MarkDuplicatesHelper (picard 3.4.0 API)

All Known Implementing Classes:: MarkDuplicates, MarkDuplicatesForFlowHelper, SimpleMarkDuplicatesWithMateCigar, UmiAwareMarkDuplicatesWithMateCigar

public interface MarkDuplicatesHelper

Method Summary

Modifier and Type

Method

Description

ReadEndsForMarkDuplicates

buildReadEnds(htsjdk.samtools.SAMFileHeader header, long index, htsjdk.samtools.SAMRecord rec, boolean useBarcodes)

void

generateDuplicateIndexes(boolean useBarcodes, boolean indexOpticalDuplicates)

short

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

Method Details
- 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)