Class CollectJumpingLibraryMetrics


  • @DocumentedFeature
    public class CollectJumpingLibraryMetrics
    extends CommandLineProgram
    Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.
    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="BAM file(s) of reads with duplicates marked")
        public List<File> INPUT
      • OUTPUT

        @Argument(shortName="O",
                  doc="File to which metrics should be written")
        public File OUTPUT
      • MINIMUM_MAPPING_QUALITY

        @Argument(shortName="MQ",
                  doc="Mapping quality minimum cutoff")
        public Integer MINIMUM_MAPPING_QUALITY
      • TAIL_LIMIT

        @Argument(shortName="T",
                  doc="When calculating mean and stdev stop when the bins in the tail of the distribution contain fewer than mode/TAIL_LIMIT items")
        public int TAIL_LIMIT
      • CHIMERA_KB_MIN

        @Argument(doc="Jumps greater than or equal to the greater of this value or 2 times the mode of the outward-facing pairs are considered chimeras")
        public int CHIMERA_KB_MIN
    • Constructor Detail

      • CollectJumpingLibraryMetrics

        public CollectJumpingLibraryMetrics()
    • Method Detail

      • doWork

        protected int doWork()
        Calculates the detailed statistics about the jumping library and then generates the results.
        Specified by:
        doWork in class CommandLineProgram
        Returns:
        program exit status.