Package picard.sam

Class MostDistantPrimaryAlignmentSelectionStrategy

  • All Implemented Interfaces:
    PrimaryAlignmentSelectionStrategy

    public class MostDistantPrimaryAlignmentSelectionStrategy
    extends Object
    implements PrimaryAlignmentSelectionStrategy
    For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size. If such a pair of alignments cannot be found, either because one end is not aligned, or because all alignment pairs are chimeric, then select the best MAPQ for each end independently. The primary alignments are then correlated so that their mate info points to each other, but all non-primary alignments are uncorrelated.
    • Constructor Detail

      • MostDistantPrimaryAlignmentSelectionStrategy

        public MostDistantPrimaryAlignmentSelectionStrategy()