Class ConvertSequencingArtifactToOxoG

java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.artifacts.ConvertSequencingArtifactToOxoG

@DocumentedFeature public class ConvertSequencingArtifactToOxoG extends CommandLineProgram
  • Field Details

    • OXOG_METRICS_EXT

      public static final String OXOG_METRICS_EXT
      See Also:
    • INPUT_BASE

      @Argument(shortName="I", doc="Basename of the input artifact metrics file (output by CollectSequencingArtifactMetrics). If this is not specified, you must specify PRE_ADAPTER_IN and BAIT_BIAS_IN", optional=true) public File INPUT_BASE
    • PRE_ADAPTER_IN

      @Argument(doc="The pre adapter details input file. Defaults to a filename based on the input basename", optional=true) public File PRE_ADAPTER_IN
    • BAIT_BIAS_IN

      @Argument(doc="The bait bias input file. Defaults to a filename based on the input basename", optional=true) public File BAIT_BIAS_IN
    • OUTPUT_BASE

      @Argument(shortName="O", doc="Basename for output OxoG metrics. Defaults to same basename as input metrics", optional=true) public File OUTPUT_BASE
    • OXOG_OUT

      @Argument(doc="File for the output OxoG metrics. Defaults to a filename based on the output basename", optional=true) public File OXOG_OUT
  • Constructor Details

    • ConvertSequencingArtifactToOxoG

      public ConvertSequencingArtifactToOxoG()
  • Method Details

    • 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.