Field Detail

• INPUT

  @Option(shortName="I",
          doc="The input VCF/BCF file.")
  public File INPUT

• OUTPUT

  @Option(shortName="O",
          doc="The output VCF/BCF file.")
  public File OUTPUT

• CHECK_FIRST_N_RECORDS

  @Option(shortName="N",
          doc="Check only the first N records when searching for missing INFO and FORMAT fields.",
          optional=true)
  public int CHECK_FIRST_N_RECORDS

• HEADER

  @Option(shortName="H",
          doc="The replacement VCF header.",
          optional=true)
  public File HEADER

• ENFORCE_SAME_SAMPLES

  @Option(doc="Enforce that the samples are the same (and in the same order) when replacing the VCF header.",
          optional=true)
  public boolean ENFORCE_SAME_SAMPLES

Constructor Detail

• FixVcfHeader

  public FixVcfHeader()

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.

• 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.