Package | Description |
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picard.sam |
Modifier and Type | Class and Description |
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class |
BestEndMapqPrimaryAlignmentStrategy
For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and
make that the primary.
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class |
BestMapqPrimaryAlignmentSelectionStrategy
This strategy was designed for TopHat output, but could be of general utility.
|
class |
EarliestFragmentPrimaryAlignmentSelectionStrategy
When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps
the earliest base in the read.
|
class |
MostDistantPrimaryAlignmentSelectionStrategy
For a paired-end aligner that aligns each end independently, select the pair of alignments that result
in the largest insert size.
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Constructor and Description |
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AbstractAlignmentMerger(File unmappedBamFile,
File targetBamFile,
File referenceFasta,
boolean clipAdapters,
boolean bisulfiteSequence,
boolean alignedReadsOnly,
SAMProgramRecord programRecord,
List<String> attributesToRetain,
List<String> attributesToRemove,
Integer read1BasesTrimmed,
Integer read2BasesTrimmed,
List<SamPairUtil.PairOrientation> expectedOrientations,
SAMFileHeader.SortOrder sortOrder,
PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy,
boolean addMateCigar,
boolean unmapContaminantReads)
Constructor
|
SamAlignmentMerger(File unmappedBamFile,
File targetBamFile,
File referenceFasta,
SAMProgramRecord programRecord,
boolean clipAdapters,
boolean bisulfiteSequence,
boolean alignedReadsOnly,
List<File> alignedSamFile,
int maxGaps,
List<String> attributesToRetain,
List<String> attributesToRemove,
Integer read1BasesTrimmed,
Integer read2BasesTrimmed,
List<File> read1AlignedSamFile,
List<File> read2AlignedSamFile,
List<SamPairUtil.PairOrientation> expectedOrientations,
SAMFileHeader.SortOrder sortOrder,
PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy,
boolean addMateCigar,
boolean unmapContaminantReads,
int minUnclippedBases)
Constructor
|