Package picard.sam

Class BestEndMapqPrimaryAlignmentStrategy

java.lang.Object
picard.sam.BestEndMapqPrimaryAlignmentStrategy
All Implemented Interfaces:
PrimaryAlignmentSelectionStrategy

public class BestEndMapqPrimaryAlignmentStrategy extends Object implements PrimaryAlignmentSelectionStrategy
For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary. The primary alignments are then correlated so that their mate info points to each other, but all non-primary alignments are uncorrelated.
  • Constructor Details

    • BestEndMapqPrimaryAlignmentStrategy

      public BestEndMapqPrimaryAlignmentStrategy()
  • Method Details