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Hierarchy For All Packages
Package Hierarchies:
picard
,
picard.analysis
,
picard.analysis.artifacts
,
picard.analysis.directed
,
picard.analysis.replicates
,
picard.annotation
,
picard.cmdline
,
picard.cmdline.programgroups
,
picard.fastq
,
picard.filter
,
picard.fingerprint
,
picard.illumina
,
picard.illumina.parser
,
picard.illumina.parser.fakers
,
picard.illumina.parser.readers
,
picard.illumina.quality
,
picard.metrics
,
picard.pedigree
,
picard.reference
,
picard.sam
,
picard.sam.markduplicates
,
picard.sam.markduplicates.util
,
picard.sam.util
,
picard.util
,
picard.vcf
,
picard.vcf.filter
,
picard.vcf.processor
,
picard.vcf.processor.util
Class Hierarchy
java.lang.Object
picard.sam.
AbstractAlignmentMerger
picard.sam.
SamAlignmentMerger
picard.illumina.parser.readers.
AbstractIlluminaPositionFileReader
(implements htsjdk.samtools.util.CloseableIterator<T>)
picard.illumina.parser.readers.
ClocsFileReader
picard.illumina.parser.readers.
LocsFileReader
picard.illumina.parser.readers.
PosFileReader
picard.illumina.parser.readers.
AbstractIlluminaPositionFileReader.PositionInfo
htsjdk.samtools.util.AbstractIterator<E> (implements java.util.Iterator<E>)
picard.util.
AbstractInputParser
(implements htsjdk.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
picard.util.
BasicInputParser
picard.util.
CsvInputParser
picard.util.
TabbedInputParser
java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
java.util.TreeMap<K,V> (implements java.lang.Cloneable, java.util.NavigableMap<K,V>, java.io.Serializable)
picard.fingerprint.
Fingerprint
picard.pedigree.
PedFile
picard.sam.markduplicates.util.
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
picard.util.
AdapterMarker
picard.analysis.
AdapterUtility
picard.vcf.filter.
AlleleBalanceFilter
(implements picard.vcf.filter.
VariantFilter
)
picard.cmdline.programgroups.
Alpha
(implements picard.cmdline.
CommandLineProgramGroup
)
picard.util.
AsyncIterator
<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
picard.fastq.
BamToBfqWriter
picard.illumina.parser.readers.
BarcodeFileReader
(implements htsjdk.samtools.util.CloseableIterator<T>)
picard.illumina.parser.
BclData
picard.illumina.parser.readers.
BclIndexReader
picard.illumina.parser.readers.
BclQualityEvaluationStrategy
picard.illumina.parser.readers.
BclReader
(implements htsjdk.samtools.util.CloseableIterator<T>)
picard.sam.
BestEndMapqPrimaryAlignmentStrategy
(implements picard.sam.
PrimaryAlignmentSelectionStrategy
)
picard.sam.
BestMapqPrimaryAlignmentSelectionStrategy
(implements picard.sam.
PrimaryAlignmentSelectionStrategy
)
picard.vcf.
ByIntervalListVariantContextIterator
(implements java.util.Iterator<E>)
picard.vcf.
CallingMetricAccumulator
(implements picard.vcf.processor.
VariantProcessor.Accumulator
<RESULT>)
picard.vcf.
GvcfMetricAccumulator
picard.vcf.
CallingMetricAccumulator.Result
picard.fastq.
Casava18ReadNameEncoder
(implements picard.fastq.
ReadNameEncoder
)
picard.analysis.
ChimeraUtil
picard.util.
CircularByteBuffer
picard.cmdline.
ClassFinder
picard.util.
ClippingUtility
picard.illumina.parser.
ClusterData
picard.illumina.
ClusterDataToSamConverter
(implements picard.illumina.
IlluminaBasecallsConverter.ClusterDataConverter
<OUTPUT_RECORD>)
picard.illumina.quality.
CollectHiSeqXPfFailMetrics.ReadClassifier
picard.illumina.
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
picard.analysis.
CollectWgsMetrics.WgsMetricsCollector
picard.analysis.
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
picard.cmdline.
CommandLineDefaults
picard.cmdline.
CommandLineParser
picard.cmdline.
CommandLineParser.OptionDefinition
picard.cmdline.
CommandLineParser.OptionDefinitionByPrintOrderComparator
(implements java.util.Comparator<T>)
picard.cmdline.
CommandLineProgram
picard.sam.markduplicates.util.
AbstractOpticalDuplicateFinderCommandLineProgram
picard.sam.markduplicates.util.
AbstractMarkDuplicatesCommandLineProgram
picard.sam.markduplicates.
MarkDuplicates
picard.sam.markduplicates.
MarkDuplicatesWithMateCigar
picard.sam.markduplicates.
EstimateLibraryComplexity
picard.sam.
AddCommentsToBam
picard.sam.
AddOrReplaceReadGroups
picard.util.
BaitDesigner
picard.sam.
BamIndexStats
picard.fastq.
BamToBfq
picard.util.
BedToIntervalList
picard.sam.
BuildBamIndex
picard.sam.
CalculateReadGroupChecksum
picard.fingerprint.
CheckFingerprint
picard.illumina.
CheckIlluminaDirectory
picard.sam.
CheckTerminatorBlock
picard.sam.
CleanSam
picard.illumina.quality.
CollectHiSeqXPfFailMetrics
picard.illumina.
CollectIlluminaBasecallingMetrics
picard.illumina.
CollectIlluminaLaneMetrics
picard.analysis.replicates.
CollectIndependentReplicateMetrics
picard.analysis.
CollectJumpingLibraryMetrics
picard.analysis.
CollectMultipleMetrics
picard.analysis.
CollectOxoGMetrics
picard.analysis.
CollectRrbsMetrics
picard.analysis.directed.
CollectTargetedMetrics
<METRIC,COLLECTOR>
picard.analysis.directed.
CollectHsMetrics
picard.analysis.directed.
CalculateHsMetrics
picard.analysis.directed.
CollectTargetedPcrMetrics
picard.vcf.
CollectVariantCallingMetrics
picard.analysis.
CollectWgsMetrics
picard.analysis.
CollectRawWgsMetrics
picard.analysis.
CollectWgsMetricsFromSampledSites
picard.analysis.
CollectWgsMetricsWithNonZeroCoverage
picard.analysis.
CollectWgsMetricsFromQuerySorted
picard.analysis.
CompareMetrics
picard.sam.
CompareSAMs
picard.analysis.artifacts.
ConvertSequencingArtifactToOxoG
picard.sam.
CreateSequenceDictionary
picard.fingerprint.
CrosscheckReadGroupFingerprints
picard.sam.
DownsampleSam
picard.illumina.
ExtractIlluminaBarcodes
picard.reference.
ExtractSequences
picard.sam.
FastqToSam
picard.util.
FifoBuffer
picard.sam.
FilterSamReads
picard.vcf.filter.
FilterVcf
picard.sam.
FixMateInformation
picard.sam.
GatherBamFiles
picard.vcf.
GatherVcfs
picard.vcf.
GenotypeConcordance
picard.illumina.
IlluminaBasecallsToFastq
picard.illumina.
IlluminaBasecallsToSam
picard.util.
IntervalListToBed
picard.util.
IntervalListTools
picard.util.
LiftOverIntervalList
picard.vcf.
LiftoverVcf
picard.vcf.
MakeSitesOnlyVcf
picard.illumina.
MarkIlluminaAdapters
picard.sam.
MergeBamAlignment
picard.sam.
MergeSamFiles
picard.vcf.
MergeVcfs
picard.reference.
NonNFastaSize
picard.reference.
NormalizeFasta
picard.sam.
PositionBasedDownsampleSam
picard.vcf.
RenameSampleInVcf
picard.sam.
ReorderSam
picard.sam.
ReplaceSamHeader
picard.sam.
RevertOriginalBaseQualitiesAndAddMateCigar
picard.sam.
RevertSam
picard.sam.
SamFormatConverter
picard.sam.
SamToFastq
picard.util.
ScatterIntervalsByNs
picard.sam.
SetNmAndUqTags
picard.analysis.
SinglePassSamProgram
picard.analysis.
CollectAlignmentSummaryMetrics
picard.analysis.
CollectBaseDistributionByCycle
picard.analysis.
CollectGcBiasMetrics
picard.analysis.
CollectInsertSizeMetrics
picard.analysis.
CollectQualityYieldMetrics
picard.analysis.
CollectRnaSeqMetrics
picard.analysis.artifacts.
CollectSequencingArtifactMetrics
picard.analysis.
MeanQualityByCycle
picard.analysis.
QualityScoreDistribution
picard.sam.
SortSam
picard.vcf.
SortVcf
picard.sam.
SplitSamByLibrary
picard.vcf.
SplitVcfs
picard.vcf.
UpdateVcfSequenceDictionary
picard.sam.
ValidateSamFile
picard.vcf.
VcfFormatConverter
picard.vcf.
VcfToIntervalList
picard.sam.
ViewSam
picard.filter.
CountingFilter
(implements htsjdk.samtools.filter.SamRecordFilter)
picard.filter.
CountingDuplicateFilter
picard.filter.
CountingMapQFilter
picard.filter.
CountingPairedFilter
picard.cmdline.
CreateHtmlDocForProgram
picard.cmdline.
CreateHtmlDocForStandardOptions
picard.util.
DbSnpBitSetUtil
picard.util.
DbSnpBitSetUtil.DbSnpBitSets
picard.util.
DelimitedTextFileWithHeaderIterator
(implements htsjdk.samtools.util.CloseableIterator<T>)
picard.util.
DelimitedTextFileWithHeaderIterator.Row
picard.vcf.filter.
DepthFilter
(implements picard.vcf.filter.
GenotypeFilter
)
picard.sam.markduplicates.util.
DiskBasedReadEndsForMarkDuplicatesMap
(implements picard.sam.markduplicates.util.
ReadEndsForMarkDuplicatesMap
)
picard.sam.
EarliestFragmentPrimaryAlignmentSelectionStrategy
(implements picard.sam.
PrimaryAlignmentSelectionStrategy
)
picard.cmdline.programgroups.
Fasta
(implements picard.cmdline.
CommandLineProgramGroup
)
picard.util.
FileChannelJDKBugWorkAround
picard.illumina.parser.fakers.
FileFaker
picard.illumina.parser.fakers.
BarcodeFileFaker
picard.illumina.parser.fakers.
BciFileFaker
picard.illumina.parser.fakers.
BclFileFaker
picard.illumina.parser.fakers.
ClocsFileFaker
picard.illumina.parser.fakers.
FilterFileFaker
picard.illumina.parser.fakers.
LocsFileFaker
picard.illumina.parser.fakers.
MultiTileBclFileFaker
picard.illumina.parser.fakers.
MultiTileLocsFileFaker
picard.illumina.parser.fakers.
PosFileFaker
picard.vcf.filter.
FilterApplyingVariantIterator
(implements htsjdk.samtools.util.CloseableIterator<T>)
picard.illumina.parser.readers.
FilterFileReader
(implements java.util.Iterator<E>)
picard.fingerprint.
FingerprintChecker
picard.fingerprint.
FingerprintResults
picard.vcf.filter.
FisherStrandFilter
(implements picard.vcf.filter.
VariantFilter
)
picard.illumina.parser.
FourChannelIntensityData
picard.analysis.
GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
(implements picard.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>)
picard.analysis.
GcBiasUtils
picard.annotation.
Gene.Transcript
picard.annotation.
Gene.Transcript.Exon
picard.annotation.
GeneAnnotationReader
picard.vcf.
GenotypeConcordanceCounts
picard.vcf.
GenotypeConcordanceScheme
picard.vcf.
GA4GHScheme
picard.vcf.
GA4GHSchemeWithMissingAsHomRef
picard.vcf.
GenotypeConcordanceSchemeFactory
picard.vcf.
GenotypeConcordanceStates
picard.vcf.
GenotypeConcordanceStates.TruthAndCallStates
(implements java.lang.Comparable<T>)
picard.vcf.filter.
GenotypeQualityFilter
(implements picard.vcf.filter.
GenotypeFilter
)
picard.fingerprint.
GenotypeReader
picard.fingerprint.
GenotypeReader.VariantIterator
(implements htsjdk.samtools.util.CloseableIterator<T>)
picard.fingerprint.
HaplotypeBlock
(implements java.lang.Comparable<T>)
picard.fingerprint.
HaplotypeMap
picard.fingerprint.
HaplotypeProbabilities
picard.fingerprint.
HaplotypeProbabilitiesFromGenotype
picard.fingerprint.
HaplotypeProbabilitiesFromGenotypeLikelihoods
picard.fingerprint.
HaplotypeProbabilitiesFromSequence
picard.fingerprint.
HaplotypeProbabilitiesFromContaminatorSequence
picard.fingerprint.
HaplotypeProbabilityOfNormalGivenTumor
picard.cmdline.programgroups.
Illumina
(implements picard.cmdline.
CommandLineProgramGroup
)
picard.illumina.
IlluminaBasecallsConverter
<CLUSTER_OUTPUT_RECORD>
picard.illumina.parser.
IlluminaDataProvider
(implements java.lang.Iterable<T>, java.util.Iterator<E>)
picard.illumina.parser.
IlluminaDataProviderFactory
picard.illumina.parser.
IlluminaFileUtil
picard.fastq.
IlluminaReadNameEncoder
(implements picard.fastq.
ReadNameEncoder
)
picard.util.
IlluminaUtil
picard.analysis.directed.
InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
(implements picard.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>)
htsjdk.samtools.util.Interval (implements java.lang.Cloneable, java.lang.Comparable<T>, htsjdk.samtools.util.Locatable)
picard.annotation.
Gene
(implements java.lang.Iterable<T>)
picard.util.
IntervalListScatterer
picard.cmdline.programgroups.
Intervals
(implements picard.cmdline.
CommandLineProgramGroup
)
picard.util.
Iterators
picard.illumina.
LanePhasingMetricsCollector
picard.sam.markduplicates.util.
LibraryIdGenerator
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
htsjdk.samtools.metrics.MetricBase
picard.analysis.
BaseDistributionByCycleMetrics
picard.illumina.quality.
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
picard.illumina.quality.
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
picard.analysis.
CollectOxoGMetrics.CpcgMetrics
picard.analysis.
CollectQualityYieldMetrics.QualityYieldMetrics
picard.vcf.
CollectVariantCallingMetrics.VariantCallingSummaryMetrics
picard.vcf.
CollectVariantCallingMetrics.VariantCallingDetailMetrics
picard.analysis.
CollectWgsMetrics.WgsMetrics
picard.analysis.
CollectRawWgsMetrics.RawWgsMetrics
picard.analysis.
CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
picard.analysis.
CollectWgsMetricsFromSampledSites.SampledWgsMetrics
picard.analysis.
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
picard.sam.
DuplicationMetrics
picard.illumina.
ExtractIlluminaBarcodes.BarcodeMetric
picard.analysis.
FingerprintingDetailMetrics
picard.analysis.
FingerprintingSummaryMetrics
picard.metrics.
GcBiasMetrics
picard.vcf.
GenotypeConcordanceContingencyMetrics
picard.vcf.
GenotypeConcordanceDetailMetrics
picard.vcf.
GenotypeConcordanceSummaryMetrics
picard.illumina.
IlluminaBasecallingMetrics
picard.illumina.
IlluminaLaneMetrics
picard.illumina.
IlluminaPhasingMetrics
picard.analysis.
JumpingLibraryMetrics
picard.analysis.replicates.
MergeableMetricBase
picard.analysis.replicates.
IndependentReplicateMetric
picard.metrics.
MultilevelMetrics
picard.analysis.
AlignmentSummaryMetrics
picard.analysis.
GcBiasDetailMetrics
picard.analysis.
GcBiasSummaryMetrics
picard.analysis.directed.
HsMetrics
picard.analysis.
InsertSizeMetrics
picard.analysis.
RnaSeqMetrics
picard.analysis.
RrbsCpgDetailMetrics
picard.analysis.
RrbsSummaryMetrics
picard.analysis.directed.
TargetedPcrMetrics
picard.analysis.artifacts.
SequencingArtifactMetrics.BaitBiasDetailMetrics
picard.analysis.artifacts.
SequencingArtifactMetrics.BaitBiasSummaryMetrics
picard.analysis.artifacts.
SequencingArtifactMetrics.PreAdapterDetailMetrics
picard.analysis.artifacts.
SequencingArtifactMetrics.PreAdapterSummaryMetrics
picard.cmdline.programgroups.
Metrics
(implements picard.cmdline.
CommandLineProgramGroup
)
picard.util.
MetricsDoclet
picard.illumina.parser.readers.
MMapBackedIteratorFactory
picard.sam.
MostDistantPrimaryAlignmentSelectionStrategy
(implements picard.sam.
PrimaryAlignmentSelectionStrategy
)
picard.metrics.
MultiLevelCollector
<METRIC_TYPE,Histogram_KEY,ARGTYPE>
picard.analysis.
GcBiasMetricsCollector
picard.analysis.directed.
InsertSizeMetricsCollector
picard.metrics.
SAMRecordAndReferenceMultiLevelCollector
<BEAN,HKEY>
picard.analysis.
AlignmentSummaryMetricsCollector
picard.analysis.
RrbsMetricsCollector
picard.metrics.
SAMRecordMultiLevelCollector
<BEAN,HKEY>
picard.analysis.directed.
RnaSeqMetricsCollector
picard.analysis.directed.
TargetMetricsCollector
<METRIC_TYPE>
picard.analysis.directed.
HsMetricCollector
picard.analysis.directed.
TargetedPcrMetricsCollector
picard.illumina.parser.
MultiTileBclParser
picard.illumina.parser.
MultiTileParser
<OUTPUT_RECORD>
picard.illumina.parser.
MultiTileFilterParser
picard.illumina.parser.
MultiTileLocsParser
picard.cmdline.programgroups.
None
(implements picard.cmdline.
CommandLineProgramGroup
)
picard.illumina.parser.
OutputMapping
picard.vcf.
PairedVariantSubContextIterator
(implements java.util.Iterator<E>)
picard.vcf.
PairedVariantSubContextIterator.VcfTuple
picard.illumina.parser.
ParameterizedFileUtil
picard.illumina.parser.
MultiTileBclFileUtil
picard.illumina.parser.
MultiTileFileUtil
<OUTPUT_RECORD>
picard.illumina.parser.
PerTileFileUtil
picard.illumina.parser.
PerTilePerCycleFileUtil
picard.pedigree.
PedFile.PedTrio
picard.illumina.parser.
PerTileParser
<ILLUMINA_DATA>
picard.illumina.parser.
PosParser
picard.sam.markduplicates.util.
PhysicalLocationForMateCigarSet
picard.sam.util.
PhysicalLocationInt
(implements picard.sam.util.
PhysicalLocation
)
picard.sam.util.
PhysicalLocationShort
picard.sam.markduplicates.util.
PhysicalLocationForMateCigar
picard.sam.markduplicates.util.
ReadEnds
picard.sam.markduplicates.util.
ReadEndsForMarkDuplicates
(implements java.lang.Cloneable)
picard.sam.markduplicates.util.
ReadEndsForMarkDuplicatesWithBarcodes
picard.sam.markduplicates.util.
ReadEndsForMateCigar
picard.cmdline.
PicardCommandLine
picard.vcf.processor.util.
PredicateFilterDecoratingClosableIterator
<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
picard.vcf.filter.
QdFilter
(implements picard.vcf.filter.
VariantFilter
)
picard.util.
QuerySortedReadPairIteratorUtil
picard.util.
QuerySortedReadPairIteratorUtil.ReadPair
picard.illumina.parser.
Range
picard.illumina.parser.
ReadData
picard.illumina.parser.
ReadDescriptor
picard.sam.markduplicates.util.
ReadEndsForMarkDuplicatesCodec
(implements htsjdk.samtools.util.SortingCollection.Codec<T>)
picard.sam.markduplicates.util.
ReadEndsForMarkDuplicatesWithBarcodesCodec
picard.sam.util.
ReadNameParser
picard.sam.markduplicates.util.
OpticalDuplicateFinder
picard.illumina.parser.
ReadStructure
picard.illumina.parser.
ReadStructure.Substructure
(implements java.lang.Iterable<T>)
picard.annotation.
RefFlatReader
picard.util.
RExecutor
picard.cmdline.programgroups.
SamOrBam
(implements picard.cmdline.
CommandLineProgramGroup
)
picard.metrics.
SAMRecordAndReference
htsjdk.samtools.util.SamRecordWithOrdinal
picard.sam.markduplicates.util.
SamRecordWithOrdinalAndSetDuplicateReadFlag
picard.analysis.artifacts.
SequencingArtifactMetrics
picard.fingerprint.
Snp
(implements java.lang.Comparable<T>)
picard.cmdline.
StandardOptionDefinitions
picard.util.
TabbedTextFileWithHeaderParser
(implements java.lang.Iterable<T>)
picard.util.
TabbedTextFileWithHeaderParser.Row
picard.analysis.directed.
TargetMetricsCollector.Coverage
picard.analysis.directed.
TargetMetricsCollector.PerUnitTargetMetricCollector
(implements picard.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>)
picard.
Test
picard.cmdline.programgroups.
Testing
(implements picard.cmdline.
CommandLineProgramGroup
)
picard.util.
TestNGUtil
picard.util.
TestNGUtil.SingleTestUnitTest
<TestClazz>
picard.util.
TestNGUtil.TestNGParameterizable
picard.analysis.
TheoreticalSensitivity
picard.analysis.
TheoreticalSensitivity.RouletteWheel
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
java.lang.RuntimeException
picard.
PicardException
picard.annotation.
AnnotationException
picard.cmdline.
CommandLineParseException
picard.cmdline.
CommandLineParserDefinitionException
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
picard.util.
UnsignedTypeUtil
picard.vcf.processor.
VariantAccumulatorExecutor.MultiThreadedChunkBased
<A,R> (implements picard.vcf.processor.
VariantAccumulatorExecutor
<ACCUMULATOR,RESULT>)
picard.vcf.processor.
VariantIteratorProducer
picard.vcf.processor.
VariantProcessor
<RESULT,ACCUMULATOR>
picard.vcf.processor.
VariantProcessor.Builder
<A,R>
picard.vcf.processor.
VcfFileSegment
picard.vcf.processor.
VcfFileSegmentGenerator
picard.cmdline.programgroups.
VcfOrBcf
(implements picard.cmdline.
CommandLineProgramGroup
)
Interface Hierarchy
picard.util.
AdapterPair
picard.util.
AtomicIterator
<T>
picard.analysis.
CollectMultipleMetrics.ProgramInterface
picard.cmdline.
CommandLineParser.ClpEnum
picard.cmdline.
CommandLineProgramGroup
picard.vcf.filter.
GenotypeFilter
picard.illumina.
IlluminaBasecallsConverter.ClusterDataConverter
<OUTPUT_RECORD>
picard.illumina.
IlluminaBasecallsConverter.ConvertedClusterDataWriter
<OUTPUT_RECORD>
picard.metrics.
PerUnitMetricCollector
<BEAN,HKEY,ARGTYPE>
picard.sam.util.
PhysicalLocation
picard.sam.
PrimaryAlignmentSelectionStrategy
picard.sam.markduplicates.util.
ReadEndsForMarkDuplicatesMap
picard.fastq.
ReadNameEncoder
picard.vcf.processor.
VariantAccumulatorExecutor
<ACCUMULATOR,RESULT>
picard.vcf.filter.
VariantFilter
picard.vcf.processor.
VariantProcessor.Accumulator
<RESULT>
picard.vcf.processor.
VariantProcessor.AccumulatorGenerator
<ACCUMULATOR,RESULT>
picard.vcf.processor.
VariantProcessor.ResultMerger
<RESULT>
Annotation Type Hierarchy
picard.analysis.replicates.
MergeableMetricBase.MergeByAdding
(implements java.lang.annotation.Annotation)
picard.analysis.replicates.
MergeableMetricBase.MergeByAssertEquals
(implements java.lang.annotation.Annotation)
picard.analysis.replicates.
MergeableMetricBase.NoMergingIsDerived
(implements java.lang.annotation.Annotation)
picard.cmdline.
CommandLineProgramProperties
(implements java.lang.annotation.Annotation)
picard.cmdline.
NestedOptions
(implements java.lang.annotation.Annotation)
picard.cmdline.
Option
(implements java.lang.annotation.Annotation)
picard.cmdline.
PositionalArguments
(implements java.lang.annotation.Annotation)
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
picard.analysis.
AlignmentSummaryMetrics.Category
picard.analysis.
CollectMultipleMetrics.Program
(implements picard.analysis.
CollectMultipleMetrics.ProgramInterface
)
picard.analysis.
CollectWgsMetricsFromQuerySorted.FILTERING_STRINGENCY
picard.analysis.
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
picard.analysis.
MetricAccumulationLevel
picard.analysis.directed.
RnaSeqMetricsCollector.StrandSpecificity
picard.annotation.
LocusFunction
picard.annotation.
RefFlatReader.RefFlatColumns
picard.fingerprint.
DiploidGenotype
picard.fingerprint.
DiploidHaplotype
picard.fingerprint.
HaplotypeProbabilities.Genotype
picard.illumina.
IlluminaBasecallsToFastq.ReadNameFormat
picard.illumina.parser.
IlluminaDataType
picard.illumina.parser.
IlluminaFileUtil.SupportedIlluminaFormat
picard.illumina.parser.
IlluminaMetricsCode
picard.illumina.parser.
IntensityChannel
picard.illumina.parser.
ReadType
picard.illumina.parser.
TileTemplateRead
picard.illumina.quality.
CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
picard.pedigree.
Sex
picard.sam.
FilterSamReads.Filter
picard.sam.
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
picard.sam.
ValidateSamFile.Mode
picard.sam.
ViewSam.AlignmentStatus
picard.sam.
ViewSam.PfStatus
picard.sam.markduplicates.
MarkDuplicates.DuplicateTaggingPolicy
picard.sam.markduplicates.
MarkDuplicates.DuplicateType
picard.util.
BaitDesigner.DesignStrategy
picard.util.
IlluminaUtil.IlluminaAdapterPair
(implements picard.util.
AdapterPair
)
picard.util.
IntervalListScatterer.Mode
picard.util.
IntervalListTools.Action
(implements picard.cmdline.
CommandLineParser.ClpEnum
)
picard.util.
VariantType
picard.vcf.
GenotypeConcordanceStateCodes
picard.vcf.
GenotypeConcordanceStates.TruthState
picard.vcf.
GenotypeConcordanceStates.CallState
picard.vcf.
GenotypeConcordanceStates.ContingencyState
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