Package picard.sam
Interface PrimaryAlignmentSelectionStrategy
- All Known Implementing Classes:
BestEndMapqPrimaryAlignmentStrategy
,BestMapqPrimaryAlignmentSelectionStrategy
,EarliestFragmentPrimaryAlignmentSelectionStrategy
,MostDistantPrimaryAlignmentSelectionStrategy
public interface PrimaryAlignmentSelectionStrategy
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever
strategy is appropriate. Any pre-existing primary designation is ignored, so if the aligner has selected an
appropriate primary alignment, this class should not be called.
-
Method Summary
Modifier and TypeMethodDescriptionvoid
pickPrimaryAlignment
(picard.sam.HitsForInsert hitsForInsert) When this method returns, one alignment has been marked as primary according to the implementation's strategy.
-
Method Details
-
pickPrimaryAlignment
void pickPrimaryAlignment(picard.sam.HitsForInsert hitsForInsert) When this method returns, one alignment has been marked as primary according to the implementation's strategy.
-