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 Type
    Method
    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 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.