Class ReadEndsForMateCigar

  • All Implemented Interfaces:
    PhysicalLocation

    public class ReadEndsForMateCigar
    extends ReadEnds
    A class to store individual records for MarkDuplicatesWithMateCigar. This aids in comparing records to determine which need to be compared when we mark duplicates. We also store the original SAMRecord and its ordinal in the input file (in SamRecordWithOrdinal) to access optional tags (mate cigar) and other information.
    • Field Detail

      • samRecordWithOrdinal

        public htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal
    • Constructor Detail

      • ReadEndsForMateCigar

        public ReadEndsForMateCigar​(htsjdk.samtools.SAMFileHeader header,
                                    htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal,
                                    OpticalDuplicateFinder opticalDuplicateFinder,
                                    short libraryId)
        Builds a read ends object that represents a single read.
      • ReadEndsForMateCigar

        public ReadEndsForMateCigar​(ReadEndsForMateCigar other,
                                    htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal)
        Creates a shallow copy from the "other"
    • Method Detail

      • getSamRecordIndex

        public htsjdk.samtools.util.SamRecordWithOrdinal getSamRecordIndex()
        A number of convenience functions
      • getRecord

        public htsjdk.samtools.SAMRecord getRecord()
      • getRecordReadName

        public String getRecordReadName()
      • getReadEndSetForOpticalDuplicates

        public Set<ReadEnds> getReadEndSetForOpticalDuplicates()
        Gets the read ends for optical duplicate tracking