Uses of Interface
picard.sam.PrimaryAlignmentSelectionStrategy

Packages that use PrimaryAlignmentSelectionStrategy

Package	Description
picard.sam

Uses of PrimaryAlignmentSelectionStrategy in picard.sam

Classes in picard.sam that implement PrimaryAlignmentSelectionStrategy

Modifier and Type	Class and Description
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.
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.

Constructors in picard.sam with parameters of type PrimaryAlignmentSelectionStrategy

Constructor and Description
AbstractAlignmentMerger(java.io.File unmappedBamFile, java.io.File targetBamFile, java.io.File referenceFasta, boolean clipAdapters, boolean bisulfiteSequence, boolean alignedReadsOnly, htsjdk.samtools.SAMProgramRecord programRecord, java.util.List<java.lang.String> attributesToRetain, java.util.List<java.lang.String> attributesToRemove, java.lang.Integer read1BasesTrimmed, java.lang.Integer read2BasesTrimmed, java.util.List<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations, htsjdk.samtools.SAMFileHeader.SortOrder sortOrder, PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy, boolean addMateCigar, boolean unmapContaminantReads) Constructor
SamAlignmentMerger(java.io.File unmappedBamFile, java.io.File targetBamFile, java.io.File referenceFasta, htsjdk.samtools.SAMProgramRecord programRecord, boolean clipAdapters, boolean bisulfiteSequence, boolean alignedReadsOnly, java.util.List<java.io.File> alignedSamFile, int maxGaps, java.util.List<java.lang.String> attributesToRetain, java.util.List<java.lang.String> attributesToRemove, java.lang.Integer read1BasesTrimmed, java.lang.Integer read2BasesTrimmed, java.util.List<java.io.File> read1AlignedSamFile, java.util.List<java.io.File> read2AlignedSamFile, java.util.List<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations, htsjdk.samtools.SAMFileHeader.SortOrder sortOrder, PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy, boolean addMateCigar, boolean unmapContaminantReads, int minUnclippedBases) Constructor