Package picard.analysis

Class CollectRrbsMetrics

java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.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 Details

    • INPUT

      @Argument(doc="The SAM/BAM/CRAM 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

    • DETAIL_FILE_EXTENSION

      public static final String DETAIL_FILE_EXTENSION
      See Also:

    • SUMMARY_FILE_EXTENSION

      public static final String SUMMARY_FILE_EXTENSION
      See Also:

    • PDF_FILE_EXTENSION

      public static final String PDF_FILE_EXTENSION
      See Also:

  • Constructor Details

    • CollectRrbsMetrics

      public CollectRrbsMetrics()

  • Method Details

    • makeReferenceArgumentCollection

      protected ReferenceArgumentCollection makeReferenceArgumentCollection()
      Overrides:
      makeReferenceArgumentCollection in class CommandLineProgram

    • 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.