Package picard.analysis

Class CollectUmiPrevalenceMetrics

java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.CollectUmiPrevalenceMetrics
@DocumentedFeature @ExperimentalFeature public class CollectUmiPrevalenceMetrics extends CommandLineProgram
A CLP that, tallies the number of UMIs in a duplicate set across the entire bam and produces a histogram.

  • Field Details

    • INPUT

      @Argument(shortName="I", doc="Input (indexed) BAM/CRAM file.") public PicardHtsPath INPUT

    • OUTPUT

      @Argument(shortName="O", doc="Write metrics to this file") public File OUTPUT

    • MINIMUM_MQ

      @Argument(shortName="MQ", doc="minimal value for the mapping quality of the reads to be used in the estimation.", optional=true, minValue=0.0, maxValue=255.0) public Integer MINIMUM_MQ

    • BARCODE_TAG

      @Argument(doc="Barcode SAM tag.", optional=true) public String BARCODE_TAG

    • BARCODE_BQ

      @Argument(doc="Barcode Quality SAM tag.", optional=true) public String BARCODE_BQ

    • MINIMUM_BARCODE_BQ

      @Argument(shortName="BQ", doc="minimal value for the base quality of all the bases in a molecular barcode, for it to be used.", optional=true, minValue=0.0, maxValue=255.0) public Integer MINIMUM_BARCODE_BQ

    • FILTER_UNPAIRED_READS

      @Argument(shortName="FUR", doc="Whether to filter unpaired reads from the input.", optional=true) public boolean FILTER_UNPAIRED_READS

    • PROGRESS_STEP_INTERVAL

      @Argument(fullName="PROGRESS_STEP_INTERVAL", doc="The interval between which progress will be displayed.", optional=true) public int PROGRESS_STEP_INTERVAL

  • Constructor Details

    • CollectUmiPrevalenceMetrics

      public CollectUmiPrevalenceMetrics()

  • Method Details

    • doWork

      protected int doWork()
      Description copied from class: CommandLineProgram
      Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
      Specified by:
      doWork in class CommandLineProgram
      Returns:
      program exit status.