs' field.

getProteinLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'proteinLength' field.

getProteinLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'proteinLength' field.

getProteinPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'proteinPosition' field.

getProteinPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'proteinPosition' field.

getQuality() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'quality' field.

getQuality() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'quality' field.

getQualityScores() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'qualityScores' field.

getQualityScores() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'qualityScores' field.

getQualityScores() - Method in class org.bdgenomics.formats.avro.Read.Builder

Gets the value of the 'qualityScores' field.

getQualityScores() - Method in class org.bdgenomics.formats.avro.Read

Gets the value of the 'qualityScores' field.

getRank() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'rank' field.

getRank() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'rank' field.

getReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'readDepth' field.

getReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'readDepth' field.

getReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'readDepth' field.

getReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'readDepth' field.

getReadGroupId() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'readGroupId' field.

getReadGroupId() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'readGroupId' field.

getReadGroupId() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Gets the value of the 'readGroupId' field.

getReadGroupId() - Method in class org.bdgenomics.formats.avro.Fragment

Gets the value of the 'readGroupId' field.

getReadGroupSampleId() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'readGroupSampleId' field.

getReadGroupSampleId() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'readGroupSampleId' field.

getReadInFragment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'readInFragment' field.

getReadInFragment() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'readInFragment' field.

getReadMapped() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'readMapped' field.

getReadMapped() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'readMapped' field.

getReadName() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'readName' field.

getReadName() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'readName' field.

getReadNegativeStrand() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'readNegativeStrand' field.

getReadNegativeStrand() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'readNegativeStrand' field.

getReadPaired() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'readPaired' field.

getReadPaired() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'readPaired' field.

getReadPositionRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'readPositionRankSum' field.

getReadPositionRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'readPositionRankSum' field.

getReferenceAllele() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'referenceAllele' field.

getReferenceAllele() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'referenceAllele' field.

getReferenceForwardReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'referenceForwardReadDepth' field.

getReferenceForwardReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'referenceForwardReadDepth' field.

getReferenceName() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'referenceName' field.

getReferenceName() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'referenceName' field.

getReferenceName() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'referenceName' field.

getReferenceName() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'referenceName' field.

getReferenceName() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'referenceName' field.

getReferenceName() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'referenceName' field.

getReferenceName() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'referenceName' field.

getReferenceName() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'referenceName' field.

getReferenceReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'referenceReadDepth' field.

getReferenceReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'referenceReadDepth' field.

getReferenceReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'referenceReadDepth' field.

getReferenceReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'referenceReadDepth' field.

getReferenceReverseReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'referenceReverseReadDepth' field.

getReferenceReverseReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'referenceReverseReadDepth' field.

getReverseReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'reverseReadDepth' field.

getReverseReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'reverseReadDepth' field.

getRmsMapQ() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'rmsMapQ' field.

getRmsMapQ() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'rmsMapQ' field.

getRunDateEpoch() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'runDateEpoch' field.

getRunDateEpoch() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'runDateEpoch' field.

getSampleDescription() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'sampleDescription' field.

getSampleDescription() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'sampleDescription' field.

getSampleId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'sampleId' field.

getSampleId() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'sampleId' field.

getSampleId() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'sampleId' field.

getSampleId() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'sampleId' field.

getSampleId() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'sampleId' field.

getSampleId() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'sampleId' field.

getSchema() - Method in class org.bdgenomics.formats.avro.Alignment

getSchema() - Method in class org.bdgenomics.formats.avro.Dbxref

getSchema() - Method in class org.bdgenomics.formats.avro.Feature

getSchema() - Method in class org.bdgenomics.formats.avro.Fragment

getSchema() - Method in class org.bdgenomics.formats.avro.Genotype

getSchema() - Method in class org.bdgenomics.formats.avro.OntologyTerm

getSchema() - Method in class org.bdgenomics.formats.avro.ProcessingStep

getSchema() - Method in class org.bdgenomics.formats.avro.Read

getSchema() - Method in class org.bdgenomics.formats.avro.ReadGroup

getSchema() - Method in class org.bdgenomics.formats.avro.Reference

getSchema() - Method in class org.bdgenomics.formats.avro.Sample

getSchema() - Method in class org.bdgenomics.formats.avro.Sequence

getSchema() - Method in class org.bdgenomics.formats.avro.Slice

getSchema() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

getSchema() - Method in class org.bdgenomics.formats.avro.Variant

getSchema() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

getSchema() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

getScore() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'score' field.

getScore() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'score' field.

getSecondaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'secondaryAlignment' field.

getSecondaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'secondaryAlignment' field.

getSequence() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'sequence' field.

getSequence() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'sequence' field.

getSequence() - Method in class org.bdgenomics.formats.avro.Read.Builder

Gets the value of the 'sequence' field.

getSequence() - Method in class org.bdgenomics.formats.avro.Read

Gets the value of the 'sequence' field.

getSequence() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Gets the value of the 'sequence' field.

getSequence() - Method in class org.bdgenomics.formats.avro.Sequence

Gets the value of the 'sequence' field.

getSequence() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'sequence' field.

getSequence() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'sequence' field.

getSequencingCenter() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Gets the value of the 'sequencingCenter' field.

getSequencingCenter() - Method in class org.bdgenomics.formats.avro.ReadGroup

Gets the value of the 'sequencingCenter' field.

getSlices() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'slices' field.

getSlices() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'slices' field.

getSomatic() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'somatic' field.

getSomatic() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'somatic' field.

getSource() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'source' field.

getSource() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'source' field.

getSourceAccessions() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Gets the value of the 'sourceAccessions' field.

getSourceAccessions() - Method in class org.bdgenomics.formats.avro.Reference

Gets the value of the 'sourceAccessions' field.

getSourceUri() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Gets the value of the 'sourceUri' field.

getSourceUri() - Method in class org.bdgenomics.formats.avro.Reference

Gets the value of the 'sourceUri' field.

getSpecies() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Gets the value of the 'species' field.

getSpecies() - Method in class org.bdgenomics.formats.avro.Reference

Gets the value of the 'species' field.

getSplitFromMultiAllelic() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'splitFromMultiAllelic' field.

getSplitFromMultiAllelic() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'splitFromMultiAllelic' field.

getSplitFromMultiAllelic() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'splitFromMultiAllelic' field.

getSplitFromMultiAllelic() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'splitFromMultiAllelic' field.

getStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'start' field.

getStart() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'start' field.

getStart() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'start' field.

getStart() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'start' field.

getStart() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'start' field.

getStart() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'start' field.

getStart() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'start' field.

getStart() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'start' field.

getStart() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Gets the value of the 'start' field.

getStart() - Method in class org.bdgenomics.formats.avro.Variant

Gets the value of the 'start' field.

getStrand() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'strand' field.

getStrand() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'strand' field.

getStrand() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'strand' field.

getStrand() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'strand' field.

getStrandBiasComponents() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'strandBiasComponents' field.

getStrandBiasComponents() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'strandBiasComponents' field.

getSupplementaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Gets the value of the 'supplementaryAlignment' field.

getSupplementaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment

Gets the value of the 'supplementaryAlignment' field.

getTarget() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'target' field.

getTarget() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'target' field.

getThousandGenomes() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'thousandGenomes' field.

getThousandGenomes() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'thousandGenomes' field.

getTotal() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'total' field.

getTotal() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'total' field.

getTotalLength() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Gets the value of the 'totalLength' field.

getTotalLength() - Method in class org.bdgenomics.formats.avro.Slice

Gets the value of the 'totalLength' field.

getTranscriptEffects() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'transcriptEffects' field.

getTranscriptEffects() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'transcriptEffects' field.

getTranscriptHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Gets the value of the 'transcriptHgvs' field.

getTranscriptHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Gets the value of the 'transcriptHgvs' field.

getTranscriptId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Gets the value of the 'transcriptId' field.

getTranscriptId() - Method in class org.bdgenomics.formats.avro.Feature

Gets the value of the 'transcriptId' field.

getValidated() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Gets the value of the 'validated' field.

getValidated() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Gets the value of the 'validated' field.

getVariant() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'variant' field.

getVariant() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'variant' field.

getVariantBuilder() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the Builder instance for the 'variant' field and creates one if it doesn't exist yet.

getVariantCallingAnnotations() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the value of the 'variantCallingAnnotations' field.

getVariantCallingAnnotations() - Method in class org.bdgenomics.formats.avro.Genotype

Gets the value of the 'variantCallingAnnotations' field.

getVariantCallingAnnotationsBuilder() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Gets the Builder instance for the 'variantCallingAnnotations' field and creates one if it doesn't exist yet.

getVersion() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Gets the value of the 'version' field.

getVersion() - Method in class org.bdgenomics.formats.avro.ProcessingStep

Gets the value of the 'version' field.

getVqslod() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Gets the value of the 'vqslod' field.

getVqslod() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Gets the value of the 'vqslod' field.

H

hapMap2 - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

hapMap3 - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

hasAccession() - Method in class org.bdgenomics.formats.avro.Dbxref.Builder

Checks whether the 'accession' field has been set.

hasAccession() - Method in class org.bdgenomics.formats.avro.OntologyTerm.Builder

Checks whether the 'accession' field has been set.

hasAliases() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'aliases' field has been set.

hasAlignments() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Checks whether the 'alignments' field has been set.

hasAlleleCount() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'alleleCount' field has been set.

hasAlleleFrequency() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'alleleFrequency' field has been set.

hasAlleles() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'alleles' field has been set.

hasAlphabet() - Method in class org.bdgenomics.formats.avro.Read.Builder

Checks whether the 'alphabet' field has been set.

hasAlphabet() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Checks whether the 'alphabet' field has been set.

hasAlphabet() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'alphabet' field has been set.

hasAlternateAllele() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'alternateAllele' field has been set.

hasAlternateAllele() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'alternateAllele' field has been set.

hasAlternateReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'alternateReadDepth' field has been set.

hasAncestralAllele() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'ancestralAllele' field has been set.

hasAnnotation() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'annotation' field has been set.

hasAnnotationBuilder() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'annotation' field has an active Builder instance Annotation for this variant, if any.

hasAssembly() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Checks whether the 'assembly' field has been set.

hasAttributes() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'attributes' field has been set.

hasAttributes() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'attributes' field has been set.

hasAttributes() - Method in class org.bdgenomics.formats.avro.Read.Builder

Checks whether the 'attributes' field has been set.

hasAttributes() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Checks whether the 'attributes' field has been set.

hasAttributes() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Checks whether the 'attributes' field has been set.

hasAttributes() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'attributes' field has been set.

hasAttributes() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'attributes' field has been set.

hasAttributes() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'attributes' field has been set.

hasBaseQRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'baseQRankSum' field has been set.

hasBasesTrimmedFromEnd() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'basesTrimmedFromEnd' field has been set.

hasBasesTrimmedFromStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'basesTrimmedFromStart' field has been set.

hasBiotype() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'biotype' field has been set.

hasCdnaLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'cdnaLength' field has been set.

hasCdnaPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'cdnaPosition' field has been set.

hasCdsLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'cdsLength' field has been set.

hasCdsPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'cdsPosition' field has been set.

hasCigar() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'cigar' field has been set.

hasCigar() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'cigar' field has been set.

hasCircular() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'circular' field has been set.

hasCommandLine() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Checks whether the 'commandLine' field has been set.

hasCulprit() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'culprit' field has been set.

hasDb() - Method in class org.bdgenomics.formats.avro.Dbxref.Builder

Checks whether the 'db' field has been set.

hasDb() - Method in class org.bdgenomics.formats.avro.OntologyTerm.Builder

Checks whether the 'db' field has been set.

hasDbSnp() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'dbSnp' field has been set.

hasDbxrefs() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'dbxrefs' field has been set.

hasDerivesFrom() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'derivesFrom' field has been set.

hasDescription() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Checks whether the 'description' field has been set.

hasDescription() - Method in class org.bdgenomics.formats.avro.Read.Builder

Checks whether the 'description' field has been set.

hasDescription() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'description' field has been set.

hasDescription() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Checks whether the 'description' field has been set.

hasDescription() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'description' field has been set.

hasDistance() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'distance' field has been set.

hasDownsampled() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'downsampled' field has been set.

hasDuplicateRead() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'duplicateRead' field has been set.

hasEffects() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'effects' field has been set.

hasEnd() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'end' field has been set.

hasEnd() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'end' field has been set.

hasEnd() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'end' field has been set.

hasEnd() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'end' field has been set.

hasEnd() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'end' field has been set.

hasExonId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'exonId' field has been set.

hasExpectedAlleleDosage() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'expectedAlleleDosage' field has been set.

hasFailedVendorQualityChecks() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'failedVendorQualityChecks' field has been set.

hasFeatureId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'featureId' field has been set.

hasFeatureId() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'featureId' field has been set.

hasFeatureType() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'featureType' field has been set.

hasFeatureType() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'featureType' field has been set.

hasFiltersApplied() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'filtersApplied' field has been set.

hasFiltersApplied() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'filtersApplied' field has been set.

hasFiltersFailed() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'filtersFailed' field has been set.

hasFiltersFailed() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'filtersFailed' field has been set.

hasFiltersPassed() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'filtersPassed' field has been set.

hasFiltersPassed() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'filtersPassed' field has been set.

hasFisherStrandBiasPValue() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'fisherStrandBiasPValue' field has been set.

hasFlowOrder() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'flowOrder' field has been set.

hasForwardReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'forwardReadDepth' field has been set.

hasFrame() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'frame' field has been set.

hasGap() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'gap' field has been set.

hasGeneId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'geneId' field has been set.

hasGeneId() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'geneId' field has been set.

hasGeneName() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'geneName' field has been set.

hasGenomicHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'genomicHgvs' field has been set.

hasGenotypeLikelihoods() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'genotypeLikelihoods' field has been set.

hasGenotypePosteriors() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'genotypePosteriors' field has been set.

hasGenotypePriors() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'genotypePriors' field has been set.

hasGenotypeQuality() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'genotypeQuality' field has been set.

hasHapMap2() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'hapMap2' field has been set.

hasHapMap3() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'hapMap3' field has been set.

hasId() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Checks whether the 'id' field has been set.

hasId() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'id' field has been set.

hasId() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Checks whether the 'id' field has been set.

hasIndex() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Checks whether the 'index' field has been set.

hasIndex() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'index' field has been set.

hasInsertSize() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'insertSize' field has been set.

hasInsertSize() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Checks whether the 'insertSize' field has been set.

hasKeySequence() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'keySequence' field has been set.

hasLength() - Method in class org.bdgenomics.formats.avro.Read.Builder

Checks whether the 'length' field has been set.

hasLength() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Checks whether the 'length' field has been set.

hasLength() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Checks whether the 'length' field has been set.

hasLength() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'length' field has been set.

hasLibrary() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'library' field has been set.

hasMappingQuality() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'mappingQuality' field has been set.

hasMapq0Reads() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'mapq0Reads' field has been set.

hasMateAlignmentStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'mateAlignmentStart' field has been set.

hasMateMapped() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'mateMapped' field has been set.

hasMateNegativeStrand() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'mateNegativeStrand' field has been set.

hasMateReferenceName() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'mateReferenceName' field has been set.

hasMd5() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Checks whether the 'md5' field has been set.

hasMessages() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'messages' field has been set.

hasMinReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'minReadDepth' field has been set.

hasMismatchingPositions() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'mismatchingPositions' field has been set.

hasMqRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'mqRankSum' field has been set.

hasName() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'name' field has been set.

hasName() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Checks whether the 'name' field has been set.

hasName() - Method in class org.bdgenomics.formats.avro.Read.Builder

Checks whether the 'name' field has been set.

hasName() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Checks whether the 'name' field has been set.

hasName() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Checks whether the 'name' field has been set.

hasName() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Checks whether the 'name' field has been set.

hasName() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'name' field has been set.

hasNames() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'names' field has been set.

hasNonReferenceLikelihoods() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'nonReferenceLikelihoods' field has been set.

hasNotes() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'notes' field has been set.

hasOntologyTerms() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'ontologyTerms' field has been set.

hasOriginalCigar() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'originalCigar' field has been set.

hasOriginalQualityScores() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'originalQualityScores' field has been set.

hasOriginalStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'originalStart' field has been set.

hasParentIds() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'parentIds' field has been set.

hasPhase() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'phase' field has been set.

hasPhased() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'phased' field has been set.

hasPhaseQuality() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'phaseQuality' field has been set.

hasPhaseSetId() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'phaseSetId' field has been set.

hasPlatform() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'platform' field has been set.

hasPlatformModel() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'platformModel' field has been set.

hasPlatformUnit() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'platformUnit' field has been set.

hasPredictedMedianInsertSize() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'predictedMedianInsertSize' field has been set.

hasPreviousId() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Checks whether the 'previousId' field has been set.

hasPrimaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'primaryAlignment' field has been set.

hasProcessingDescription() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'processingDescription' field has been set.

hasProcessingSteps() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'processingSteps' field has been set.

hasProcessingSteps() - Method in class org.bdgenomics.formats.avro.Sample.Builder

Checks whether the 'processingSteps' field has been set.

hasProgramName() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Checks whether the 'programName' field has been set.

hasProperPair() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'properPair' field has been set.

hasProteinHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'proteinHgvs' field has been set.

hasProteinLength() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'proteinLength' field has been set.

hasProteinPosition() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'proteinPosition' field has been set.

hasQuality() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'quality' field has been set.

hasQualityScores() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'qualityScores' field has been set.

hasQualityScores() - Method in class org.bdgenomics.formats.avro.Read.Builder

Checks whether the 'qualityScores' field has been set.

hasRank() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'rank' field has been set.

hasReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'readDepth' field has been set.

hasReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'readDepth' field has been set.

hasReadGroupId() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'readGroupId' field has been set.

hasReadGroupId() - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Checks whether the 'readGroupId' field has been set.

hasReadGroupSampleId() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'readGroupSampleId' field has been set.

hasReadInFragment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'readInFragment' field has been set.

hasReadMapped() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'readMapped' field has been set.

hasReadName() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'readName' field has been set.

hasReadNegativeStrand() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'readNegativeStrand' field has been set.

hasReadPaired() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'readPaired' field has been set.

hasReadPositionRankSum() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'readPositionRankSum' field has been set.

hasReferenceAllele() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'referenceAllele' field has been set.

hasReferenceForwardReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'referenceForwardReadDepth' field has been set.

hasReferenceName() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'referenceName' field has been set.

hasReferenceName() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'referenceName' field has been set.

hasReferenceName() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'referenceName' field has been set.

hasReferenceName() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'referenceName' field has been set.

hasReferenceReadDepth() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'referenceReadDepth' field has been set.

hasReferenceReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'referenceReadDepth' field has been set.

hasReferenceReverseReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'referenceReverseReadDepth' field has been set.

hasReverseReadDepth() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'reverseReadDepth' field has been set.

hasRmsMapQ() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'rmsMapQ' field has been set.

hasRunDateEpoch() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'runDateEpoch' field has been set.

hasSampleDescription() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'sampleDescription' field has been set.

hasSampleId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'sampleId' field has been set.

hasSampleId() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'sampleId' field has been set.

hasSampleId() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'sampleId' field has been set.

hasScore() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'score' field has been set.

hasSecondaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'secondaryAlignment' field has been set.

hasSequence() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'sequence' field has been set.

hasSequence() - Method in class org.bdgenomics.formats.avro.Read.Builder

Checks whether the 'sequence' field has been set.

hasSequence() - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Checks whether the 'sequence' field has been set.

hasSequence() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'sequence' field has been set.

hasSequencingCenter() - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Checks whether the 'sequencingCenter' field has been set.

hasSlices() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'slices' field has been set.

hasSomatic() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'somatic' field has been set.

hasSource() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'source' field has been set.

hasSourceAccessions() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Checks whether the 'sourceAccessions' field has been set.

hasSourceUri() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Checks whether the 'sourceUri' field has been set.

hasSpecies() - Method in class org.bdgenomics.formats.avro.Reference.Builder

Checks whether the 'species' field has been set.

hasSplitFromMultiAllelic() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'splitFromMultiAllelic' field has been set.

hasSplitFromMultiAllelic() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'splitFromMultiAllelic' field has been set.

hasStart() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'start' field has been set.

hasStart() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'start' field has been set.

hasStart() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'start' field has been set.

hasStart() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'start' field has been set.

hasStart() - Method in class org.bdgenomics.formats.avro.Variant.Builder

Checks whether the 'start' field has been set.

hasStrand() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'strand' field has been set.

hasStrand() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'strand' field has been set.

hasStrandBiasComponents() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'strandBiasComponents' field has been set.

hasSupplementaryAlignment() - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Checks whether the 'supplementaryAlignment' field has been set.

hasTarget() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'target' field has been set.

hasThousandGenomes() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'thousandGenomes' field has been set.

hasTotal() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'total' field has been set.

hasTotalLength() - Method in class org.bdgenomics.formats.avro.Slice.Builder

Checks whether the 'totalLength' field has been set.

hasTranscriptEffects() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'transcriptEffects' field has been set.

hasTranscriptHgvs() - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Checks whether the 'transcriptHgvs' field has been set.

hasTranscriptId() - Method in class org.bdgenomics.formats.avro.Feature.Builder

Checks whether the 'transcriptId' field has been set.

hasValidated() - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Checks whether the 'validated' field has been set.

hasVariant() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'variant' field has been set.

hasVariantBuilder() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'variant' field has an active Builder instance The variant called at this site.

hasVariantCallingAnnotations() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'variantCallingAnnotations' field has been set.

hasVariantCallingAnnotationsBuilder() - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Checks whether the 'variantCallingAnnotations' field has an active Builder instance Statistics collected at this site, if available.

hasVersion() - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Checks whether the 'version' field has been set.

hasVqslod() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Checks whether the 'vqslod' field has been set.

I

id - Variable in class org.bdgenomics.formats.avro.ProcessingStep

Deprecated.

id - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

id - Variable in class org.bdgenomics.formats.avro.Sample

Deprecated.

index - Variable in class org.bdgenomics.formats.avro.Reference

Deprecated.

index - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

insertSize - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

insertSize - Variable in class org.bdgenomics.formats.avro.Fragment

Deprecated.

K

keySequence - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

L

length - Variable in class org.bdgenomics.formats.avro.Read

Deprecated.

length - Variable in class org.bdgenomics.formats.avro.Reference

Deprecated.

length - Variable in class org.bdgenomics.formats.avro.Sequence

Deprecated.

length - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

library - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

M

mappingQuality - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

mapq0Reads - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

mateAlignmentStart - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

mateMapped - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

mateNegativeStrand - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

mateReferenceName - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

md5 - Variable in class org.bdgenomics.formats.avro.Reference

Deprecated.

messages - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

minReadDepth - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

mismatchingPositions - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

mqRankSum - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

N

name - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

name - Variable in class org.bdgenomics.formats.avro.Fragment

Deprecated.

name - Variable in class org.bdgenomics.formats.avro.Read

Deprecated.

name - Variable in class org.bdgenomics.formats.avro.Reference

Deprecated.

name - Variable in class org.bdgenomics.formats.avro.Sample

Deprecated.

name - Variable in class org.bdgenomics.formats.avro.Sequence

Deprecated.

name - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

names - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

newBuilder() - Static method in class org.bdgenomics.formats.avro.Alignment

Creates a new Alignment RecordBuilder.

newBuilder(Alignment.Builder) - Static method in class org.bdgenomics.formats.avro.Alignment

Creates a new Alignment RecordBuilder by copying an existing Builder.

newBuilder(Alignment) - Static method in class org.bdgenomics.formats.avro.Alignment

Creates a new Alignment RecordBuilder by copying an existing Alignment instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.Dbxref

Creates a new Dbxref RecordBuilder.

newBuilder(Dbxref.Builder) - Static method in class org.bdgenomics.formats.avro.Dbxref

Creates a new Dbxref RecordBuilder by copying an existing Builder.

newBuilder(Dbxref) - Static method in class org.bdgenomics.formats.avro.Dbxref

Creates a new Dbxref RecordBuilder by copying an existing Dbxref instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.Feature

Creates a new Feature RecordBuilder.

newBuilder(Feature.Builder) - Static method in class org.bdgenomics.formats.avro.Feature

Creates a new Feature RecordBuilder by copying an existing Builder.

newBuilder(Feature) - Static method in class org.bdgenomics.formats.avro.Feature

Creates a new Feature RecordBuilder by copying an existing Feature instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.Fragment

Creates a new Fragment RecordBuilder.

newBuilder(Fragment.Builder) - Static method in class org.bdgenomics.formats.avro.Fragment

Creates a new Fragment RecordBuilder by copying an existing Builder.

newBuilder(Fragment) - Static method in class org.bdgenomics.formats.avro.Fragment

Creates a new Fragment RecordBuilder by copying an existing Fragment instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.Genotype

Creates a new Genotype RecordBuilder.

newBuilder(Genotype.Builder) - Static method in class org.bdgenomics.formats.avro.Genotype

Creates a new Genotype RecordBuilder by copying an existing Builder.

newBuilder(Genotype) - Static method in class org.bdgenomics.formats.avro.Genotype

Creates a new Genotype RecordBuilder by copying an existing Genotype instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.OntologyTerm

Creates a new OntologyTerm RecordBuilder.

newBuilder(OntologyTerm.Builder) - Static method in class org.bdgenomics.formats.avro.OntologyTerm

Creates a new OntologyTerm RecordBuilder by copying an existing Builder.

newBuilder(OntologyTerm) - Static method in class org.bdgenomics.formats.avro.OntologyTerm

Creates a new OntologyTerm RecordBuilder by copying an existing OntologyTerm instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.ProcessingStep

Creates a new ProcessingStep RecordBuilder.

newBuilder(ProcessingStep.Builder) - Static method in class org.bdgenomics.formats.avro.ProcessingStep

Creates a new ProcessingStep RecordBuilder by copying an existing Builder.

newBuilder(ProcessingStep) - Static method in class org.bdgenomics.formats.avro.ProcessingStep

Creates a new ProcessingStep RecordBuilder by copying an existing ProcessingStep instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.Read

Creates a new Read RecordBuilder.

newBuilder(Read.Builder) - Static method in class org.bdgenomics.formats.avro.Read

Creates a new Read RecordBuilder by copying an existing Builder.

newBuilder(Read) - Static method in class org.bdgenomics.formats.avro.Read

Creates a new Read RecordBuilder by copying an existing Read instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.ReadGroup

Creates a new ReadGroup RecordBuilder.

newBuilder(ReadGroup.Builder) - Static method in class org.bdgenomics.formats.avro.ReadGroup

Creates a new ReadGroup RecordBuilder by copying an existing Builder.

newBuilder(ReadGroup) - Static method in class org.bdgenomics.formats.avro.ReadGroup

Creates a new ReadGroup RecordBuilder by copying an existing ReadGroup instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.Reference

Creates a new Reference RecordBuilder.

newBuilder(Reference.Builder) - Static method in class org.bdgenomics.formats.avro.Reference

Creates a new Reference RecordBuilder by copying an existing Builder.

newBuilder(Reference) - Static method in class org.bdgenomics.formats.avro.Reference

Creates a new Reference RecordBuilder by copying an existing Reference instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.Sample

Creates a new Sample RecordBuilder.

newBuilder(Sample.Builder) - Static method in class org.bdgenomics.formats.avro.Sample

Creates a new Sample RecordBuilder by copying an existing Builder.

newBuilder(Sample) - Static method in class org.bdgenomics.formats.avro.Sample

Creates a new Sample RecordBuilder by copying an existing Sample instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.Sequence

Creates a new Sequence RecordBuilder.

newBuilder(Sequence.Builder) - Static method in class org.bdgenomics.formats.avro.Sequence

Creates a new Sequence RecordBuilder by copying an existing Builder.

newBuilder(Sequence) - Static method in class org.bdgenomics.formats.avro.Sequence

Creates a new Sequence RecordBuilder by copying an existing Sequence instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.Slice

Creates a new Slice RecordBuilder.

newBuilder(Slice.Builder) - Static method in class org.bdgenomics.formats.avro.Slice

Creates a new Slice RecordBuilder by copying an existing Builder.

newBuilder(Slice) - Static method in class org.bdgenomics.formats.avro.Slice

Creates a new Slice RecordBuilder by copying an existing Slice instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.TranscriptEffect

Creates a new TranscriptEffect RecordBuilder.

newBuilder(TranscriptEffect.Builder) - Static method in class org.bdgenomics.formats.avro.TranscriptEffect

Creates a new TranscriptEffect RecordBuilder by copying an existing Builder.

newBuilder(TranscriptEffect) - Static method in class org.bdgenomics.formats.avro.TranscriptEffect

Creates a new TranscriptEffect RecordBuilder by copying an existing TranscriptEffect instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.Variant

Creates a new Variant RecordBuilder.

newBuilder(Variant.Builder) - Static method in class org.bdgenomics.formats.avro.Variant

Creates a new Variant RecordBuilder by copying an existing Builder.

newBuilder(Variant) - Static method in class org.bdgenomics.formats.avro.Variant

Creates a new Variant RecordBuilder by copying an existing Variant instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.VariantAnnotation

Creates a new VariantAnnotation RecordBuilder.

newBuilder(VariantAnnotation.Builder) - Static method in class org.bdgenomics.formats.avro.VariantAnnotation

Creates a new VariantAnnotation RecordBuilder by copying an existing Builder.

newBuilder(VariantAnnotation) - Static method in class org.bdgenomics.formats.avro.VariantAnnotation

Creates a new VariantAnnotation RecordBuilder by copying an existing VariantAnnotation instance.

newBuilder() - Static method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Creates a new VariantCallingAnnotations RecordBuilder.

newBuilder(VariantCallingAnnotations.Builder) - Static method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Creates a new VariantCallingAnnotations RecordBuilder by copying an existing Builder.

newBuilder(VariantCallingAnnotations) - Static method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Creates a new VariantCallingAnnotations RecordBuilder by copying an existing VariantCallingAnnotations instance.

nonReferenceLikelihoods - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

notes - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

O

OntologyTerm - Class in org.bdgenomics.formats.avro

OntologyTerm() - Constructor for class org.bdgenomics.formats.avro.OntologyTerm

Default constructor.

OntologyTerm(String, String) - Constructor for class org.bdgenomics.formats.avro.OntologyTerm

All-args constructor.

OntologyTerm.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for OntologyTerm instances.

ontologyTerms - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

org.bdgenomics.formats.avro - package org.bdgenomics.formats.avro

originalCigar - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

originalQualityScores - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

originalStart - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

P

parentIds - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

phase - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

phased - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

phaseQuality - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

phaseSetId - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

platform - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

platformModel - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

platformUnit - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

predictedMedianInsertSize - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

previousId - Variable in class org.bdgenomics.formats.avro.ProcessingStep

Deprecated.

primaryAlignment - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

processingDescription - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

ProcessingStep - Class in org.bdgenomics.formats.avro

ProcessingStep() - Constructor for class org.bdgenomics.formats.avro.ProcessingStep

Default constructor.

ProcessingStep(String, String, String, String, String, String) - Constructor for class org.bdgenomics.formats.avro.ProcessingStep

All-args constructor.

ProcessingStep.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for ProcessingStep instances.

processingSteps - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

processingSteps - Variable in class org.bdgenomics.formats.avro.Sample

Deprecated.

programName - Variable in class org.bdgenomics.formats.avro.ProcessingStep

Deprecated.

properPair - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

proteinHgvs - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

proteinLength - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

proteinPosition - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

PROTOCOL - Static variable in interface org.bdgenomics.formats.avro.BDG.Callback

PROTOCOL - Static variable in interface org.bdgenomics.formats.avro.BDG

put(int, Object) - Method in class org.bdgenomics.formats.avro.Alignment

put(int, Object) - Method in class org.bdgenomics.formats.avro.Dbxref

put(int, Object) - Method in class org.bdgenomics.formats.avro.Feature

put(int, Object) - Method in class org.bdgenomics.formats.avro.Fragment

put(int, Object) - Method in class org.bdgenomics.formats.avro.Genotype

put(int, Object) - Method in class org.bdgenomics.formats.avro.OntologyTerm

put(int, Object) - Method in class org.bdgenomics.formats.avro.ProcessingStep

put(int, Object) - Method in class org.bdgenomics.formats.avro.Read

put(int, Object) - Method in class org.bdgenomics.formats.avro.ReadGroup

put(int, Object) - Method in class org.bdgenomics.formats.avro.Reference

put(int, Object) - Method in class org.bdgenomics.formats.avro.Sample

put(int, Object) - Method in class org.bdgenomics.formats.avro.Sequence

put(int, Object) - Method in class org.bdgenomics.formats.avro.Slice

put(int, Object) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

put(int, Object) - Method in class org.bdgenomics.formats.avro.Variant

put(int, Object) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

put(int, Object) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Q

quality - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

qualityScores - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

qualityScores - Variable in class org.bdgenomics.formats.avro.Read

Deprecated.

R

rank - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

Read - Class in org.bdgenomics.formats.avro

Read() - Constructor for class org.bdgenomics.formats.avro.Read

Default constructor.

Read(String, String, Alphabet, String, Long, String, Map<String, String>) - Constructor for class org.bdgenomics.formats.avro.Read

All-args constructor.

Read.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for Read instances.

readDepth - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

readDepth - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.Alignment

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.Dbxref

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.Feature

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.Fragment

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.Genotype

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.OntologyTerm

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.ProcessingStep

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.Read

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.ReadGroup

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.Reference

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.Sample

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.Sequence

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.Slice

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.Variant

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

readExternal(ObjectInput) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

ReadGroup - Class in org.bdgenomics.formats.avro

ReadGroup() - Constructor for class org.bdgenomics.formats.avro.ReadGroup

Default constructor.

ReadGroup(String, String, String, Long, String, String, String, Integer, String, String, String, String, List<ProcessingStep>) - Constructor for class org.bdgenomics.formats.avro.ReadGroup

All-args constructor.

ReadGroup.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for ReadGroup instances.

readGroupId - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

readGroupId - Variable in class org.bdgenomics.formats.avro.Fragment

Deprecated.

readGroupSampleId - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

readInFragment - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

readMapped - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

readName - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

readNegativeStrand - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

readPaired - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

readPositionRankSum - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

Reference - Class in org.bdgenomics.formats.avro

Reference() - Constructor for class org.bdgenomics.formats.avro.Reference

Default constructor.

Reference(String, Long, String, String, String, List<String>, String, Integer) - Constructor for class org.bdgenomics.formats.avro.Reference

All-args constructor.

Reference.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for Reference instances.

referenceAllele - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

referenceForwardReadDepth - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

referenceName - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

referenceName - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

referenceName - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

referenceName - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

referenceReadDepth - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

referenceReadDepth - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

referenceReverseReadDepth - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

reverseReadDepth - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

rmsMapQ - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

runDateEpoch - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

S

Sample - Class in org.bdgenomics.formats.avro

Sample() - Constructor for class org.bdgenomics.formats.avro.Sample

Default constructor.

Sample(String, String, Map<String, String>, List<ProcessingStep>) - Constructor for class org.bdgenomics.formats.avro.Sample

All-args constructor.

Sample.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for Sample instances.

sampleDescription - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

sampleId - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

sampleId - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

sampleId - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.Alignment

SCHEMA$ - Static variable in enum org.bdgenomics.formats.avro.Alphabet

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.Dbxref

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.Feature

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.Fragment

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.Genotype

SCHEMA$ - Static variable in enum org.bdgenomics.formats.avro.GenotypeAllele

SCHEMA$ - Static variable in enum org.bdgenomics.formats.avro.GenotypeType

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.OntologyTerm

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.ProcessingStep

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.Read

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.ReadGroup

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.Reference

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.Sample

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.Sequence

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.Slice

SCHEMA$ - Static variable in enum org.bdgenomics.formats.avro.Strand

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.TranscriptEffect

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.Variant

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.VariantAnnotation

SCHEMA$ - Static variable in enum org.bdgenomics.formats.avro.VariantAnnotationMessage

SCHEMA$ - Static variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

score - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

secondaryAlignment - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

sequence - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

sequence - Variable in class org.bdgenomics.formats.avro.Read

Deprecated.

Sequence - Class in org.bdgenomics.formats.avro

Sequence() - Constructor for class org.bdgenomics.formats.avro.Sequence

Default constructor.

Sequence(String, String, Alphabet, String, Long, Map<String, String>) - Constructor for class org.bdgenomics.formats.avro.Sequence

All-args constructor.

sequence - Variable in class org.bdgenomics.formats.avro.Sequence

Deprecated.

sequence - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

Sequence.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for Sequence instances.

sequencingCenter - Variable in class org.bdgenomics.formats.avro.ReadGroup

Deprecated.

setAccession(String) - Method in class org.bdgenomics.formats.avro.Dbxref.Builder

Sets the value of the 'accession' field.

setAccession(String) - Method in class org.bdgenomics.formats.avro.Dbxref

Sets the value of the 'accession' field.

setAccession(String) - Method in class org.bdgenomics.formats.avro.OntologyTerm.Builder

Sets the value of the 'accession' field.

setAccession(String) - Method in class org.bdgenomics.formats.avro.OntologyTerm

Sets the value of the 'accession' field.

setAliases(List<String>) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'aliases' field.

setAliases(List<String>) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'aliases' field.

setAlignments(List<Alignment>) - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Sets the value of the 'alignments' field.

setAlignments(List<Alignment>) - Method in class org.bdgenomics.formats.avro.Fragment

Sets the value of the 'alignments' field.

setAlleleCount(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'alleleCount' field.

setAlleleCount(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'alleleCount' field.

setAlleleFrequency(Float) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'alleleFrequency' field.

setAlleleFrequency(Float) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'alleleFrequency' field.

setAlleles(List<GenotypeAllele>) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'alleles' field.

setAlleles(List<GenotypeAllele>) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'alleles' field.

setAlphabet(Alphabet) - Method in class org.bdgenomics.formats.avro.Read.Builder

Sets the value of the 'alphabet' field.

setAlphabet(Alphabet) - Method in class org.bdgenomics.formats.avro.Read

Sets the value of the 'alphabet' field.

setAlphabet(Alphabet) - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Sets the value of the 'alphabet' field.

setAlphabet(Alphabet) - Method in class org.bdgenomics.formats.avro.Sequence

Sets the value of the 'alphabet' field.

setAlphabet(Alphabet) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'alphabet' field.

setAlphabet(Alphabet) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'alphabet' field.

setAlternateAllele(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'alternateAllele' field.

setAlternateAllele(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'alternateAllele' field.

setAlternateAllele(String) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'alternateAllele' field.

setAlternateAllele(String) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'alternateAllele' field.

setAlternateReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'alternateReadDepth' field.

setAlternateReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'alternateReadDepth' field.

setAncestralAllele(String) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'ancestralAllele' field.

setAncestralAllele(String) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'ancestralAllele' field.

setAnnotation(VariantAnnotation) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'annotation' field.

setAnnotation(VariantAnnotation) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'annotation' field.

setAnnotationBuilder(VariantAnnotation.Builder) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the Builder instance for the 'annotation' field Annotation for this variant, if any.

setAssembly(String) - Method in class org.bdgenomics.formats.avro.Reference.Builder

Sets the value of the 'assembly' field.

setAssembly(String) - Method in class org.bdgenomics.formats.avro.Reference

Sets the value of the 'assembly' field.

setAttributes(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'attributes' field.

setAttributes(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.Read.Builder

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.Read

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.Sample.Builder

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.Sample

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.Sequence

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'attributes' field.

setAttributes(Map<String, String>) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'attributes' field.

setBaseQRankSum(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'baseQRankSum' field.

setBaseQRankSum(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'baseQRankSum' field.

setBasesTrimmedFromEnd(Integer) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'basesTrimmedFromEnd' field.

setBasesTrimmedFromEnd(Integer) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'basesTrimmedFromEnd' field.

setBasesTrimmedFromStart(Integer) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'basesTrimmedFromStart' field.

setBasesTrimmedFromStart(Integer) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'basesTrimmedFromStart' field.

setBiotype(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'biotype' field.

setBiotype(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'biotype' field.

setCdnaLength(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'cdnaLength' field.

setCdnaLength(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'cdnaLength' field.

setCdnaPosition(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'cdnaPosition' field.

setCdnaPosition(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'cdnaPosition' field.

setCdsLength(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'cdsLength' field.

setCdsLength(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'cdsLength' field.

setCdsPosition(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'cdsPosition' field.

setCdsPosition(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'cdsPosition' field.

setCigar(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'cigar' field.

setCigar(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'cigar' field.

setCigar(String) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'cigar' field.

setCigar(String) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'cigar' field.

setCircular(Boolean) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'circular' field.

setCircular(Boolean) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'circular' field.

setCommandLine(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Sets the value of the 'commandLine' field.

setCommandLine(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep

Sets the value of the 'commandLine' field.

setCulprit(String) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'culprit' field.

setCulprit(String) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'culprit' field.

setDb(String) - Method in class org.bdgenomics.formats.avro.Dbxref.Builder

Sets the value of the 'db' field.

setDb(String) - Method in class org.bdgenomics.formats.avro.Dbxref

Sets the value of the 'db' field.

setDb(String) - Method in class org.bdgenomics.formats.avro.OntologyTerm.Builder

Sets the value of the 'db' field.

setDb(String) - Method in class org.bdgenomics.formats.avro.OntologyTerm

Sets the value of the 'db' field.

setDbSnp(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'dbSnp' field.

setDbSnp(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'dbSnp' field.

setDbxrefs(List<Dbxref>) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'dbxrefs' field.

setDbxrefs(List<Dbxref>) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'dbxrefs' field.

setDerivesFrom(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'derivesFrom' field.

setDerivesFrom(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'derivesFrom' field.

setDescription(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Sets the value of the 'description' field.

setDescription(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep

Sets the value of the 'description' field.

setDescription(String) - Method in class org.bdgenomics.formats.avro.Read.Builder

Sets the value of the 'description' field.

setDescription(String) - Method in class org.bdgenomics.formats.avro.Read

Sets the value of the 'description' field.

setDescription(String) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'description' field.

setDescription(String) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'description' field.

setDescription(String) - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Sets the value of the 'description' field.

setDescription(String) - Method in class org.bdgenomics.formats.avro.Sequence

Sets the value of the 'description' field.

setDescription(String) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'description' field.

setDescription(String) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'description' field.

setDistance(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'distance' field.

setDistance(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'distance' field.

setDownsampled(Boolean) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'downsampled' field.

setDownsampled(Boolean) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'downsampled' field.

setDuplicateRead(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'duplicateRead' field.

setDuplicateRead(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'duplicateRead' field.

setEffects(List<String>) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'effects' field.

setEffects(List<String>) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'effects' field.

setEnd(Long) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'end' field.

setEnd(Long) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'end' field.

setEnd(Long) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'end' field.

setEnd(Long) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'end' field.

setEnd(Long) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'end' field.

setEnd(Long) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'end' field.

setEnd(Long) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'end' field.

setEnd(Long) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'end' field.

setEnd(Long) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'end' field.

setEnd(Long) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'end' field.

setExonId(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'exonId' field.

setExonId(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'exonId' field.

setExpectedAlleleDosage(Float) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'expectedAlleleDosage' field.

setExpectedAlleleDosage(Float) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'expectedAlleleDosage' field.

setFailedVendorQualityChecks(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'failedVendorQualityChecks' field.

setFailedVendorQualityChecks(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'failedVendorQualityChecks' field.

setFeatureId(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'featureId' field.

setFeatureId(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'featureId' field.

setFeatureId(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'featureId' field.

setFeatureId(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'featureId' field.

setFeatureType(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'featureType' field.

setFeatureType(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'featureType' field.

setFeatureType(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'featureType' field.

setFeatureType(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'featureType' field.

setFiltersApplied(Boolean) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'filtersApplied' field.

setFiltersApplied(Boolean) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'filtersApplied' field.

setFiltersApplied(Boolean) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'filtersApplied' field.

setFiltersApplied(Boolean) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'filtersApplied' field.

setFiltersFailed(List<String>) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'filtersFailed' field.

setFiltersFailed(List<String>) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'filtersFailed' field.

setFiltersFailed(List<String>) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'filtersFailed' field.

setFiltersFailed(List<String>) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'filtersFailed' field.

setFiltersPassed(Boolean) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'filtersPassed' field.

setFiltersPassed(Boolean) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'filtersPassed' field.

setFiltersPassed(Boolean) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'filtersPassed' field.

setFiltersPassed(Boolean) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'filtersPassed' field.

setFisherStrandBiasPValue(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'fisherStrandBiasPValue' field.

setFisherStrandBiasPValue(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'fisherStrandBiasPValue' field.

setFlowOrder(String) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'flowOrder' field.

setFlowOrder(String) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'flowOrder' field.

setForwardReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'forwardReadDepth' field.

setForwardReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'forwardReadDepth' field.

setFrame(Integer) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'frame' field.

setFrame(Integer) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'frame' field.

setGap(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'gap' field.

setGap(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'gap' field.

setGeneId(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'geneId' field.

setGeneId(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'geneId' field.

setGeneId(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'geneId' field.

setGeneId(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'geneId' field.

setGeneName(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'geneName' field.

setGeneName(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'geneName' field.

setGenomicHgvs(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'genomicHgvs' field.

setGenomicHgvs(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'genomicHgvs' field.

setGenotypeLikelihoods(List<Double>) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'genotypeLikelihoods' field.

setGenotypeLikelihoods(List<Double>) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'genotypeLikelihoods' field.

setGenotypePosteriors(List<Float>) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'genotypePosteriors' field.

setGenotypePosteriors(List<Float>) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'genotypePosteriors' field.

setGenotypePriors(List<Float>) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'genotypePriors' field.

setGenotypePriors(List<Float>) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'genotypePriors' field.

setGenotypeQuality(Integer) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'genotypeQuality' field.

setGenotypeQuality(Integer) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'genotypeQuality' field.

setHapMap2(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'hapMap2' field.

setHapMap2(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'hapMap2' field.

setHapMap3(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'hapMap3' field.

setHapMap3(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'hapMap3' field.

setId(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Sets the value of the 'id' field.

setId(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep

Sets the value of the 'id' field.

setId(String) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'id' field.

setId(String) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'id' field.

setId(String) - Method in class org.bdgenomics.formats.avro.Sample.Builder

Sets the value of the 'id' field.

setId(String) - Method in class org.bdgenomics.formats.avro.Sample

Sets the value of the 'id' field.

setIndex(Integer) - Method in class org.bdgenomics.formats.avro.Reference.Builder

Sets the value of the 'index' field.

setIndex(Integer) - Method in class org.bdgenomics.formats.avro.Reference

Sets the value of the 'index' field.

setIndex(Integer) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'index' field.

setIndex(Integer) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'index' field.

setInsertSize(Long) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'insertSize' field.

setInsertSize(Long) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'insertSize' field.

setInsertSize(Integer) - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Sets the value of the 'insertSize' field.

setInsertSize(Integer) - Method in class org.bdgenomics.formats.avro.Fragment

Sets the value of the 'insertSize' field.

setKeySequence(String) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'keySequence' field.

setKeySequence(String) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'keySequence' field.

setLength(Long) - Method in class org.bdgenomics.formats.avro.Read.Builder

Sets the value of the 'length' field.

setLength(Long) - Method in class org.bdgenomics.formats.avro.Read

Sets the value of the 'length' field.

setLength(Long) - Method in class org.bdgenomics.formats.avro.Reference.Builder

Sets the value of the 'length' field.

setLength(Long) - Method in class org.bdgenomics.formats.avro.Reference

Sets the value of the 'length' field.

setLength(Long) - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Sets the value of the 'length' field.

setLength(Long) - Method in class org.bdgenomics.formats.avro.Sequence

Sets the value of the 'length' field.

setLength(Long) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'length' field.

setLength(Long) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'length' field.

setLibrary(String) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'library' field.

setLibrary(String) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'library' field.

setMappingQuality(Integer) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'mappingQuality' field.

setMappingQuality(Integer) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'mappingQuality' field.

setMapq0Reads(Integer) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'mapq0Reads' field.

setMapq0Reads(Integer) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'mapq0Reads' field.

setMateAlignmentStart(Long) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'mateAlignmentStart' field.

setMateAlignmentStart(Long) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'mateAlignmentStart' field.

setMateMapped(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'mateMapped' field.

setMateMapped(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'mateMapped' field.

setMateNegativeStrand(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'mateNegativeStrand' field.

setMateNegativeStrand(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'mateNegativeStrand' field.

setMateReferenceName(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'mateReferenceName' field.

setMateReferenceName(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'mateReferenceName' field.

setMd5(String) - Method in class org.bdgenomics.formats.avro.Reference.Builder

Sets the value of the 'md5' field.

setMd5(String) - Method in class org.bdgenomics.formats.avro.Reference

Sets the value of the 'md5' field.

setMessages(List<VariantAnnotationMessage>) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'messages' field.

setMessages(List<VariantAnnotationMessage>) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'messages' field.

setMinReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'minReadDepth' field.

setMinReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'minReadDepth' field.

setMismatchingPositions(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'mismatchingPositions' field.

setMismatchingPositions(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'mismatchingPositions' field.

setMqRankSum(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'mqRankSum' field.

setMqRankSum(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'mqRankSum' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Fragment

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Read.Builder

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Read

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Reference.Builder

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Reference

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Sample.Builder

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Sample

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Sequence

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'name' field.

setName(String) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'name' field.

setNames(List<String>) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'names' field.

setNames(List<String>) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'names' field.

setNonReferenceLikelihoods(List<Double>) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'nonReferenceLikelihoods' field.

setNonReferenceLikelihoods(List<Double>) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'nonReferenceLikelihoods' field.

setNotes(List<String>) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'notes' field.

setNotes(List<String>) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'notes' field.

setOntologyTerms(List<OntologyTerm>) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'ontologyTerms' field.

setOntologyTerms(List<OntologyTerm>) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'ontologyTerms' field.

setOriginalCigar(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'originalCigar' field.

setOriginalCigar(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'originalCigar' field.

setOriginalQualityScores(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'originalQualityScores' field.

setOriginalQualityScores(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'originalQualityScores' field.

setOriginalStart(Long) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'originalStart' field.

setOriginalStart(Long) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'originalStart' field.

setParentIds(List<String>) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'parentIds' field.

setParentIds(List<String>) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'parentIds' field.

setPhase(Integer) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'phase' field.

setPhase(Integer) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'phase' field.

setPhased(Boolean) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'phased' field.

setPhased(Boolean) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'phased' field.

setPhaseQuality(Integer) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'phaseQuality' field.

setPhaseQuality(Integer) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'phaseQuality' field.

setPhaseSetId(Integer) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'phaseSetId' field.

setPhaseSetId(Integer) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'phaseSetId' field.

setPlatform(String) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'platform' field.

setPlatform(String) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'platform' field.

setPlatformModel(String) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'platformModel' field.

setPlatformModel(String) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'platformModel' field.

setPlatformUnit(String) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'platformUnit' field.

setPlatformUnit(String) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'platformUnit' field.

setPredictedMedianInsertSize(Integer) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'predictedMedianInsertSize' field.

setPredictedMedianInsertSize(Integer) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'predictedMedianInsertSize' field.

setPreviousId(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Sets the value of the 'previousId' field.

setPreviousId(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep

Sets the value of the 'previousId' field.

setPrimaryAlignment(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'primaryAlignment' field.

setPrimaryAlignment(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'primaryAlignment' field.

setProcessingDescription(String) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'processingDescription' field.

setProcessingDescription(String) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'processingDescription' field.

setProcessingSteps(List<ProcessingStep>) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'processingSteps' field.

setProcessingSteps(List<ProcessingStep>) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'processingSteps' field.

setProcessingSteps(List<ProcessingStep>) - Method in class org.bdgenomics.formats.avro.Sample.Builder

Sets the value of the 'processingSteps' field.

setProcessingSteps(List<ProcessingStep>) - Method in class org.bdgenomics.formats.avro.Sample

Sets the value of the 'processingSteps' field.

setProgramName(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Sets the value of the 'programName' field.

setProgramName(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep

Sets the value of the 'programName' field.

setProperPair(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'properPair' field.

setProperPair(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'properPair' field.

setProteinHgvs(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'proteinHgvs' field.

setProteinHgvs(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'proteinHgvs' field.

setProteinLength(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'proteinLength' field.

setProteinLength(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'proteinLength' field.

setProteinPosition(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'proteinPosition' field.

setProteinPosition(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'proteinPosition' field.

setQuality(Double) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'quality' field.

setQuality(Double) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'quality' field.

setQualityScores(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'qualityScores' field.

setQualityScores(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'qualityScores' field.

setQualityScores(String) - Method in class org.bdgenomics.formats.avro.Read.Builder

Sets the value of the 'qualityScores' field.

setQualityScores(String) - Method in class org.bdgenomics.formats.avro.Read

Sets the value of the 'qualityScores' field.

setRank(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'rank' field.

setRank(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'rank' field.

setReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'readDepth' field.

setReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'readDepth' field.

setReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'readDepth' field.

setReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'readDepth' field.

setReadGroupId(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'readGroupId' field.

setReadGroupId(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'readGroupId' field.

setReadGroupId(String) - Method in class org.bdgenomics.formats.avro.Fragment.Builder

Sets the value of the 'readGroupId' field.

setReadGroupId(String) - Method in class org.bdgenomics.formats.avro.Fragment

Sets the value of the 'readGroupId' field.

setReadGroupSampleId(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'readGroupSampleId' field.

setReadGroupSampleId(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'readGroupSampleId' field.

setReadInFragment(Integer) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'readInFragment' field.

setReadInFragment(Integer) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'readInFragment' field.

setReadMapped(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'readMapped' field.

setReadMapped(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'readMapped' field.

setReadName(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'readName' field.

setReadName(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'readName' field.

setReadNegativeStrand(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'readNegativeStrand' field.

setReadNegativeStrand(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'readNegativeStrand' field.

setReadPaired(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'readPaired' field.

setReadPaired(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'readPaired' field.

setReadPositionRankSum(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'readPositionRankSum' field.

setReadPositionRankSum(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'readPositionRankSum' field.

setReferenceAllele(String) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'referenceAllele' field.

setReferenceAllele(String) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'referenceAllele' field.

setReferenceForwardReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'referenceForwardReadDepth' field.

setReferenceForwardReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'referenceForwardReadDepth' field.

setReferenceName(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'referenceName' field.

setReferenceName(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'referenceName' field.

setReferenceName(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'referenceName' field.

setReferenceName(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'referenceName' field.

setReferenceName(String) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'referenceName' field.

setReferenceName(String) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'referenceName' field.

setReferenceName(String) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'referenceName' field.

setReferenceName(String) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'referenceName' field.

setReferenceReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'referenceReadDepth' field.

setReferenceReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'referenceReadDepth' field.

setReferenceReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'referenceReadDepth' field.

setReferenceReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'referenceReadDepth' field.

setReferenceReverseReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'referenceReverseReadDepth' field.

setReferenceReverseReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'referenceReverseReadDepth' field.

setReverseReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'reverseReadDepth' field.

setReverseReadDepth(Integer) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'reverseReadDepth' field.

setRmsMapQ(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'rmsMapQ' field.

setRmsMapQ(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'rmsMapQ' field.

setRunDateEpoch(Long) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'runDateEpoch' field.

setRunDateEpoch(Long) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'runDateEpoch' field.

setSampleDescription(String) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'sampleDescription' field.

setSampleDescription(String) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'sampleDescription' field.

setSampleId(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'sampleId' field.

setSampleId(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'sampleId' field.

setSampleId(String) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'sampleId' field.

setSampleId(String) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'sampleId' field.

setSampleId(String) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'sampleId' field.

setSampleId(String) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'sampleId' field.

setScore(Double) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'score' field.

setScore(Double) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'score' field.

setSecondaryAlignment(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'secondaryAlignment' field.

setSecondaryAlignment(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'secondaryAlignment' field.

setSequence(String) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'sequence' field.

setSequence(String) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'sequence' field.

setSequence(String) - Method in class org.bdgenomics.formats.avro.Read.Builder

Sets the value of the 'sequence' field.

setSequence(String) - Method in class org.bdgenomics.formats.avro.Read

Sets the value of the 'sequence' field.

setSequence(String) - Method in class org.bdgenomics.formats.avro.Sequence.Builder

Sets the value of the 'sequence' field.

setSequence(String) - Method in class org.bdgenomics.formats.avro.Sequence

Sets the value of the 'sequence' field.

setSequence(String) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'sequence' field.

setSequence(String) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'sequence' field.

setSequencingCenter(String) - Method in class org.bdgenomics.formats.avro.ReadGroup.Builder

Sets the value of the 'sequencingCenter' field.

setSequencingCenter(String) - Method in class org.bdgenomics.formats.avro.ReadGroup

Sets the value of the 'sequencingCenter' field.

setSlices(Integer) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'slices' field.

setSlices(Integer) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'slices' field.

setSomatic(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'somatic' field.

setSomatic(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'somatic' field.

setSource(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'source' field.

setSource(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'source' field.

setSourceAccessions(List<String>) - Method in class org.bdgenomics.formats.avro.Reference.Builder

Sets the value of the 'sourceAccessions' field.

setSourceAccessions(List<String>) - Method in class org.bdgenomics.formats.avro.Reference

Sets the value of the 'sourceAccessions' field.

setSourceUri(String) - Method in class org.bdgenomics.formats.avro.Reference.Builder

Sets the value of the 'sourceUri' field.

setSourceUri(String) - Method in class org.bdgenomics.formats.avro.Reference

Sets the value of the 'sourceUri' field.

setSpecies(String) - Method in class org.bdgenomics.formats.avro.Reference.Builder

Sets the value of the 'species' field.

setSpecies(String) - Method in class org.bdgenomics.formats.avro.Reference

Sets the value of the 'species' field.

setSplitFromMultiAllelic(Boolean) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'splitFromMultiAllelic' field.

setSplitFromMultiAllelic(Boolean) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'splitFromMultiAllelic' field.

setSplitFromMultiAllelic(Boolean) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'splitFromMultiAllelic' field.

setSplitFromMultiAllelic(Boolean) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'splitFromMultiAllelic' field.

setStart(Long) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'start' field.

setStart(Long) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'start' field.

setStart(Long) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'start' field.

setStart(Long) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'start' field.

setStart(Long) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'start' field.

setStart(Long) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'start' field.

setStart(Long) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'start' field.

setStart(Long) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'start' field.

setStart(Long) - Method in class org.bdgenomics.formats.avro.Variant.Builder

Sets the value of the 'start' field.

setStart(Long) - Method in class org.bdgenomics.formats.avro.Variant

Sets the value of the 'start' field.

setStrand(Strand) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'strand' field.

setStrand(Strand) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'strand' field.

setStrand(Strand) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'strand' field.

setStrand(Strand) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'strand' field.

setStrandBiasComponents(List<Integer>) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'strandBiasComponents' field.

setStrandBiasComponents(List<Integer>) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'strandBiasComponents' field.

setSupplementaryAlignment(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment.Builder

Sets the value of the 'supplementaryAlignment' field.

setSupplementaryAlignment(Boolean) - Method in class org.bdgenomics.formats.avro.Alignment

Sets the value of the 'supplementaryAlignment' field.

setTarget(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'target' field.

setTarget(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'target' field.

setThousandGenomes(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'thousandGenomes' field.

setThousandGenomes(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'thousandGenomes' field.

setTotal(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'total' field.

setTotal(Integer) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'total' field.

setTotalLength(Long) - Method in class org.bdgenomics.formats.avro.Slice.Builder

Sets the value of the 'totalLength' field.

setTotalLength(Long) - Method in class org.bdgenomics.formats.avro.Slice

Sets the value of the 'totalLength' field.

setTranscriptEffects(List<TranscriptEffect>) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'transcriptEffects' field.

setTranscriptEffects(List<TranscriptEffect>) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'transcriptEffects' field.

setTranscriptHgvs(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect.Builder

Sets the value of the 'transcriptHgvs' field.

setTranscriptHgvs(String) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Sets the value of the 'transcriptHgvs' field.

setTranscriptId(String) - Method in class org.bdgenomics.formats.avro.Feature.Builder

Sets the value of the 'transcriptId' field.

setTranscriptId(String) - Method in class org.bdgenomics.formats.avro.Feature

Sets the value of the 'transcriptId' field.

setValidated(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation.Builder

Sets the value of the 'validated' field.

setValidated(Boolean) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Sets the value of the 'validated' field.

setVariant(Variant) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'variant' field.

setVariant(Variant) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'variant' field.

setVariantBuilder(Variant.Builder) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the Builder instance for the 'variant' field The variant called at this site.

setVariantCallingAnnotations(VariantCallingAnnotations) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the value of the 'variantCallingAnnotations' field.

setVariantCallingAnnotations(VariantCallingAnnotations) - Method in class org.bdgenomics.formats.avro.Genotype

Sets the value of the 'variantCallingAnnotations' field.

setVariantCallingAnnotationsBuilder(VariantCallingAnnotations.Builder) - Method in class org.bdgenomics.formats.avro.Genotype.Builder

Sets the Builder instance for the 'variantCallingAnnotations' field Statistics collected at this site, if available.

setVersion(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep.Builder

Sets the value of the 'version' field.

setVersion(String) - Method in class org.bdgenomics.formats.avro.ProcessingStep

Sets the value of the 'version' field.

setVqslod(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations.Builder

Sets the value of the 'vqslod' field.

setVqslod(Float) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Sets the value of the 'vqslod' field.

Slice - Class in org.bdgenomics.formats.avro

Slice() - Constructor for class org.bdgenomics.formats.avro.Slice

Default constructor.

Slice(String, String, Alphabet, String, Long, Long, Strand, Long, Long, Integer, Integer, Map<String, String>) - Constructor for class org.bdgenomics.formats.avro.Slice

All-args constructor.

Slice.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for Slice instances.

slices - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

somatic - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

source - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

sourceAccessions - Variable in class org.bdgenomics.formats.avro.Reference

Deprecated.

sourceUri - Variable in class org.bdgenomics.formats.avro.Reference

Deprecated.

species - Variable in class org.bdgenomics.formats.avro.Reference

Deprecated.

splitFromMultiAllelic - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

splitFromMultiAllelic - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

start - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

start - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

start - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

start - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

start - Variable in class org.bdgenomics.formats.avro.Variant

Deprecated.

strand - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

strand - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

Strand - Enum in org.bdgenomics.formats.avro

strandBiasComponents - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

supplementaryAlignment - Variable in class org.bdgenomics.formats.avro.Alignment

Deprecated.

T

target - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

thousandGenomes - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.Alignment

Serializes this Alignment to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.Dbxref

Serializes this Dbxref to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.Feature

Serializes this Feature to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.Fragment

Serializes this Fragment to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.Genotype

Serializes this Genotype to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.OntologyTerm

Serializes this OntologyTerm to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.ProcessingStep

Serializes this ProcessingStep to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.Read

Serializes this Read to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.ReadGroup

Serializes this ReadGroup to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.Reference

Serializes this Reference to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.Sample

Serializes this Sample to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.Sequence

Serializes this Sequence to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.Slice

Serializes this Slice to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.TranscriptEffect

Serializes this TranscriptEffect to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.Variant

Serializes this Variant to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.VariantAnnotation

Serializes this VariantAnnotation to a ByteBuffer.

toByteBuffer() - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Serializes this VariantCallingAnnotations to a ByteBuffer.

total - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

totalLength - Variable in class org.bdgenomics.formats.avro.Slice

Deprecated.

TranscriptEffect - Class in org.bdgenomics.formats.avro

TranscriptEffect() - Constructor for class org.bdgenomics.formats.avro.TranscriptEffect

Default constructor.

TranscriptEffect(String, List<String>, String, String, String, String, String, Integer, Integer, String, String, String, Integer, Integer, Integer, Integer, Integer, Integer, Integer, List<VariantAnnotationMessage>) - Constructor for class org.bdgenomics.formats.avro.TranscriptEffect

All-args constructor.

TranscriptEffect.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for TranscriptEffect instances.

transcriptEffects - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

transcriptHgvs - Variable in class org.bdgenomics.formats.avro.TranscriptEffect

Deprecated.

transcriptId - Variable in class org.bdgenomics.formats.avro.Feature

Deprecated.

V

validated - Variable in class org.bdgenomics.formats.avro.VariantAnnotation

Deprecated.

valueOf(String) - Static method in enum org.bdgenomics.formats.avro.Alphabet

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.bdgenomics.formats.avro.GenotypeAllele

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.bdgenomics.formats.avro.GenotypeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.bdgenomics.formats.avro.Strand

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.bdgenomics.formats.avro.VariantAnnotationMessage

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.bdgenomics.formats.avro.Alphabet

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.bdgenomics.formats.avro.GenotypeAllele

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.bdgenomics.formats.avro.GenotypeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.bdgenomics.formats.avro.Strand

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.bdgenomics.formats.avro.VariantAnnotationMessage

Returns an array containing the constants of this enum type, in the order they are declared.

variant - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

Variant - Class in org.bdgenomics.formats.avro

Variant() - Constructor for class org.bdgenomics.formats.avro.Variant

Default constructor.

Variant(String, Long, Long, List<String>, Boolean, String, String, Double, Boolean, Boolean, List<String>, VariantAnnotation) - Constructor for class org.bdgenomics.formats.avro.Variant

All-args constructor.

Variant.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for Variant instances.

VariantAnnotation - Class in org.bdgenomics.formats.avro

VariantAnnotation() - Constructor for class org.bdgenomics.formats.avro.VariantAnnotation

Default constructor.

VariantAnnotation(String, Integer, Integer, Integer, Integer, Integer, Integer, Integer, Float, String, Boolean, Boolean, Boolean, Boolean, Boolean, Boolean, List<TranscriptEffect>, Map<String, String>) - Constructor for class org.bdgenomics.formats.avro.VariantAnnotation

All-args constructor.

VariantAnnotation.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for VariantAnnotation instances.

VariantAnnotationMessage - Enum in org.bdgenomics.formats.avro

variantCallingAnnotations - Variable in class org.bdgenomics.formats.avro.Genotype

Deprecated.

VariantCallingAnnotations - Class in org.bdgenomics.formats.avro

VariantCallingAnnotations() - Constructor for class org.bdgenomics.formats.avro.VariantCallingAnnotations

Default constructor.

VariantCallingAnnotations(Boolean, Boolean, List<String>, Boolean, Float, Float, Float, Integer, Float, Float, List<Float>, List<Float>, Float, String, Map<String, String>) - Constructor for class org.bdgenomics.formats.avro.VariantCallingAnnotations

All-args constructor.

VariantCallingAnnotations.Builder - Class in org.bdgenomics.formats.avro

RecordBuilder for VariantCallingAnnotations instances.

version - Variable in class org.bdgenomics.formats.avro.ProcessingStep

Deprecated.

vqslod - Variable in class org.bdgenomics.formats.avro.VariantCallingAnnotations

Deprecated.

W

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.Alignment

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.Dbxref

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.Feature

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.Fragment

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.Genotype

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.OntologyTerm

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.ProcessingStep

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.Read

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.ReadGroup

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.Reference

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.Sample

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.Sequence

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.Slice

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.TranscriptEffect

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.Variant

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.VariantAnnotation

writeExternal(ObjectOutput) - Method in class org.bdgenomics.formats.avro.VariantCallingAnnotations

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