Package picard.vcf

Class FixVcfHeader


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

      • INPUT

        @Argument(shortName="I",
                  doc="The input VCF/BCF file.")
        public File 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
      • HEADER

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

      • FixVcfHeader

        public FixVcfHeader()
    • 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.
      • 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.