Field Detail

• INPUT

  @Option(doc="The BAM or SAM file to fix.",
          shortName="I")
  public File INPUT

• OUTPUT

  @Option(doc="The fixed BAM or SAM output file. ",
          shortName="O")
  public File OUTPUT

• IS_BISULFITE_SEQUENCE

  @Option(doc="Whether the file contains bisulfite sequence (used when calculating the NM tag).")
  public boolean IS_BISULFITE_SEQUENCE

Constructor Detail

• SetNmMdAndUqTags

  public SetNmMdAndUqTags​()

Method Detail

• 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.

• main

  public static void main​(String[] argv)

• 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.