Class Hierarchy
- java.lang.Object
- org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates
- org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates.Relative
- org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
- picard.sam.AbstractAlignmentMerger
- org.broadinstitute.hellbender.utils.codecs.AbstractBCICodec<F> (implements htsjdk.tribble.FeatureCodec<FEATURE_TYPE,SOURCE>, org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodec<F,S>)
- java.util.AbstractCollection<E> (implements java.util.Collection<E>)
- org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.sv.AbstractEvidenceSortMerger<F> (implements org.broadinstitute.hellbender.utils.codecs.FeatureSink<F>)
- java.util.concurrent.AbstractExecutorService (implements java.util.concurrent.ExecutorService)
- htsjdk.tribble.AbstractFeatureCodec<FEATURE_TYPE,SOURCE> (implements htsjdk.tribble.FeatureCodec<FEATURE_TYPE,SOURCE>)
- org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec
- htsjdk.tribble.AsciiFeatureCodec<T>
- org.jgrapht.graph.AbstractGraph<V,E> (implements org.jgrapht.Graph<V,E>)
- org.jgrapht.graph.AbstractBaseGraph<V,E> (implements java.lang.Cloneable, org.jgrapht.Graph<V,E>, java.io.Serializable)
- org.jgrapht.graph.DefaultDirectedGraph<V,E> (implements org.jgrapht.DirectedGraph<V,E>)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph<V,E>
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph (implements org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KmerSearchableGraph<V,E>)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqGraph
- picard.illumina.parser.readers.AbstractIlluminaPositionFileReader (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
- org.apache.commons.math3.distribution.AbstractIntegerDistribution (implements org.apache.commons.math3.distribution.IntegerDistribution, java.io.Serializable)
- htsjdk.samtools.util.AbstractIterator<E> (implements java.util.Iterator<E>)
- java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
- java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
- htsjdk.samtools.util.CollectionUtil.DefaultingMap<K,V>
- java.util.LinkedHashMap<K,V> (implements java.util.Map<K,V>)
- org.broadinstitute.hellbender.utils.LRUCache<K,V>
- java.util.TreeMap<K,V> (implements java.lang.Cloneable, java.util.NavigableMap<K,V>, java.io.Serializable)
- picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
- htsjdk.samtools.util.AbstractProgressLogger (implements htsjdk.samtools.util.ProgressLoggerInterface)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph.MyEdgeFactory (implements org.jgrapht.EdgeFactory<V,E>)
- org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractRecordCollection<METADATA,RECORD>
- picard.analysis.AbstractWgsMetricsCollector<T>
- org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
- org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState
- org.broadinstitute.hellbender.engine.ActivityProfileStateIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileStateRange
- picard.util.AdapterMarker
- org.broadinstitute.hellbender.transformers.AdapterTrimTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- picard.analysis.AdapterUtility
- org.broadinstitute.hellbender.utils.mcmc.AdaptiveMetropolisSampler
- org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult
- org.broadinstitute.hellbender.tools.funcotator.AliasProvider
- org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedAssembly
- org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
- org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig
- org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.GoodAndBadMappings
- org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContigGenerator
- org.broadinstitute.hellbender.engine.AlignmentAndReferenceContext
- org.broadinstitute.hellbender.engine.AlignmentContext (implements org.broadinstitute.hellbender.utils.HasGenomeLocation, htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.utils.locusiterator.AlignmentContextIteratorBuilder
- org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval
- org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine
- picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- org.broadinstitute.hellbender.utils.read.AlignmentUtils
- org.broadinstitute.hellbender.utils.read.AlignmentUtils.MismatchCount
- picard.vcf.filter.AlleleBalanceFilter (implements picard.vcf.filter.VariantFilter)
- org.broadinstitute.hellbender.utils.downsampling.AlleleBiasedDownsamplingUtils
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleFiltering
- org.broadinstitute.hellbender.tools.walkers.mutect.filtering.AlleleFilterUtils
- org.broadinstitute.hellbender.tools.walkers.annotator.AlleleFraction (implements org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeAnnotation)
- org.broadinstitute.hellbender.tools.copynumber.segmentation.AlleleFractionKernelSegmenter
- org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionModeller
- org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionPrior
- org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
- org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AlleleFrequencyUtils
- org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods<EVIDENCE,A> (implements org.broadinstitute.hellbender.utils.genotyper.AlleleList<A>, org.broadinstitute.hellbender.utils.genotyper.SampleList)
- org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods.BestAllele
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleLikelihoodWriter (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.utils.genotyper.AlleleList.ActualPermutation<A> (implements org.broadinstitute.hellbender.utils.genotyper.AlleleListPermutation<A>)
- org.broadinstitute.hellbender.utils.genotyper.AlleleList.NonPermutation<A> (implements org.broadinstitute.hellbender.utils.genotyper.AlleleListPermutation<A>)
- org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.AllelePileupCounter
- org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth (implements org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeAnnotation)
- org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
- picard.util.AlleleSubsettingUtils
- org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.copynumber.datacollection.AllelicCountCollector
- org.broadinstitute.hellbender.utils.iterators.AllLocusIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
- org.broadinstitute.hellbender.tools.walkers.varianteval.util.AnalysisModuleScanner
- org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis.ReportTypeCounts
- org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval (implements htsjdk.tribble.Feature, htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
- org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalHeader
- org.broadinstitute.hellbender.tools.funcotator.AnnotatedIntervalToSegmentVariantContextConverter
- org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalUtils
- org.broadinstitute.hellbender.tools.spark.sv.discovery.AnnotatedVariantProducer (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationKey<T>
- org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationMap
- org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
- org.broadinstitute.hellbender.utils.svd.ApacheSingularValueDecomposer (implements org.broadinstitute.hellbender.utils.svd.SingularValueDecomposer)
- org.broadinstitute.hellbender.tools.spark.transforms.ApplyBQSRSparkFn
- org.broadinstitute.hellbender.tools.ApplyBQSRUniqueArgumentCollection (implements java.io.Serializable)
- picard.arrays.illumina.ArraysControlInfo
- org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior
- org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPriorCollection
- org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
- org.broadinstitute.hellbender.utils.read.ArtificialReadIterator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
- org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
- org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_InbreedingCoeff (implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StandardAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth (implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StandardAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation)
- org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality (implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StandardAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation)
- org.broadinstitute.hellbender.tools.walkers.annotator.AS_StrandBiasMutectAnnotation (implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardMutectAnnotation)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
- org.broadinstitute.hellbender.tools.walkers.annotator.AssemblyComplexity (implements org.broadinstitute.hellbender.tools.walkers.annotator.JumboInfoAnnotation)
- org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigAlignmentsRDDProcessor
- org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments
- org.broadinstitute.hellbender.engine.AssemblyRegion (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.engine.AssemblyRegionFromActivityProfileStateIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.engine.AssemblyRegionIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.engine.spark.AssemblyRegionReadShardArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.Result
- org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerContext
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
- org.broadinstitute.hellbender.utils.runtime.AsynchronousStreamWriter<T>
- picard.util.AsyncIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
- org.broadinstitute.hellbender.utils.collections.AutoCloseableCollection<C> (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.utils.AutoCloseableReference<T> (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AutosomalRecessiveConstants
- org.broadinstitute.hellbender.tools.sv.BafEvidence (implements org.broadinstitute.hellbender.tools.sv.SVFeature)
- org.broadinstitute.hellbender.utils.baq.BAQ (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.baq.BAQ.BAQCalculationResult
- picard.util.BarcodeEditDistanceQuery
- picard.illumina.BarcodeExtractor
- picard.illumina.BarcodeExtractor.BarcodeMatch
- picard.illumina.parser.readers.BarcodeFileReader (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.illumina.parser.readers.BaseBclReader
- picard.illumina.parser.readers.BclReader (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.illumina.parser.readers.CbclReader (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.illumina.parser.readers.BaseBclReader.CycleData
- picard.illumina.parser.readers.BaseBclReader.TileData
- picard.cmdline.programgroups.BaseCallingProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.illumina.BasecallsConverter<CLUSTER_OUTPUT_RECORD>
- picard.illumina.BasecallsConverterBuilder<CLUSTER_OUTPUT_RECORD>
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MultiSampleEdge
- picard.sam.SamErrorMetric.BaseErrorAggregation<CALCULATOR>
- picard.sam.SamErrorMetric.BaseErrorCalculator (implements picard.sam.SamErrorMetric.BaseCalculator)
- org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection (implements java.io.Serializable)
- picard.illumina.parser.BaseIlluminaDataProvider (implements java.lang.AutoCloseable, java.lang.Iterable<T>, java.util.Iterator<E>)
- org.broadinstitute.hellbender.transformers.BaseQualityClipReadTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityHistogram (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- org.broadinstitute.hellbender.transformers.BaseQualityReadTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine.BQSRReferenceWindowFunction (implements org.broadinstitute.hellbender.utils.SerializableFunction<T,R>)
- org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn
- org.broadinstitute.hellbender.utils.BaseUtils
- org.broadinstitute.hellbender.utils.BaseUtils.HmerIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex
- org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicSomaticShortMutationValidator
- org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.utils.clustering.BayesianGaussianMixtureModeller (implements java.io.Serializable)
- picard.illumina.parser.BclData
- picard.illumina.parser.readers.BclIndexReader
- picard.illumina.parser.readers.BclQualityEvaluationStrategy
- org.broadinstitute.hellbender.utils.read.mergealignment.BestEndMapqPrimaryAlignmentStrategy (implements org.broadinstitute.hellbender.utils.read.mergealignment.PrimaryAlignmentSelectionStrategy)
- picard.sam.BestEndMapqPrimaryAlignmentStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- org.broadinstitute.hellbender.utils.read.mergealignment.BestMapqPrimaryAlignmentSelectionStrategy (implements org.broadinstitute.hellbender.utils.read.mergealignment.PrimaryAlignmentSelectionStrategy)
- picard.sam.BestMapqPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BetaBinomialCluster (implements org.broadinstitute.hellbender.tools.walkers.mutect.clustering.AlleleFractionCluster)
- org.broadinstitute.hellbender.tools.walkers.readorientation.BetaDistributionShape
- org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.BGMMVariantAnnotationsModel (implements org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsModel)
- org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.BGMMVariantAnnotationsScorer (implements java.io.Serializable, org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsScorer)
- org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils
- org.broadinstitute.hellbender.utils.BinaryTableReader<R> (implements java.lang.AutoCloseable, java.util.Iterator<E>)
- org.broadinstitute.hellbender.utils.BinaryTableWriter<R> (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster (implements org.broadinstitute.hellbender.tools.walkers.mutect.clustering.AlleleFractionCluster)
- org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream
- org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.IndexEntry
- org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Reader<T> (implements htsjdk.tribble.FeatureReader<T>)
- org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer<F> (implements org.broadinstitute.hellbender.utils.codecs.FeatureSink<F>)
- org.broadinstitute.hellbender.transformers.BQSRReadTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications
- org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointDensityFilter (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
- org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidenceClusterer (implements java.util.function.Function<T,R>)
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference
- org.broadinstitute.hellbender.utils.gcs.BucketUtils
- picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- org.broadinstitute.hellbender.utils.logging.BunnyLog
- org.broadinstitute.hellbender.tools.spark.bwa.BwaArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.bwa.BwaMemAlignmentUtils
- org.broadinstitute.hellbender.utils.bwa.BwaMemIndexCache
- org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkEngine (implements java.lang.AutoCloseable)
- picard.vcf.ByIntervalListVariantContextIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.utils.iterators.ByteArrayIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile (implements htsjdk.samtools.reference.ReferenceSequenceFile, java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.CalledHaplotypes
- picard.vcf.CallingMetricAccumulator (implements picard.vcf.processor.VariantProcessor.Accumulator<RESULT>)
- picard.vcf.CallingMetricAccumulator.Result
- org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser
- picard.fastq.Casava18ReadNameEncoder (implements picard.fastq.ReadNameEncoder)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.ChainPruner<V,E>
- picard.analysis.ChimeraUtil
- org.broadinstitute.hellbender.tools.walkers.annotator.ChromosomeCounts (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation)
- org.broadinstitute.hellbender.utils.read.CigarBuilder
- org.broadinstitute.hellbender.utils.read.CigarBuilder.Result
- org.broadinstitute.hellbender.utils.read.CigarUtils
- picard.util.CircularByteBuffer
- org.broadinstitute.hellbender.utils.ClassUtils
- org.broadinstitute.hellbender.utils.clipping.ClippingOp
- picard.util.ClippingUtility
- org.broadinstitute.hellbender.tools.ClipReads.ClippingData
- org.broadinstitute.hellbender.utils.iterators.CloseAtEndIterator<E> (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder
- org.broadinstitute.hellbender.tools.sv.concordance.ClosestSVFinder.ClosestPair
- picard.illumina.parser.ClusterData
- picard.illumina.ClusterDataToSamConverter (implements picard.illumina.BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD>)
- org.broadinstitute.hellbender.tools.sv.cluster.ClusteringParameters
- org.broadinstitute.hellbender.tools.spark.sv.utils.CNVInputReader
- picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection
- picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier
- picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
- picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence.BAFSiteIterator (implements java.util.Iterator<E>)
- picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection (implements picard.cmdline.argumentcollections.IntervalArgumentCollection)
- picard.cmdline.CommandLineDefaults
- org.broadinstitute.barclay.argparser.CommandLinePluginDescriptor<T>
- org.broadinstitute.hellbender.cmdline.CommandLineProgram (implements org.broadinstitute.barclay.argparser.CommandLinePluginProvider)
- picard.cmdline.CommandLineProgram
- picard.cmdline.CommandLineSyntaxTranslater
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.CommonSuffixSplitter
- org.broadinstitute.hellbender.tools.validation.CompareMatrix (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.CompressedDataList<T> (implements java.lang.Iterable<T>)
- org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord
- org.broadinstitute.hellbender.utils.config.ConfigFactory
- org.apache.hadoop.conf.Configured (implements org.apache.hadoop.conf.Configurable)
- org.apache.hadoop.fs.FileSystem (implements java.io.Closeable, org.apache.hadoop.security.token.DelegationTokenIssuer, org.apache.hadoop.fs.PathCapabilities)
- org.apache.hadoop.fs.FilterFileSystem
- org.apache.hadoop.fs.ChecksumFileSystem
- org.apache.hadoop.fs.LocalFileSystem
- org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilterSpark (implements org.apache.spark.api.java.function.Function<T1,R>)
- org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
- org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationRecord
- org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter
- org.broadinstitute.hellbender.utils.recalibration.covariates.ContextCovariate (implements org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate)
- org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ContigChimericAlignmentIterativeInterpreter
- org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.CopyNumberAnnotations
- org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
- org.broadinstitute.hellbender.tools.copynumber.formats.CopyNumberFormatsUtils
- org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyNumberPosteriorDistribution
- org.broadinstitute.hellbender.cmdline.programgroups.CopyNumberProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
- org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.copynumber.segmentation.CopyRatioKernelSegmenter
- org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioModeller
- org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment (implements htsjdk.samtools.util.Locatable)
- picard.analysis.CounterManager
- picard.analysis.CounterManager.Counter
- picard.filter.CountingFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- org.broadinstitute.hellbender.engine.filters.CountingVariantFilter (implements org.broadinstitute.hellbender.engine.filters.VariantFilter)
- org.broadinstitute.hellbender.tools.walkers.annotator.CountNs (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- org.broadinstitute.hellbender.utils.recalibration.covariates.CovariateKeyCache
- org.broadinstitute.hellbender.tools.walkers.annotator.Coverage (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardMutectAnnotation)
- org.broadinstitute.hellbender.cmdline.programgroups.CoverageAnalysisProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter (implements java.io.Closeable)
- org.broadinstitute.hellbender.tools.copynumber.formats.records.CoveragePerContig
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantCanonicalRepresentation
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInducingAssemblyContig
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInterpreter
- picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- org.broadinstitute.hellbender.utils.config.CustomBooleanConverter (implements org.aeonbits.owner.Converter<T>)
- org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator
- org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate (implements org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate)
- org.broadinstitute.hellbender.utils.tsv.DataLine
- org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory (implements java.io.Closeable)
- org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
- org.broadinstitute.hellbender.tools.walkers.mutect.clustering.Datum
- org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.variant.DbSnpBitSetUtil
- picard.util.DbSnpBitSetUtil
- org.broadinstitute.hellbender.utils.variant.DbSnpBitSetUtil.DbSnpBitSets
- picard.util.DbSnpBitSetUtil.DbSnpBitSets
- org.broadinstitute.hellbender.utils.mcmc.DecileCollection (implements java.io.Serializable)
- picard.util.DelimitedTextFileWithHeaderIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.util.DelimitedTextFileWithHeaderIterator.Row
- org.broadinstitute.hellbender.cmdline.DeprecatedToolsRegistry
- org.broadinstitute.hellbender.tools.sv.DepthEvidence (implements org.broadinstitute.hellbender.tools.sv.SVFeature)
- org.broadinstitute.hellbender.tools.sv.DepthEvidenceSortMerger (implements org.broadinstitute.hellbender.utils.codecs.FeatureSink<F>)
- picard.vcf.filter.DepthFilter (implements picard.vcf.filter.GenotypeFilter)
- org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoveragePartitionedDataStore
- org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
- org.broadinstitute.hellbender.tools.walkers.readorientation.DepthOneHistograms
- org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerAlleleBySample (implements org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardMutectAnnotation)
- org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerSampleHC (implements org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardHCAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardMutectAnnotation)
- picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.utils.Dirichlet
- org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence (implements org.broadinstitute.hellbender.tools.sv.SVFeature)
- picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap (implements picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap)
- org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType
- org.broadinstitute.barclay.help.DocWorkUnit (implements java.lang.Comparable<T>)
- org.broadinstitute.barclay.help.DocWorkUnitHandler
- org.broadinstitute.barclay.help.DefaultDocWorkUnitHandler
- org.broadinstitute.hellbender.utils.dragstr.DoubleSequence
- org.broadinstitute.hellbender.tools.DownsampleableSparkReadShard (implements java.io.Serializable, org.broadinstitute.hellbender.engine.Shard<T>)
- org.broadinstitute.hellbender.utils.downsampling.Downsampler<T> (implements org.broadinstitute.hellbender.utils.iterators.PushPullTransformer<T>)
- org.broadinstitute.hellbender.utils.downsampling.DownsamplingMethod (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel (implements org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingModel)
- org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel.ReadFeatherEndForwardComparator (implements java.util.Comparator<T>, java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel.ReadFeatherEndReverseComparator (implements java.util.Comparator<T>, java.io.Serializable)
- org.broadinstitute.hellbender.transformers.DRAGENMappingQualityReadTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters
- org.broadinstitute.hellbender.tools.dragstr.DragstrLocus (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase
- org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils
- org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils.BinaryTableIndex
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.DragstrPairHMMInputScoreImputator (implements org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputator)
- org.broadinstitute.hellbender.utils.dragstr.DragstrParams
- org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder
- org.broadinstitute.hellbender.utils.dragstr.DragstrParamUtils
- org.broadinstitute.hellbender.utils.pairhmm.DragstrReadSTRAnalyzer
- org.broadinstitute.hellbender.utils.dragstr.DragstrReferenceAnalyzer
- picard.sam.DuplicationMetricsFactory
- org.broadinstitute.hellbender.transformers.DUSTReadTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.utils.read.mergealignment.EarliestFragmentPrimaryAlignmentSelectionStrategy (implements org.broadinstitute.hellbender.utils.read.mergealignment.PrimaryAlignmentSelectionStrategy)
- picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader (implements java.util.Iterator<E>)
- picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
- picard.cmdline.argumentcollections.EmptyOutputArgumentCollection (implements picard.cmdline.argumentcollections.OutputArgumentCollection)
- org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities
- org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext
- org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
- org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLinkClusterer
- org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollectorSpark (implements org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark<T>, java.io.Serializable)
- org.broadinstitute.hellbender.cmdline.programgroups.ExampleProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsCollectorSpark (implements org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark<T>, java.io.Serializable)
- org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
- picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor (implements java.lang.Runnable)
- org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
- org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterConstants
- org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterUtils
- org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
- org.broadinstitute.hellbender.tools.walkers.variantutils.FamilyLikelihoods
- org.broadinstitute.hellbender.engine.FeatureContext
- org.broadinstitute.hellbender.engine.FeatureDataSource<T> (implements java.lang.AutoCloseable, org.broadinstitute.hellbender.engine.GATKDataSource<T>)
- org.broadinstitute.hellbender.engine.FeatureManager (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodecFinder
- org.broadinstitute.hellbender.utils.io.FeatureOutputStream<F> (implements org.broadinstitute.hellbender.utils.codecs.FeatureSink<F>)
- org.broadinstitute.hellbender.tools.walkers.annotator.FeaturizedReadSets (implements org.broadinstitute.hellbender.tools.walkers.annotator.JumboGenotypeAnnotation)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.FermiLiteAssemblyHandler
- picard.illumina.parser.fakers.FileFaker
- org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
- picard.vcf.filter.FilterApplyingVariantIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.illumina.parser.readers.FilterFileReader (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsConstants
- org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsUtils
- org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteringOutputStats
- org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
- org.broadinstitute.hellbender.engine.spark.FindAssemblyRegionsSpark
- org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.AssembledEvidenceResults
- org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.IntPair
- picard.fingerprint.FingerprintChecker
- picard.fingerprint.FingerprintIdDetails
- picard.fingerprint.FingerprintResults
- picard.fingerprint.FingerprintUtils
- org.broadinstitute.hellbender.utils.FisherExactTest
- picard.vcf.filter.FisherStrandFilter (implements picard.vcf.filter.VariantFilter)
- org.broadinstitute.hellbender.tools.FlagStat.FlagStatus (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.funcotator.FlankSettings
- org.broadinstitute.hellbender.tools.spark.utils.FlatMapGluer<I,O> (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase.LocalContext
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine (implements org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine)
- org.broadinstitute.hellbender.tools.FlowBasedArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.engine.filters.flow.FlowBasedHmerBasedReadFilterHelper
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHMMEngine (implements org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine)
- org.broadinstitute.hellbender.utils.read.FlowBasedKeyCodec
- org.broadinstitute.hellbender.cmdline.programgroups.FlowBasedProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
- org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils.ReadGroupInfo
- org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper.MappedFeature (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper.ReadContext (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.read.Fragment (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.utils.fragments.FragmentCollection<T>
- org.broadinstitute.hellbender.tools.walkers.annotator.FragmentDepthPerAlleleBySample (implements org.broadinstitute.hellbender.tools.walkers.annotator.JumboGenotypeAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardMutectAnnotation)
- org.broadinstitute.hellbender.utils.fragments.FragmentUtils
- org.broadinstitute.hellbender.tools.funcotator.filtrationRules.FuncotationFilter
- org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHomvarFilter
- org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ClinVarFilter
- org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LmmFilter
- org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LofFilter
- org.broadinstitute.hellbender.tools.funcotator.filtrationRules.TwoPassFuncotationFilter
- org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHetvarFilter
- org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
- org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadataUtils
- org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
- org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
- org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
- org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.genomicsdb.GATKGenomicsDBUtils
- org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.read.GATKReadToBDGAlignmentRecordConverter
- org.broadinstitute.hellbender.engine.spark.GATKRegistrator (implements org.apache.spark.serializer.KryoRegistrator)
- org.broadinstitute.hellbender.utils.report.GATKReport
- org.broadinstitute.hellbender.utils.report.GATKReportColumn
- org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat
- org.broadinstitute.hellbender.utils.report.GATKReportTable
- org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils
- org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
- org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines
- org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
- org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.AlleleMapper
- org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
- org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
- org.broadinstitute.hellbender.tools.copynumber.denoising.GCBiasCorrector
- picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- picard.analysis.GcBiasUtils
- org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation (implements org.broadinstitute.hellbender.tools.funcotator.Funcotation)
- org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
- org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature (implements java.lang.Comparable<T>, htsjdk.tribble.Feature)
- org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.OptionalField<T>
- org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData
- picard.annotation.Gene.Transcript
- picard.annotation.Gene.Transcript.Exon
- picard.annotation.GeneAnnotationReader
- org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.Coverage
- org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.SingleStrandFeatureCoverage
- org.broadinstitute.hellbender.utils.GenomeLoc (implements java.lang.Comparable<T>, org.broadinstitute.hellbender.utils.HasGenomeLocation, htsjdk.samtools.util.Locatable, java.io.Serializable)
- org.broadinstitute.hellbender.utils.GenomeLocParser
- org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBConstants
- org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions
- org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection (implements java.lang.Cloneable, java.io.Serializable)
- picard.vcf.GenotypeConcordance.Alleles
- picard.vcf.GenotypeConcordanceCounts
- picard.vcf.GenotypeConcordanceScheme
- picard.vcf.GenotypeConcordanceSchemeFactory
- picard.vcf.GenotypeConcordanceStates
- picard.vcf.GenotypeConcordanceStates.TruthAndCallStates (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.utils.GenotypeCounts
- org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine
- org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
- org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculators
- org.broadinstitute.hellbender.utils.genotyper.GenotypePriorCalculator
- picard.vcf.filter.GenotypeQualityFilter (implements picard.vcf.filter.GenotypeFilter)
- org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeSummaries (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- org.broadinstitute.hellbender.utils.GenotypeUtils
- picard.cmdline.programgroups.GenotypingArraysProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData<A> (implements org.broadinstitute.hellbender.utils.genotyper.AlleleList<A>, org.broadinstitute.hellbender.utils.genotyper.SampleList)
- org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine<Config>
- org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingLikelihoods<A> (implements org.broadinstitute.hellbender.utils.genotyper.AlleleList<A>, org.broadinstitute.hellbender.utils.genotyper.SampleList)
- org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
- org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVVariantComposer<DATA>
- org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyModelArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.mcmc.GibbsSampler<V,S,T>
- org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyperEngine
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphUtils
- picard.util.GraphUtils
- picard.util.GraphUtils.Graph<Node>
- org.broadinstitute.barclay.help.GSONWorkUnit
- org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner (implements org.broadinstitute.hellbender.utils.iterators.PushPullTransformer<T>)
- org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter (implements htsjdk.variant.variantcontext.writer.VariantContextWriter)
- org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMDestination
- org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecallerArgumentCollection (implements java.io.Serializable)
- picard.fingerprint.HaplotypeBlock (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine (implements org.broadinstitute.hellbender.engine.AssemblyRegionEvaluator)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingDebugger
- org.broadinstitute.hellbender.tools.walkers.annotator.HaplotypeFilteringAnnotation (implements org.broadinstitute.hellbender.tools.walkers.annotator.JumboInfoAnnotation)
- picard.fingerprint.HaplotypeMap
- picard.fingerprint.HaplotypeProbabilities
- org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeRegionWalker
- org.broadinstitute.hellbender.tools.copynumber.formats.collections.HDF5SimpleCountCollection
- org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals (implements org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals)
- org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
- org.broadinstitute.hellbender.utils.read.HeaderlessSAMRecordCoordinateComparator (implements java.util.Comparator<T>, java.io.Serializable)
- org.broadinstitute.hellbender.utils.help.HelpConstants
- picard.util.help.HelpConstants
- org.broadinstitute.barclay.help.HelpDoclet (implements jdk.javadoc.doclet.Doclet)
- org.broadinstitute.hellbender.tools.walkers.genotyper.HeterogeneousPloidyModel (implements org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel)
- org.broadinstitute.hellbender.tools.walkers.annotator.HeterozygosityCalculator
- org.broadinstitute.hellbender.utils.Histogram
- org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
- org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel (implements org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel)
- org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants
- org.broadinstitute.hellbender.tools.htsgetreader.HtsgetErrorResponse
- org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder
- org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse
- org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse.Block
- htsjdk.io.HtsPath (implements htsjdk.io.IOPath, java.io.Serializable)
- org.broadinstitute.hellbender.utils.HttpUtils
- org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.IGVUtils
- picard.arrays.illumina.IlluminaAdpcFileWriter (implements java.lang.AutoCloseable)
- picard.arrays.illumina.IlluminaAdpcFileWriter.Record
- picard.arrays.illumina.IlluminaBPMLocusEntry
- picard.illumina.parser.IlluminaDataProviderFactory
- picard.illumina.parser.IlluminaFileUtil
- picard.arrays.illumina.IlluminaManifest
- picard.arrays.illumina.IlluminaManifestRecord
- picard.fastq.IlluminaReadNameEncoder (implements picard.fastq.ReadNameEncoder)
- picard.util.IlluminaUtil
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ImpreciseVariantDetector
- org.broadinstitute.hellbender.tools.walkers.genotyper.IndependentSampleGenotypesModel (implements org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingModel)
- org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList<A> (implements org.broadinstitute.hellbender.utils.genotyper.AlleleList<A>)
- org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList (implements org.broadinstitute.hellbender.utils.genotyper.SampleList)
- org.broadinstitute.hellbender.utils.IndexRange
- org.broadinstitute.hellbender.utils.IndexUtils
- picard.arrays.illumina.InfiniumDataFile
- picard.arrays.illumina.InfiniumFileTOC
- picard.arrays.illumina.InfiniumGTCRecord
- picard.arrays.illumina.InfiniumNormalizationManifest
- picard.arrays.illumina.InfiniumTransformation
- picard.arrays.illumina.InfiniumVcfFields
- org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord
- org.broadinstitute.hellbender.utils.runtime.InputStreamSettings
- org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution (implements java.io.Serializable)
- picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- org.broadinstitute.hellbender.tools.spark.pipelines.metrics.InsertSizeMetricsCollectorSpark (implements org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark<T>, java.io.Serializable)
- org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.copynumber.gcnv.IntegerCopyNumberState (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.utils.IntegrationUtils
- htsjdk.samtools.util.Interval (implements java.lang.Cloneable, java.lang.Comparable<T>, htsjdk.tribble.Feature)
- org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.IntervalCoverageFinder (implements java.lang.Iterable<T>)
- picard.util.IntervalList.IntervalListScatter (implements java.lang.Iterable<T>)
- picard.util.IntervalList.IntervalListScattererByBaseCount (implements picard.util.IntervalList.IntervalListScatterer)
- picard.util.IntervalList.IntervalListScattererByIntervalCount (implements picard.util.IntervalList.IntervalListScatterer)
- org.broadinstitute.hellbender.utils.iterators.IntervalLocusIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.utils.iterators.IntervalOverlappingIterator<T> (implements java.util.Iterator<E>)
- picard.cmdline.programgroups.IntervalsManipulationProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.utils.IntervalUtils
- org.broadinstitute.hellbender.engine.spark.IntervalWalkerContext
- org.broadinstitute.hellbender.tools.spark.utils.IntHistogram
- org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.CDF
- org.broadinstitute.hellbender.utils.IntToDoubleFunctionCache
- org.broadinstitute.hellbender.utils.io.IOUtils
- picard.util.Iterators
- org.broadinstitute.hellbender.transformers.IUPACReadTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.utils.spark.JoinReadsWithVariants
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph.ThreadingNode
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph.ThreadingTree
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotypeFinder<V,E>
- org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.KernelSegmenter<DATA>
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
- org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerCleaner (implements java.lang.Iterable<T>)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerCounter
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.KMerCounter
- org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
- org.broadinstitute.hellbender.utils.KV<K,V>
- org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
- picard.illumina.LanePhasingMetricsCollector
- org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine
- org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
- picard.sam.markduplicates.util.LibraryIdGenerator
- org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
- org.broadinstitute.hellbender.utils.locusiterator.LIBSDownsamplingInfo (implements java.io.Serializable)
- picard.util.LiftoverUtils
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.copynumber.formats.records.LinearCopyRatio (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.LocalAssembler.ContigImpl (implements org.broadinstitute.hellbender.tools.LocalAssembler.Contig)
- org.broadinstitute.hellbender.tools.LocalAssembler.ContigRCImpl (implements org.broadinstitute.hellbender.tools.LocalAssembler.Contig)
- org.broadinstitute.hellbender.tools.LocalAssembler.Kmer
- org.broadinstitute.hellbender.tools.LocalAssembler.Path
- org.broadinstitute.hellbender.tools.LocalAssembler.PathBuilder
- org.broadinstitute.hellbender.tools.LocalAssembler.PathPartContig (implements org.broadinstitute.hellbender.tools.LocalAssembler.PathPart)
- org.broadinstitute.hellbender.tools.LocalAssembler.PathPartGap (implements org.broadinstitute.hellbender.tools.LocalAssembler.PathPart)
- org.broadinstitute.hellbender.tools.LocalAssembler.SequenceRC (implements java.lang.CharSequence, java.lang.Comparable<T>)
- org.broadinstitute.hellbender.tools.LocalAssembler.TransitPairCount
- org.broadinstitute.hellbender.tools.LocalAssembler.Traversal
- org.broadinstitute.hellbender.tools.LocalAssembler.TraversalEndpointComparator (implements java.util.Comparator<T>)
- org.broadinstitute.hellbender.tools.LocalAssembler.WalkData
- org.broadinstitute.hellbender.tools.LocalAssembler.WalkDataFactory
- org.broadinstitute.hellbender.tools.funcotator.dataSources.LocatableFuncotationCreator
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LocationAndAlleles
- org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.engine.spark.LocusWalkerContext
- org.broadinstitute.hellbender.utils.LoggingUtils
- org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LongHomopolymerHaplotypeCollapsingEngine
- org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
- org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
- org.broadinstitute.hellbender.Main
- org.broadinstitute.hellbender.utils.MannWhitneyU
- org.broadinstitute.hellbender.utils.MannWhitneyU.RankedData
- org.broadinstitute.hellbender.utils.MannWhitneyU.Result
- org.broadinstitute.hellbender.utils.MannWhitneyU.TestStatistic
- org.broadinstitute.hellbender.transformers.MappingQualityReadTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityZero (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- picard.sam.markduplicates.MarkDuplicatesForFlowHelper (implements picard.sam.markduplicates.MarkDuplicatesHelper)
- org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
- org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.PairedEnds
- org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment
- org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation (implements picard.sam.util.PhysicalLocation)
- org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
- org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment
- org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
- org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Passthrough
- org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils
- org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils.IndexPair<T>
- org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils.TransientFieldPhysicalLocationComparator (implements java.util.Comparator<T>, java.io.Serializable)
- picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator (implements htsjdk.samtools.SAMRecordIterator)
- picard.sam.markduplicates.util.MarkQueue
- picard.fingerprint.MatchResults (implements java.lang.Comparable<T>)
- picard.util.MathUtil
- picard.util.MathUtil.LogMath
- org.broadinstitute.hellbender.utils.MathUtils
- org.broadinstitute.hellbender.utils.MathUtils.RunningAverage
- org.broadinstitute.hellbender.utils.MatrixSummaryUtils
- picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap (implements picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap)
- org.broadinstitute.hellbender.utils.samples.MendelianViolation
- org.broadinstitute.hellbender.tools.copynumber.formats.metadata.MetadataUtils
- org.broadinstitute.hellbender.cmdline.programgroups.MetagenomicsProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.cmdline.programgroups.MethylationProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.cmdline.argumentcollections.MetricAccumulationLevelArgumentCollection (implements java.io.Serializable)
- htsjdk.samtools.metrics.MetricBase
- org.broadinstitute.hellbender.metrics.MetricsArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.metrics.MetricsUtils
- org.broadinstitute.hellbender.utils.mcmc.MinibatchSliceSampler<DATA>
- org.broadinstitute.hellbender.utils.variant.MinimalVariant (implements org.broadinstitute.hellbender.utils.variant.GATKVariant, java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.transformers.MisencodedBaseQualityReadTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.tools.walkers.validation.MixingFraction
- picard.illumina.parser.readers.MMapBackedIteratorFactory
- org.broadinstitute.hellbender.cmdline.ModeArgumentUtils
- org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment.SimplePosteriorSummary
- org.broadinstitute.hellbender.tools.walkers.consensus.MoleculeID
- org.broadinstitute.hellbender.utils.read.mergealignment.MostDistantPrimaryAlignmentSelectionStrategy (implements org.broadinstitute.hellbender.utils.read.mergealignment.PrimaryAlignmentSelectionStrategy)
- picard.sam.MostDistantPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- org.broadinstitute.hellbender.tools.copynumber.models.MultidimensionalModeller
- org.broadinstitute.hellbender.engine.MultiFeatureWalker.DictSource
- org.broadinstitute.hellbender.engine.MultiFeatureWalker.MergingIterator<F> (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.engine.MultiFeatureWalker.PQContext<F>
- org.broadinstitute.hellbender.engine.MultiFeatureWalker.PQEntry<F> (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.utils.read.mergealignment.MultiHitAlignedReadIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard (implements org.broadinstitute.hellbender.engine.MultiIntervalShard<T>)
- org.broadinstitute.hellbender.metrics.MultiLevelCollector<METRIC_TYPE,HISTOGRAM_KEY,ARGTYPE>
- picard.metrics.MultiLevelCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE>
- org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector<METRIC_TYPE,HISTOGRAM_KEY,ARGTYPE,UNIT_COLLECTOR> (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.copynumber.segmentation.MultisampleMultidimensionalKernelSegmenter
- picard.illumina.parser.MultiTileBclParser
- picard.illumina.parser.MultiTileParser<OUTPUT_RECORD>
- org.broadinstitute.hellbender.engine.MultiVariantDataSource (implements java.lang.AutoCloseable, org.broadinstitute.hellbender.engine.GATKDataSource<T>)
- org.broadinstitute.hellbender.cmdline.argumentcollections.MultiVariantInputArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.alignment.MummerExecutor
- org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine (implements org.broadinstitute.hellbender.engine.AssemblyRegionEvaluator, java.lang.AutoCloseable)
- org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
- org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
- org.broadinstitute.hellbender.tools.walkers.mutect.Mutect3DatasetEngine (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.tools.walkers.mutect.MutectStats
- org.broadinstitute.hellbender.tools.copynumber.utils.genotyping.NaiveHeterozygousPileupGenotypingUtils
- org.broadinstitute.hellbender.tools.copynumber.utils.genotyping.NaiveHeterozygousPileupGenotypingUtils.NaiveHeterozygousPileupGenotypingResult
- org.broadinstitute.hellbender.utils.NativeUtils
- org.broadinstitute.hellbender.utils.NaturalLogUtils
- org.broadinstitute.hellbender.transformers.NDNCigarReadTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector (implements org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadErrorCorrector)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector.CorrectionSet
- org.broadinstitute.hellbender.utils.collections.NestedIntegerArray<T> (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.collections.NestedIntegerArray.Leaf<T>
- org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
- org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeterResults
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NonSymmetricalPairHMMInputScoreImputator (implements org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputator)
- org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype
- org.broadinstitute.hellbender.utils.Nucleotide.Counter
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.OccurrenceMatrix<R,C>
- org.broadinstitute.hellbender.utils.svd.OjAlgoSingularValueDecomposer (implements org.broadinstitute.hellbender.utils.svd.SingularValueDecomposer)
- org.broadinstitute.hellbender.utils.logging.OneShotLogger
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OnRampBase.CSVReader
- org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.OptimizationUtils
- org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalFeatureInputArgumentCollection (implements java.io.Serializable)
- picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalTextOutputArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalVariantInputArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.annotator.OrientationBiasReadCounts (implements org.broadinstitute.hellbender.tools.walkers.annotator.JumboGenotypeAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardMutectAnnotation)
- org.broadinstitute.hellbender.tools.walkers.annotator.OriginalAlignment (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- picard.cmdline.programgroups.OtherProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.illumina.parser.OutputMapping
- org.broadinstitute.hellbender.tools.funcotator.OutputRenderer (implements java.lang.AutoCloseable)
- java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
- org.apache.commons.io.output.ThresholdingOutputStream
- org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings
- org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
- org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.Splice
- org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.SplitRead
- picard.sam.util.Pair<X,Y> (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervals
- org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree<V> (implements java.lang.Iterable<T>)
- org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.PairedStrandedIntervalTreeIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.PairedStrandedIntervalTreeOverlapperIterator (implements java.util.Iterator<E>)
- picard.vcf.PairedVariantSubContextIterator (implements java.util.Iterator<E>)
- picard.vcf.PairedVariantSubContextIterator.VcfTuple
- org.broadinstitute.hellbender.utils.pairhmm.PairHMM (implements java.io.Closeable)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine (implements org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine)
- org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMNativeArgumentCollection
- org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.utils.mcmc.Parameter<T,U>
- picard.illumina.parser.ParameterizedFileUtil
- org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel<V1,S1,T1>
- org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel.GibbsBuilder<V2,S2,T2>
- org.broadinstitute.hellbender.utils.mcmc.ParameterizedState<T>
- org.broadinstitute.hellbender.utils.param.ParamUtils
- org.broadinstitute.hellbender.tools.spark.sv.evidence.PartitionCrossingChecker
- org.apache.spark.Partitioner (implements scala.Serializable)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path<V,E>
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotype<V,E>
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype<V,E>
- org.broadinstitute.hellbender.utils.nio.PathLineIterator (implements java.lang.AutoCloseable, java.lang.Iterable<T>)
- picard.pedigree.PedFile.PedTrio
- org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation (implements org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation)
- org.broadinstitute.hellbender.utils.samples.PedReader
- org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection<X>
- org.broadinstitute.hellbender.tools.copynumber.utils.optimization.PersistenceOptimizer
- picard.illumina.parser.PerTileParser<ILLUMINA_DATA>
- org.broadinstitute.hellbender.tools.examples.metrics.multi.PerUnitExampleMultiMetricsCollector (implements org.broadinstitute.hellbender.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>, java.io.Serializable)
- org.broadinstitute.hellbender.metrics.PerUnitInsertSizeMetricsCollector (implements org.broadinstitute.hellbender.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>, java.io.Serializable)
- picard.sam.util.PGTagArgumentCollection
- picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
- picard.sam.util.PhysicalLocationInt (implements picard.sam.util.PhysicalLocation)
- picard.cmdline.PicardCommandLine
- org.broadinstitute.hellbender.utils.pileup.PileupBasedAlleles
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
- org.broadinstitute.hellbender.utils.pileup.PileupElement
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupReadErrorCorrector (implements org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadErrorCorrector)
- org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary.PileupSummaryComparator (implements java.util.Comparator<T>)
- org.broadinstitute.hellbender.tools.sv.cluster.PloidyTable
- org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils
- org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions
- org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.PowerCalculationUtils
- picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
- org.broadinstitute.hellbender.utils.read.PrimaryAlignmentKey (implements java.lang.Comparable<T>)
- picard.sam.util.PrimaryAlignmentKey (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.utils.runtime.ProcessControllerAckResult
- org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase<CAPTURE_POLICY>
- org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase.OutputCapture (implements java.util.concurrent.Callable<V>)
- org.broadinstitute.hellbender.utils.runtime.ProcessOutput
- org.broadinstitute.hellbender.utils.runtime.ProcessSettings
- org.broadinstitute.hellbender.engine.ProgressMeter
- org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec<A,B> (implements htsjdk.tribble.FeatureCodec<FEATURE_TYPE,SOURCE>)
- picard.util.PropertyUtils
- org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo
- org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
- org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaAligner
- org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaAlignerSpark (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaFilter
- org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaUtils
- org.broadinstitute.hellbender.tools.spark.pathseq.PSFilter (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterEmptyLogger (implements org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterLogger)
- org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterFileLogger (implements org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterLogger)
- org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerCollection
- org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
- org.broadinstitute.hellbender.tools.spark.pathseq.PSPairedUnpairedSplitterSpark
- org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenAlignmentHit
- org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
- org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
- org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreFileLogger (implements org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreLogger)
- org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer
- org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyConstants
- org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyDatabase
- org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
- org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
- org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils
- org.broadinstitute.hellbender.utils.iterators.PushToPullIterator<T> (implements java.lang.Iterable<T>, java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.PythonSklearnVariantAnnotationsModel (implements org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsModel)
- org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.PythonSklearnVariantAnnotationsScorer (implements java.io.Serializable, org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsScorer)
- picard.vcf.filter.QdFilter (implements picard.vcf.filter.VariantFilter)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval (implements java.util.Map.Entry<K,V>)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameFinder (implements java.util.function.Function<T,R>)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameIntervalFinder (implements java.util.function.Function<T,R>)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameKmerizer (implements java.util.function.Function<T,R>)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.QNamesForKmersFinder (implements java.util.function.Function<T,R>)
- org.broadinstitute.hellbender.tools.walkers.annotator.QualByDepth (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation)
- org.broadinstitute.hellbender.utils.recalibration.covariates.QualityScoreCovariate (implements org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate)
- org.broadinstitute.hellbender.utils.QualityUtils
- org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityYieldMetricsCollectorSpark (implements org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark<T>, java.io.Serializable)
- org.broadinstitute.hellbender.utils.recalibration.QualQuantizer
- org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.QualInterval (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.utils.recalibration.QuantizationInfo (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.bigquery.QueryRecord (implements org.apache.avro.generic.GenericRecord)
- picard.util.QuerySortedReadPairIteratorUtil
- picard.util.QuerySortedReadPairIteratorUtil.ReadPair
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OffRampBase
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.AssemblerOffRamp
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PreFilterOffRamp
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OnRampBase
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils.GATKReadComparator (implements java.util.Comparator<T>)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils.HaplotypeComparator (implements java.util.Comparator<T>)
- picard.illumina.parser.Range
- org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest (implements org.broadinstitute.hellbender.tools.walkers.annotator.Annotation, org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation)
- picard.sam.SamErrorMetric.ReadBaseStratification
- picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier<T,R> (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadClassifier (implements java.util.function.Function<T,R>)
- org.broadinstitute.hellbender.utils.clipping.ReadClipper
- org.broadinstitute.hellbender.utils.read.ReadConstants
- org.broadinstitute.hellbender.engine.ReadContextData (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.read.ReadCoordinateComparator (implements java.util.Comparator<T>, java.io.Serializable)
- org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
- picard.illumina.parser.ReadData
- picard.cmdline.programgroups.ReadDataManipulationProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.illumina.parser.ReadDescriptor
- picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
- java.io.Reader (implements java.io.Closeable, java.lang.Readable)
- org.broadinstitute.hellbender.tools.readersplitters.ReaderSplitter<T>
- org.broadinstitute.hellbender.engine.filters.ReadFilter (implements java.util.function.Predicate<T>, java.io.Serializable)
- org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
- org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
- org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
- org.broadinstitute.hellbender.tools.spark.utils.ReadFilterSparkifier (implements org.apache.spark.api.java.function.Function<T1,R>)
- org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate (implements org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate)
- org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
- org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics
- org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds
- org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics
- picard.sam.util.ReadNameParser (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.qc.ReadPair
- org.broadinstitute.hellbender.utils.pileup.ReadPileup (implements java.lang.Iterable<T>)
- org.broadinstitute.hellbender.utils.read.ReadQueryNameComparator (implements java.util.Comparator<T>, java.io.Serializable)
- org.broadinstitute.hellbender.utils.recalibration.ReadRecalibrationInfo
- org.broadinstitute.hellbender.engine.ReadsContext (implements java.lang.Iterable<T>)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadsForQNamesFinder (implements java.lang.Iterable<T>)
- org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey
- org.broadinstitute.hellbender.engine.ReadsPathDataSource (implements org.broadinstitute.hellbender.engine.ReadsDataSource)
- org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink
- org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource (implements java.io.Serializable)
- picard.illumina.parser.ReadStructure
- picard.illumina.parser.ReadStructure.Substructure (implements java.lang.Iterable<T>)
- org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.spark.utils.ReadTransformerSparkifier (implements org.apache.spark.api.java.function.Function<T1,R>)
- org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
- org.broadinstitute.hellbender.utils.read.ReadUtils
- org.broadinstitute.hellbender.engine.spark.ReadWalkerContext
- org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
- org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentEngine
- org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF.AlleleLengthComparator (implements java.util.Comparator<T>)
- org.broadinstitute.hellbender.utils.variant.writers.ReblockingOptions
- org.broadinstitute.hellbender.utils.recalibration.RecalDatum (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
- org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables (implements java.lang.Iterable<T>, java.io.Serializable)
- org.broadinstitute.hellbender.utils.recalibration.RecalUtils
- org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData<T>
- org.broadinstitute.hellbender.tools.walkers.annotator.ReferenceBases (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- org.broadinstitute.hellbender.utils.reference.ReferenceBases (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceResult
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RefVsAnyResult
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceUtils
- org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger
- org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.VCWithNewAlleles
- org.broadinstitute.hellbender.engine.ReferenceContext (implements org.broadinstitute.hellbender.engine.BasicReference, java.lang.Iterable<T>, htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.engine.ReferenceFileSource (implements org.broadinstitute.hellbender.engine.ReferenceDataSource)
- org.broadinstitute.hellbender.engine.spark.datasources.ReferenceFileSparkSource (implements org.broadinstitute.hellbender.engine.spark.datasources.ReferenceSparkSource, java.io.Serializable)
- org.broadinstitute.hellbender.engine.spark.datasources.ReferenceHadoopSparkSource (implements org.broadinstitute.hellbender.engine.spark.datasources.ReferenceSparkSource, java.io.Serializable)
- org.broadinstitute.hellbender.cmdline.argumentcollections.ReferenceInputArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.engine.ReferenceMemorySource (implements org.broadinstitute.hellbender.engine.ReferenceDataSource)
- org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource (implements org.broadinstitute.hellbender.engine.spark.datasources.ReferenceSparkSource, java.io.Serializable)
- org.broadinstitute.hellbender.tools.reference.ReferencePair
- picard.cmdline.programgroups.ReferenceProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable (implements java.lang.Iterable<T>)
- org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableEntry
- org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable.TableRow
- org.broadinstitute.hellbender.engine.ReferenceShard (implements java.io.Serializable)
- org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSparkSource (implements org.broadinstitute.hellbender.engine.spark.datasources.ReferenceSparkSource, java.io.Serializable)
- org.broadinstitute.hellbender.utils.reference.ReferenceUtils
- org.broadinstitute.hellbender.engine.spark.datasources.ReferenceWindowFunctions
- org.broadinstitute.hellbender.engine.spark.datasources.ReferenceWindowFunctions.FixedWindowFunction (implements org.broadinstitute.hellbender.utils.SerializableFunction<T,R>)
- picard.annotation.RefFlatReader
- picard.util.ReflectionUtil
- org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature (implements htsjdk.tribble.Feature, org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqTranscript)
- picard.sam.util.RepresentativeReadIndexer
- picard.sam.markduplicates.util.RepresentativeReadIndexerCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
- org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredFeatureInputArgumentCollection (implements java.io.Serializable)
- picard.cmdline.argumentcollections.RequiredOutputArgumentCollection (implements picard.cmdline.argumentcollections.OutputArgumentCollection)
- picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredVariantInputArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.io.Resource
- picard.util.RExecutor
- org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation)
- picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- org.broadinstitute.hellbender.utils.runtime.RuntimeUtils
- picard.sam.util.SamComparison
- picard.sam.util.SAMComparisonArgumentCollection
- org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter (implements org.broadinstitute.hellbender.utils.read.GATKReadWriter)
- org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupElement
- org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature (implements htsjdk.tribble.Feature)
- org.broadinstitute.hellbender.utils.samples.Sample (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.utils.samples.SampleDB
- org.broadinstitute.hellbender.utils.samples.SampleDBBuilder
- org.broadinstitute.hellbender.tools.walkers.annotator.SampleList (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- org.broadinstitute.hellbender.tools.genomicsdb.SampleNameMap
- org.broadinstitute.hellbender.tools.funcotator.metadata.SamplePairExtractor
- org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator (implements htsjdk.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
- org.broadinstitute.hellbender.metrics.SAMRecordAndReference
- picard.metrics.SAMRecordAndReference
- htsjdk.samtools.SAMRecordSparkCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
- org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter (implements org.broadinstitute.hellbender.utils.read.GATKRead, java.io.Serializable)
- org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
- htsjdk.samtools.util.SamRecordWithOrdinal
- picard.fastq.SamToBfqWriter
- org.broadinstitute.hellbender.utils.SATagBuilder
- picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.RelevantAttributes (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.SegmentExonOverlaps
- org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.SegmentExonUtils
- org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
- org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
- picard.util.SequenceDictionaryUtils
- picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection.NoValidationCollection (implements org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection)
- org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection.StandardValidationCollection (implements org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection)
- picard.analysis.artifacts.SequencingArtifactMetrics
- com.esotericsoftware.kryo.Serializer<T>
- org.broadinstitute.hellbender.utils.collections.SetSizeUtils
- org.broadinstitute.hellbender.engine.ShardBoundary (implements htsjdk.samtools.util.Locatable, java.io.Serializable)
- org.broadinstitute.hellbender.engine.ShardBoundaryShard<T> (implements java.io.Serializable, org.broadinstitute.hellbender.engine.Shard<T>)
- org.broadinstitute.hellbender.utils.iterators.ShardedIntervalIterator (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter (implements htsjdk.variant.variantcontext.writer.VariantContextWriter)
- org.broadinstitute.hellbender.engine.ShardToMultiIntervalShardAdapter<T> (implements org.broadinstitute.hellbender.engine.MultiIntervalShard<T>, java.io.Serializable, org.broadinstitute.hellbender.engine.Shard<T>)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedSequenceMerger
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedVertexSequenceSplitter
- org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- htsjdk.variant.variantcontext.SimpleAllele (implements htsjdk.variant.variantcontext.Allele)
- org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.SimpleAnnotatedIntervalWriter (implements org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalWriter)
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera.DistancesBetweenAlignmentsOnRefAndOnRead
- org.broadinstitute.hellbender.tools.copynumber.caller.SimpleCopyRatioCaller
- org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount (implements htsjdk.tribble.Feature, htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging.SimpleGermlineTagger
- org.broadinstitute.hellbender.utils.SimpleInterval (implements htsjdk.samtools.util.Locatable, java.io.Serializable)
- org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleLocatableMetadata (implements org.broadinstitute.hellbender.tools.copynumber.formats.metadata.LocatableMetadata)
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence.ChimericContigAlignmentEvidenceAnnotations (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyInterpreter
- org.broadinstitute.hellbender.transformers.SimpleRepeatMaskTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleLocatableMetadata (implements org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SampleLocatableMetadata)
- org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleMetadata (implements org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SampleMetadata, java.io.Serializable)
- org.broadinstitute.hellbender.utils.svd.SimpleSVD (implements org.broadinstitute.hellbender.utils.svd.SVD)
- org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter (implements java.io.Closeable)
- org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter.LineBuilder
- picard.util.SingleBarcodeDistanceMetric
- org.broadinstitute.hellbender.tools.walkers.groundtruth.SingleFileLocationTranslator
- org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner<T,U> (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.tools.sv.SiteDepth (implements org.broadinstitute.hellbender.tools.sv.SVFeature)
- org.broadinstitute.hellbender.utils.mcmc.SliceSampler
- org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignmentConstants
- org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanIntelAligner (implements org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner)
- org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner (implements org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner)
- picard.fingerprint.Snp (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil
- org.broadinstitute.hellbender.tools.walkers.featuremapping.SNVMapper (implements org.broadinstitute.hellbender.tools.walkers.featuremapping.FeatureMapper)
- org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
- org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine
- org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.engine.spark.SparkCommandLineArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.engine.spark.SparkContextFactory
- org.broadinstitute.hellbender.utils.spark.SparkConverter
- org.broadinstitute.hellbender.engine.spark.SparkSharder
- org.broadinstitute.hellbender.utils.svd.SparkSingularValueDecomposer (implements org.broadinstitute.hellbender.utils.svd.SingularValueDecomposer)
- org.broadinstitute.hellbender.utils.spark.SparkUtils
- org.broadinstitute.hellbender.tools.sv.SplitReadEvidence (implements org.broadinstitute.hellbender.tools.sv.SVFeature)
- org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
- org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList (implements java.lang.Iterable<T>, java.io.Serializable)
- picard.cmdline.StandardOptionDefinitions
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.StandardPairHMMInputScoreImputator (implements org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputator)
- org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader (implements org.broadinstitute.hellbender.utils.bigquery.GATKAvroReader)
- org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter.EStep
- org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasBySample (implements org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardMutectAnnotation)
- org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
- org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases
- org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager<K,V> (implements java.util.Map<K,V>)
- org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable
- org.broadinstitute.hellbender.utils.runtime.StreamingToolConstants
- org.broadinstitute.hellbender.utils.runtime.StreamOutput
- org.broadinstitute.hellbender.transformers.StripMateNumberTransformer (implements org.broadinstitute.hellbender.transformers.ReadTransformer)
- org.broadinstitute.hellbender.utils.dragstr.STRTableFile (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.utils.dragstr.STRTableFileBuilder (implements java.lang.AutoCloseable)
- org.broadinstitute.hellbender.cmdline.programgroups.StructuralVariantDiscoveryProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix<EVIDENCE,A> (implements org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix<EVIDENCE,A>)
- org.broadinstitute.hellbender.tools.spark.sv.discovery.SVAlignmentLengthFilter (implements org.broadinstitute.hellbender.tools.spark.sv.discovery.StructuralVariantFilter)
- org.broadinstitute.hellbender.tools.sv.SVAlleleCounter
- org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine
- org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine.GTFIntervalTreesContainer
- org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateEngine.SVSegment
- org.broadinstitute.hellbender.tools.sv.SVCallRecord (implements org.broadinstitute.hellbender.tools.sv.SVLocatable)
- org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils
- org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine
- org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine.OutputCluster
- org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineFactory
- org.broadinstitute.hellbender.tools.sv.cluster.SVClusterLinkage<T>
- org.broadinstitute.hellbender.tools.sv.concordance.SVConcordanceAnnotator
- org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisedCopyRatioResult
- org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisingUtils
- org.broadinstitute.hellbender.utils.svd.SVDFactory
- org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures
- org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData
- org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.ReferenceData
- org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.SampleSpecificData
- org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryUtils
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead (implements org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembler.BasesAndQuals)
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping (implements htsjdk.samtools.util.Locatable)
- org.broadinstitute.hellbender.tools.sv.SVFeaturesHeader
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVFileUtils
- org.broadinstitute.hellbender.utils.SVInterval (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.utils.SVIntervalTree<V> (implements java.lang.Iterable<T>)
- org.broadinstitute.hellbender.utils.SVIntervalTree.FwdIterator
- org.broadinstitute.hellbender.utils.SVIntervalTree.OverlapIterator
- org.broadinstitute.hellbender.utils.SVIntervalTree.RevIterator
- org.broadinstitute.hellbender.utils.SVIntervalTree.ValuesIterator<V1> (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer.ASCIICharSequence (implements java.lang.CharSequence)
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVLocation (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.tools.spark.sv.discovery.SVMappingQualityFilter (implements org.broadinstitute.hellbender.tools.spark.sv.discovery.StructuralVariantFilter)
- org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVReferenceUtils
- org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils.IteratorFilter<T> (implements java.util.Iterator<E>)
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFReader
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFWriter
- org.broadinstitute.hellbender.utils.smithwaterman.SWNativeAlignerWrapper (implements org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner)
- picard.util.TabbedTextFileWithHeaderParser (implements java.lang.AutoCloseable, java.lang.Iterable<T>)
- picard.util.TabbedTextFileWithHeaderParser.Row
- org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
- org.broadinstitute.hellbender.utils.codecs.table.TableFeature (implements htsjdk.tribble.Feature)
- org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation (implements org.broadinstitute.hellbender.tools.funcotator.Funcotation)
- org.broadinstitute.hellbender.utils.tsv.TableReader<R> (implements java.io.Closeable, java.lang.Iterable<T>)
- org.broadinstitute.hellbender.utils.bigquery.TableReference
- org.broadinstitute.hellbender.utils.tsv.TableUtils
- org.broadinstitute.hellbender.utils.tsv.TableWriter<R> (implements java.io.Closeable)
- org.broadinstitute.hellbender.tools.walkers.annotator.TandemRepeat (implements org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.StandardMutectAnnotation)
- picard.analysis.directed.TargetMetricsCollector.Coverage
- picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- picard.Test
- picard.cmdline.programgroups.Testing (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.cmdline.TestProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.utils.text.TextFormattingUtils
- org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec
- org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MDElement
- picard.analysis.TheoreticalSensitivity
- picard.analysis.TheoreticalSensitivity.RouletteWheel
- picard.util.ThreadPoolExecutorUtil
- org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator
- java.lang.Throwable (implements java.io.Serializable)
- picard.illumina.parser.Tile
- picard.illumina.parser.TileIndex (implements java.lang.Iterable<T>)
- picard.illumina.parser.TileIndex.TileIndexRecord
- picard.illumina.parser.readers.TileMetricsOutReader (implements java.util.Iterator<E>)
- picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- picard.illumina.parser.TileMetricsUtil
- picard.illumina.parser.TilePhasingValue
- org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet
- org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche
- org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche.TrancheComparator<T> (implements java.util.Comparator<T>)
- org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche.TrancheTruthSensitivityComparator (implements java.util.Comparator<T>)
- org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager
- org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.SelectionMetric
- org.broadinstitute.hellbender.engine.TraversalParameters (implements java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.variantrecalling.TrimmedReadsReader
- org.broadinstitute.hellbender.utils.samples.Trio
- org.broadinstitute.hellbender.tools.funcotator.metadata.TumorNormalPair
- picard.sam.markduplicates.UmiGraph
- org.broadinstitute.hellbender.tools.walkers.annotator.UniqueAltReadCount (implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotation, org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation)
- org.broadinstitute.hellbender.utils.UniqueIDWrapper<A>
- org.broadinstitute.hellbender.utils.UnsignedTypeUtil
- picard.util.UnsignedTypeUtil
- org.broadinstitute.hellbender.utils.Utils
- picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased<A,R> (implements picard.vcf.processor.VariantAccumulatorExecutor<ACCUMULATOR,RESULT>)
- org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
- org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.VAExpression
- htsjdk.variant.variantcontext.VariantContext (implements htsjdk.tribble.Feature, htsjdk.beta.plugin.HtsRecord, java.io.Serializable)
- org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext
- org.broadinstitute.hellbender.utils.variant.VariantContextGetters
- htsjdk.variant.variantcontext.VariantContextUtils.JexlVCMatchExp
- org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter (implements org.broadinstitute.hellbender.utils.variant.GATKVariant, java.io.Serializable)
- org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager
- org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
- org.broadinstitute.hellbender.tools.walkers.varianteval.util.VariantEvalContext
- org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
- org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalReportWriter
- picard.cmdline.programgroups.VariantEvaluationProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator (implements java.lang.Comparable<T>)
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap (implements org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.StandardEval)
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants (implements org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.StandardEval)
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.GenotypeFilterSummary
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelLengthHistogram (implements org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.StandardEval)
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary (implements org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.StandardEval)
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary (implements org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.StandardEval)
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.PrintMissingComp
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator (implements org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.StandardEval)
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport (implements org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.StandardEval)
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary (implements org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.StandardEval)
- picard.cmdline.programgroups.VariantFilteringProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary
- org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary.AllowAllVariantsVariantFilter (implements org.broadinstitute.hellbender.engine.filters.VariantFilter)
- org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary.NotSymbolicOrSVVariantFilter (implements org.broadinstitute.hellbender.engine.filters.VariantFilter)
- org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary.PassesFiltersVariantFilter (implements org.broadinstitute.hellbender.engine.filters.VariantFilter)
- org.broadinstitute.hellbender.engine.filters.VariantIDsVariantFilter (implements org.broadinstitute.hellbender.engine.filters.VariantFilter)
- picard.vcf.processor.VariantIteratorProducer
- picard.cmdline.programgroups.VariantManipulationProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator
- picard.vcf.processor.VariantProcessor<RESULT,ACCUMULATOR>
- picard.vcf.processor.VariantProcessor.Builder<A,R>
- org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine
- org.broadinstitute.hellbender.tools.walkers.variantrecalling.VariantRecallerResultWriter
- org.broadinstitute.hellbender.engine.VariantShard
- org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSink
- org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSource
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier (implements java.lang.Comparable<T>, org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.Stratifier<T>)
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.AlleleCount
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.AlleleFrequency
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.CompFeatureInput (implements org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.RequiredStratification)
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Contig
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.CpG
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Degeneracy
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.EvalFeatureInput (implements org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.RequiredStratification)
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Family
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Filter
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FilterType
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FunctionalClass
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.IndelSize
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.IntervalStratification
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.JexlExpression (implements org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.StandardStratification)
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Novelty (implements org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.StandardStratification)
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.OneBPIndel
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Sample
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.TandemRepeat
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantType
- org.broadinstitute.hellbender.engine.filters.VariantTypesVariantFilter (implements org.broadinstitute.hellbender.engine.filters.VariantFilter)
- org.broadinstitute.hellbender.engine.spark.VariantWalkerContext
- picard.vcf.processor.VcfFileSegment
- picard.vcf.processor.VcfFileSegmentGenerator
- org.broadinstitute.hellbender.tools.funcotator.metadata.VcfFuncotationMetadata (implements org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadata)
- picard.vcf.processor.VcfPathSegment
- picard.vcf.processor.VcfPathSegmentGenerator
- org.broadinstitute.hellbender.utils.variant.VcfUtils
- picard.vcf.VcfUtils
- picard.analysis.WgsMetricsProcessorImpl<T> (implements picard.analysis.WgsMetricsProcessor)
- org.broadinstitute.hellbender.utils.text.XReadLines (implements java.lang.AutoCloseable, java.lang.Iterable<T>, java.util.Iterator<E>)
- org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature (implements htsjdk.tribble.Feature)
- org.broadinstitute.hellbender.utils.ZipUtils
Interface Hierarchy
- org.broadinstitute.hellbender.utils.illumina.AdapterPair
- picard.util.AdapterPair
- org.broadinstitute.hellbender.tools.walkers.mutect.clustering.AlleleFractionCluster
- org.broadinstitute.hellbender.utils.genotyper.AlleleList<A>
- org.broadinstitute.hellbender.tools.walkers.annotator.Annotation
- org.broadinstitute.hellbender.engine.AssemblyRegionEvaluator
- picard.util.AtomicIterator<T>
- java.lang.AutoCloseable
- picard.sam.SamErrorMetric.BaseCalculator
- picard.illumina.BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD>
- org.broadinstitute.hellbender.engine.BasicReference
- org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.WriteFunc<F>
- picard.analysis.CollectMultipleMetrics.ProgramInterface
- org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark.SparkCollectorProvider
- java.util.function.Consumer<T>
- org.broadinstitute.hellbender.utils.mcmc.DataCollection
- org.broadinstitute.hellbender.tools.dragstr.DragstrLocus.WriteAction
- org.broadinstitute.hellbender.tools.walkers.featuremapping.FeatureMapper
- org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodec<F,S>
- org.broadinstitute.hellbender.utils.codecs.FeatureSink<F>
- org.broadinstitute.hellbender.tools.funcotator.Funcotation
- org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadata
- java.util.function.Function<T,R>
- picard.vcf.filter.GenotypeFilter
- org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingModel
- org.broadinstitute.hellbender.utils.HasGenomeLocation
- org.broadinstitute.hellbender.utils.functional.IntBiConsumer
- picard.cmdline.argumentcollections.IntervalArgumentCollection
- picard.util.IntervalList.IntervalListScatterer
- org.broadinstitute.hellbender.utils.IntervalPileup
- org.broadinstitute.hellbender.utils.IntervalPileup.Element
- org.broadinstitute.hellbender.utils.IntervalPileup.Insert
- org.broadinstitute.hellbender.utils.functional.IntToDoubleBiFunction
- java.lang.Iterable<T>
- org.broadinstitute.hellbender.utils.bigquery.GATKAvroReader (also extends htsjdk.samtools.util.CloseableIterator<T>)
- org.broadinstitute.hellbender.engine.GATKDataSource<T>
- org.broadinstitute.hellbender.engine.MultiIntervalShard<T>
- org.broadinstitute.hellbender.engine.Shard<T> (also extends htsjdk.samtools.util.Locatable)
- java.util.Iterator<E>
- htsjdk.samtools.util.CloseableIterator<T> (also extends java.io.Closeable)
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KmerSearchableGraph<V,E>
- org.broadinstitute.hellbender.tools.LocalAssembler.Contig
- org.broadinstitute.hellbender.tools.LocalAssembler.PathPart
- htsjdk.samtools.util.Locatable
- htsjdk.tribble.Feature
- org.broadinstitute.hellbender.tools.sv.SVFeature
- org.broadinstitute.hellbender.utils.read.GATKRead
- org.broadinstitute.hellbender.utils.variant.GATKVariant
- org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqTranscript
- org.broadinstitute.hellbender.engine.Shard<T> (also extends java.lang.Iterable<T>)
- org.broadinstitute.hellbender.tools.spark.utils.LongIterator
- picard.sam.markduplicates.MarkDuplicatesHelper
- org.broadinstitute.hellbender.utils.MathUtils.IntToDoubleArrayFunction
- org.broadinstitute.hellbender.tools.copynumber.formats.metadata.Metadata
- org.broadinstitute.hellbender.tools.copynumber.formats.metadata.LocatableMetadata
- org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SampleMetadata
- org.broadinstitute.hellbender.engine.MultiplePassReadWalker.GATKReadConsumer
- org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter.ChecksumCalculator
- picard.cmdline.argumentcollections.OutputArgumentCollection
- org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputation
- org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputator
- org.broadinstitute.hellbender.utils.mcmc.ParameterEnum
- org.broadinstitute.hellbender.utils.mcmc.ParameterSampler<U,V,S,T>
- org.broadinstitute.hellbender.utils.collections.Permutation<E>
- picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>
- java.util.function.Predicate<T>
- org.broadinstitute.hellbender.utils.read.mergealignment.PrimaryAlignmentSelectionStrategy
- picard.sam.PrimaryAlignmentSelectionStrategy
- org.broadinstitute.hellbender.utils.iterators.PushPullTransformer<T>
- picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>
- picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
- org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadErrorCorrector
- picard.fastq.ReadNameEncoder
- picard.cmdline.argumentcollections.ReferenceArgumentCollection
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.RequiredStratification
- org.broadinstitute.hellbender.utils.genotyper.SampleList
- org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel
- org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection
- java.io.Serializable
- org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner.TriFunction<T,U,V,W>
- org.broadinstitute.hellbender.utils.svd.SingularValueDecomposer
- org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignment
- org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.StandardEval
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.StandardStratification
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager.Combiner<V>
- org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.Stratifier<T>
- java.util.function.Supplier<T>
- org.broadinstitute.hellbender.utils.svd.SVD
- org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
- org.broadinstitute.hellbender.utils.SVInterval.SVIntervalConstructorArgsValidator
- org.broadinstitute.hellbender.utils.SVIntervalTree.Entry<V1>
- org.broadinstitute.hellbender.tools.sv.SVLocatable
- picard.vcf.processor.VariantAccumulatorExecutor<ACCUMULATOR,RESULT>
- org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsModel
- org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsScorer
- picard.vcf.filter.VariantFilter
- picard.vcf.processor.VariantProcessor.Accumulator<RESULT>
- picard.vcf.processor.VariantProcessor.AccumulatorGenerator<ACCUMULATOR,RESULT>
- picard.vcf.processor.VariantProcessor.ResultMerger<RESULT>
- picard.analysis.WgsMetricsProcessor
Annotation Interface Hierarchy