Class SamLocusIterator.LocusInfo

  • All Implemented Interfaces:
    Locatable, Locus
    Enclosing class:
    SamLocusIterator

    public static final class SamLocusIterator.LocusInfo
    extends AbstractLocusInfo<SamLocusIterator.RecordAndOffset>
    The unit of iteration. Holds information about the locus (the SAMSequenceRecord and 1-based position on the reference), plus List of ReadAndOffset objects, one for each read that overlaps the locus; two more List_s_ of ReadAndOffset objects include reads that overlap the locus with insertions and deletions respectively
    • Constructor Detail

      • LocusInfo

        public LocusInfo​(SAMSequenceRecord referenceSequence,
                         int position)
        Parameters:
        referenceSequence - reference sequence at which the reads are aligned
        position - position in the sequence at which the reads are aligned