Class CollectRrbsMetrics


  • @DocumentedFeature
    public class CollectRrbsMetrics
    extends CommandLineProgram
    Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well as CpG sites across all reads in the input BAM/SAM file.
    • Field Detail

      • INPUT

        @Argument(doc="The BAM or SAM file containing aligned reads. Must be coordinate sorted",
                  shortName="I")
        public File INPUT
      • METRICS_FILE_PREFIX

        @Argument(doc="Base name for output files",
                  shortName="M")
        public String METRICS_FILE_PREFIX
      • MINIMUM_READ_LENGTH

        @Argument(doc="Minimum read length")
        public int MINIMUM_READ_LENGTH
      • C_QUALITY_THRESHOLD

        @Argument(doc="Threshold for base quality of a C base before it is considered")
        public int C_QUALITY_THRESHOLD
      • NEXT_BASE_QUALITY_THRESHOLD

        @Argument(doc="Threshold for quality of a base next to a C before the C base is considered")
        public int NEXT_BASE_QUALITY_THRESHOLD
      • MAX_MISMATCH_RATE

        @Argument(doc="Maximum percentage of mismatches in a read for it to be considered, with a range of 0-1")
        public double MAX_MISMATCH_RATE
      • SEQUENCE_NAMES

        @Argument(doc="Set of sequence names to consider, if not specified all sequences will be used",
                  optional=true)
        public Set<String> SEQUENCE_NAMES
      • ASSUME_SORTED

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

        @Argument(shortName="LEVEL",
                  doc="The level(s) at which to accumulate metrics.  ")
        public Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL
    • Constructor Detail

      • CollectRrbsMetrics

        public CollectRrbsMetrics()
    • Method Detail

      • 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.
      • 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.