Package picard.sam

Class BestMapqPrimaryAlignmentSelectionStrategy

  • All Implemented Interfaces:
    PrimaryAlignmentSelectionStrategy

    public class BestMapqPrimaryAlignmentSelectionStrategy
    extends Object
    implements PrimaryAlignmentSelectionStrategy
    This strategy was designed for TopHat output, but could be of general utility. It picks the alignment with best MAPQ. If paired-end, it is the alignment in which the sum of the MAPQs of both ends is the best. In case of ties, one is selected arbitrarily. This strategy expects pair-aware alignments, with the corresponding alignment for each mate of the pair correlated by HI (hit index) tag. If the aligner has set a pair of alignments as primary, this is used (assuming one of those alignments is not filtered out). Otherwise the alignment pair with best MapQ is selected.
    • Constructor Detail

      • BestMapqPrimaryAlignmentSelectionStrategy

        public BestMapqPrimaryAlignmentSelectionStrategy()