Package picard.sam

Class EarliestFragmentPrimaryAlignmentSelectionStrategy

  • All Implemented Interfaces:
    PrimaryAlignmentSelectionStrategy

    public class EarliestFragmentPrimaryAlignmentSelectionStrategy
    extends Object
    implements PrimaryAlignmentSelectionStrategy
    When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps the earliest base in the read. This implementation only works for fragments, not for pairs. If there are multiple alignments that all start mapping at the same offest in the read, pick the one with the best MAPQ. If there are multiple alignments that have the earliest mapping and that have the same MAPQ, pick one randomly.
    • Constructor Detail

      • EarliestFragmentPrimaryAlignmentSelectionStrategy

        public EarliestFragmentPrimaryAlignmentSelectionStrategy()