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 Type	Method and Description
void	pickPrimaryAlignment(picard.sam.HitsForInsert hitsForInsert) When this method returns, one alignment has been marked as primary according to the implementation's strategy.

Method Detail

pickPrimaryAlignment

void pickPrimaryAlignment(picard.sam.HitsForInsert hitsForInsert)

When this method returns, one alignment has been marked as primary according to the implementation's strategy.