Interface MarkDuplicatesHelper

    • Method Detail

      • generateDuplicateIndexes

        void generateDuplicateIndexes​(boolean useBarcodes,
                                      boolean indexOpticalDuplicates)
      • buildReadEnds

        ReadEndsForMarkDuplicates buildReadEnds​(htsjdk.samtools.SAMFileHeader header,
                                                long index,
                                                htsjdk.samtools.SAMRecord rec,
                                                boolean useBarcodes)
      • getReadDuplicateScore

        short getReadDuplicateScore​(htsjdk.samtools.SAMRecord rec,
                                    ReadEndsForMarkDuplicates pairedEnds)