Class AbstractMarkDuplicatesCommandLineProgram

    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="One or more input SAM, BAM or CRAM 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

        public static void finalizeAndWriteMetrics​(LibraryIdGenerator libraryIdGenerator,
                                                   htsjdk.samtools.metrics.MetricsFile<DuplicationMetrics,​Double> metricsFile,
                                                   File outputFile)
        Writes the metrics given by the libraryIdGenerator to the outputFile.
        Parameters:
        libraryIdGenerator - A LibraryIdGenerator object that contains the map from library to DuplicationMetrics for that library
        metricsFile - An empty MetricsFile object that will be filled, with "finalized" metrics and written out. It needs to be generated from a non-static context so that various commandline information is added to the header when CommandLineProgram.getMetricsFile() is called.
        outputFile - The file to write the metrics to
      • addReadToLibraryMetrics

        public static DuplicationMetrics addReadToLibraryMetrics​(htsjdk.samtools.SAMRecord rec,
                                                                 htsjdk.samtools.SAMFileHeader header,
                                                                 LibraryIdGenerator libraryIdGenerator,
                                                                 boolean flowMetrics)
      • 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.
      • addSingletonToCount

        public static void addSingletonToCount​(LibraryIdGenerator libraryIdGenerator)