Package picard.sam

Class 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 Detail

      • BestEndMapqPrimaryAlignmentStrategy

        public BestEndMapqPrimaryAlignmentStrategy()