picard.sam

Interfaces

• PrimaryAlignmentSelectionStrategy

Classes

• AbstractAlignmentMerger
• AddCommentsToBam
• AddOrReplaceReadGroups
• BamIndexStats
• BestEndMapqPrimaryAlignmentStrategy
• BestMapqPrimaryAlignmentSelectionStrategy
• BuildBamIndex
• CalculateReadGroupChecksum
• CheckTerminatorBlock
• CleanSam
• CompareSAMs
• CreateSequenceDictionary
• DownsampleSam
• DuplicationMetrics
• EarliestFragmentPrimaryAlignmentSelectionStrategy
• FastqToSam
• FilterSamReads
• FixMateInformation
• GatherBamFiles
• MergeBamAlignment
• MergeSamFiles
• MostDistantPrimaryAlignmentSelectionStrategy
• PositionBasedDownsampleSam
• ReorderSam
• ReplaceSamHeader
• RevertOriginalBaseQualitiesAndAddMateCigar
• RevertSam
• SamAlignmentMerger
• SamFormatConverter
• SamToFastq
• SetNmAndUqTags
• SortSam
• SplitSamByLibrary
• ValidateSamFile
• ViewSam

Enums

• FilterSamReads.Filter
• RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
• ValidateSamFile.Mode
• ViewSam.AlignmentStatus
• ViewSam.PfStatus