Class CollectOxoGMetrics


  • @DocumentedFeature
    public class CollectOxoGMetrics
    extends CommandLineProgram
    Class for trying to quantify the CpCG->CpCA error rate.
    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="Input BAM file for analysis.")
        public File INPUT
      • OUTPUT

        @Argument(shortName="O",
                  doc="Location of output metrics file to write.")
        public File OUTPUT
      • INTERVALS

        @Argument(doc="An optional list of intervals to restrict analysis to.",
                  optional=true)
        public File INTERVALS
      • DB_SNP

        @Argument(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.",
                  optional=true)
        public File DB_SNP
      • MINIMUM_QUALITY_SCORE

        @Argument(shortName="Q",
                  doc="The minimum base quality score for a base to be included in analysis.")
        public int MINIMUM_QUALITY_SCORE
      • MINIMUM_MAPPING_QUALITY

        @Argument(shortName="MQ",
                  doc="The minimum mapping quality score for a base to be included in analysis.")
        public int MINIMUM_MAPPING_QUALITY
      • MINIMUM_INSERT_SIZE

        @Argument(shortName="MIN_INS",
                  doc="The minimum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.")
        public int MINIMUM_INSERT_SIZE
      • MAXIMUM_INSERT_SIZE

        @Argument(shortName="MAX_INS",
                  doc="The maximum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.")
        public int MAXIMUM_INSERT_SIZE
      • INCLUDE_NON_PF_READS

        @Argument(shortName="NON_PF",
                  doc="Whether or not to include non-PF reads.")
        public boolean INCLUDE_NON_PF_READS
      • USE_OQ

        @Argument(doc="When available, use original quality scores for filtering.")
        public boolean USE_OQ
      • CONTEXT_SIZE

        @Argument(doc="The number of context bases to include on each side of the assayed G/C base.")
        public int CONTEXT_SIZE
      • CONTEXTS

        @Argument(doc="The optional set of sequence contexts to restrict analysis to. If not supplied all contexts are analyzed.",
                  optional=true)
        public Set<String> CONTEXTS
      • STOP_AFTER

        @Argument(doc="For debugging purposes: stop after visiting this many sites with at least 1X coverage.")
        public int STOP_AFTER
    • Constructor Detail

      • CollectOxoGMetrics

        public CollectOxoGMetrics()
    • Method Detail

      • customCommandLineValidation

        protected String[] customCommandLineValidation()
        Description copied from class: CommandLineProgram
        Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.
        Overrides:
        customCommandLineValidation in class CommandLineProgram
        Returns:
        null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
      • 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.