Hierarchy For Package picard.sam
Class Hierarchy
- java.lang.Object
- picard.sam.AbstractAlignmentMerger
- picard.sam.SamAlignmentMerger
- picard.sam.BestEndMapqPrimaryAlignmentStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- picard.sam.BestMapqPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- picard.cmdline.CommandLineProgram
- picard.sam.AddCommentsToBam
- picard.sam.AddOATag
- picard.sam.AddOrReplaceReadGroups
- picard.sam.BamIndexStats
- picard.sam.BuildBamIndex
- picard.sam.CalculateReadGroupChecksum
- picard.sam.CheckTerminatorBlock
- picard.sam.CleanSam
- picard.sam.CompareSAMs
- picard.sam.CreateSequenceDictionary
- picard.sam.DownsampleSam
- picard.sam.FastqToSam
- picard.sam.FilterSamReads
- picard.sam.FixMateInformation
- picard.sam.GatherBamFiles
- picard.sam.MergeBamAlignment
- picard.sam.MergeSamFiles
- picard.sam.PositionBasedDownsampleSam
- picard.sam.ReorderSam
- picard.sam.ReplaceSamHeader
- picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- picard.sam.RevertSam
- picard.sam.SamFormatConverter
- picard.sam.SamToFastq
- picard.sam.SamToFastqWithTags
- picard.sam.SetNmMdAndUqTags
- picard.sam.SetNmAndUqTags
- picard.sam.SortSam
- picard.sam.SplitSamByLibrary
- picard.sam.SplitSamByNumberOfReads
- picard.sam.ValidateSamFile
- picard.sam.ViewSam
- picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- picard.sam.DuplicationMetricsFactory
- picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- htsjdk.samtools.metrics.MetricBase
- picard.analysis.MergeableMetricBase
- picard.sam.DuplicationMetrics
- picard.sam.FlowBasedDuplicationMetrics
- picard.sam.DuplicationMetrics
- picard.sam.SamComparisonMetric
- picard.analysis.MergeableMetricBase
- picard.sam.MostDistantPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- picard.sam.AbstractAlignmentMerger
Interface Hierarchy
- picard.sam.PrimaryAlignmentSelectionStrategy
Enum Class Hierarchy
- java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
- picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- picard.sam.FilterSamReads.Filter (implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
- picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- picard.sam.RevertSam.FileType (implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
- picard.sam.ValidateSamFile.Mode
- picard.sam.ViewSam.AlignmentStatus
- picard.sam.ViewSam.PfStatus
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)