Field Detail

• INPUT

  @Argument(shortName="I",
            doc="Input SAM or BAM file.")
  public File INPUT

• ASSUME_SORTED

  @Argument(doc="If true (default), then the sort order in the header file will be ignored.",
            shortName="AS")
  public boolean ASSUME_SORTED

• STOP_AFTER

  @Argument(doc="Stop after processing N reads, mainly for debugging.")
  public int STOP_AFTER

• OUTPUT

  @Argument(shortName="O",
            doc="Base name of output files.")
  public String OUTPUT

• METRIC_ACCUMULATION_LEVEL

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

• FILE_EXTENSION

  @Argument(shortName="EXT",
            doc="Append the given file extension to all metric file names (ex. OUTPUT.insert_size_metrics.EXT). None if null",
            optional=true)
  public String FILE_EXTENSION

• PROGRAM

  @Argument(doc="Set of metrics programs to apply during the pass through the SAM file.")
  public Set<CollectMultipleMetrics.Program> PROGRAM

• INTERVALS

  @Argument(doc="An optional list of intervals to restrict analysis to. Only pertains to some of the PROGRAMs. Programs whose stand-alone CLP does not have an INTERVALS argument will silently ignore this argument.",
            optional=true)
  public File INTERVALS

• DB_SNP

  @Argument(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis by some PROGRAMs; PROGRAMs whose CLP doesn\'t allow for this argument will quietly ignore it.",
            optional=true)
  public File DB_SNP

• INCLUDE_UNPAIRED

  @Argument(shortName="UNPAIRED",
            doc="Include unpaired reads in CollectSequencingArtifactMetrics. If set to true then all paired reads will be included as well - MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored in CollectSequencingArtifactMetrics.")
  public boolean INCLUDE_UNPAIRED

Constructor Detail

• CollectMultipleMetrics

  public CollectMultipleMetrics()

Method Detail

• main

  public static void main​(String[] args)

• 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.

• setProgramsToRun

  public void setProgramsToRun​(Collection<CollectMultipleMetrics.ProgramInterface> programsToRun)

  Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones available via enum. This must be called before doWork().

• doWork

  public 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.