Field Detail

• pgTagArgumentCollection

  @ArgumentCollection
  protected final PGTagArgumentCollection pgTagArgumentCollection

• INPUT

  @Argument(shortName="I",
            doc="One or more input SAM or BAM files to analyze. Must be coordinate sorted.")
  public List<String> INPUT

• OUTPUT

  @Argument(shortName="O",
            doc="The output file to write marked records to")
  public File OUTPUT

• METRICS_FILE

  @Argument(shortName="M",
            doc="File to write duplication metrics to")
  public File METRICS_FILE

• REMOVE_DUPLICATES

  @Argument(doc="If true do not write duplicates to the output file instead of writing them with appropriate flags set.")
  public boolean REMOVE_DUPLICATES

• ASSUME_SORTED

  @Deprecated
  @Argument(shortName="AS",
            doc="If true, assume that the input file is coordinate sorted even if the header says otherwise. Deprecated, used ASSUME_SORT_ORDER=coordinate instead.",
            mutex="ASSUME_SORT_ORDER")
  public boolean ASSUME_SORTED

  Deprecated.

• ASSUME_SORT_ORDER

  @Argument(shortName="ASO",
            doc="If not null, assume that the input file has this order even if the header says otherwise.",
            optional=true,
            mutex="ASSUME_SORTED")
  public htsjdk.samtools.SAMFileHeader.SortOrder ASSUME_SORT_ORDER

• DUPLICATE_SCORING_STRATEGY

  @Argument(shortName="DS",
            doc="The scoring strategy for choosing the non-duplicate among candidates.")
  public htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy DUPLICATE_SCORING_STRATEGY

• PROGRAM_RECORD_ID

  @Argument(shortName="PG",
            doc="The program record ID for the @PG record(s) created by this program. Set to null to disable PG record creation.  This string may have a suffix appended to avoid collision with other program record IDs.",
            optional=true)
  public String PROGRAM_RECORD_ID

• PROGRAM_GROUP_VERSION

  @Argument(shortName="PG_VERSION",
            doc="Value of VN tag of PG record to be created. If not specified, the version will be detected automatically.",
            optional=true)
  public String PROGRAM_GROUP_VERSION

• PROGRAM_GROUP_COMMAND_LINE

  @Argument(shortName="PG_COMMAND",
            doc="Value of CL tag of PG record to be created. If not supplied the command line will be detected automatically.",
            optional=true)
  public String PROGRAM_GROUP_COMMAND_LINE

• PROGRAM_GROUP_NAME

  @Argument(shortName="PG_NAME",
            doc="Value of PN tag of PG record to be created.")
  public String PROGRAM_GROUP_NAME

• COMMENT

  @Argument(shortName="CO",
            doc="Comment(s) to include in the output file\'s header.",
            optional=true)
  public List<String> COMMENT

• pgIdsSeen

  protected final Set<String> pgIdsSeen

  The program groups that have been seen during the course of examining the input records.

Constructor Detail

• AbstractMarkDuplicatesCommandLineProgram

  public AbstractMarkDuplicatesCommandLineProgram()

Method Detail

• getChainedPgIds

  protected Map<String,String> getChainedPgIds​(htsjdk.samtools.SAMFileHeader outputHeader)

  We have to re-chain the program groups based on this algorithm. This returns the map from existing program group ID to new program group ID.

• finalizeAndWriteMetrics

  protected void finalizeAndWriteMetrics​(LibraryIdGenerator libraryIdGenerator)

  Writes the metrics given by the libraryIdGenerator to the METRICS_FILE.

  Parameters:

  libraryIdGenerator -

• openInputs

  protected AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator openInputs​(boolean eagerlyDecode)

  Since this may read its inputs more than once this method does all the opening and checking of the inputs.

• trackOpticalDuplicates

  public static void trackOpticalDuplicates​(List<? extends ReadEnds> ends,
                                            ReadEnds keeper,
                                            OpticalDuplicateFinder opticalDuplicateFinder,
                                            LibraryIdGenerator libraryIdGenerator)

  Looks through the set of reads and identifies how many of the duplicates are in fact optical duplicates, and stores the data in the instance level histogram. Additionally sets the transient isOpticalDuplicate flag on each read end that is identified as an optical duplicate.