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

• DETAIL_FILE_EXTENSION

  public static final String DETAIL_FILE_EXTENSION

  See Also:

  Constant Field Values

• SUMMARY_FILE_EXTENSION

  public static final String SUMMARY_FILE_EXTENSION

  See Also:

  Constant Field Values

• PDF_FILE_EXTENSION

  public static final String PDF_FILE_EXTENSION

  See Also:

  Constant Field Values

Constructor Detail

• CollectRrbsMetrics

  public CollectRrbsMetrics()

Method Detail

• makeReferenceArgumentCollection

  protected ReferenceArgumentCollection makeReferenceArgumentCollection()

  Overrides:

  makeReferenceArgumentCollection in class CommandLineProgram

• main

  public static void main​(String[] args)

• 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.