Class ReadEndsForMarkDuplicates

    • Field Detail

      • score

        public short score
      • read1IndexInFile

        public long read1IndexInFile
      • read2IndexInFile

        public long read2IndexInFile
      • duplicateSetSize

        public int duplicateSetSize
    • Constructor Detail

      • ReadEndsForMarkDuplicates

        public ReadEndsForMarkDuplicates()
    • Method Detail

      • getSizeOf

        public static int getSizeOf()
      • isSingleEndReadKnownFragment

        public static boolean isSingleEndReadKnownFragment​(htsjdk.samtools.SAMRecord rec)
        This method is used to generate the following two metrics: UNPAIRED_DUPS_WITH_TLEN UNPAIRED_DUPS_WITHOUT_TLEN It will return true if and only if the read is single ended and the exact fragment length is known (i.e. it was not quality trimmed)