Package picard.vcf

Class FixVcfHeader


@DocumentedFeature public class FixVcfHeader extends CommandLineProgram
Tool for replacing or fixing up a VCF header.
  • Field Details

    • INPUT

      @Argument(shortName="I", doc="The input VCF/BCF file.") public PicardHtsPath INPUT
    • OUTPUT

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

      @Argument(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
    • ENFORCE_SAME_SAMPLES

      @Argument(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 Details

    • FixVcfHeader

      public FixVcfHeader()
  • 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.