Class LiftOverHaplotypeMap


  • public class LiftOverHaplotypeMap
    extends CommandLineProgram
    Liftover SNPs in HaplotypeMaps from one reference to another
    • Field Detail

      • INPUT

        @Argument(doc="Haplotype database to be lifted over.",
                  shortName="I")
        public File INPUT
      • OUTPUT

        @Argument(doc="Where to write lifted-over haplotype database.",
                  shortName="O")
        public File OUTPUT
      • SEQUENCE_DICTIONARY

        @Argument(doc="Sequence dictionary to write into the output haplotype database. (Any file from which a dictionary is extractable.)",
                  shortName="SD")
        public File SEQUENCE_DICTIONARY
      • CHAIN

        @Argument(doc="Chain file that guides LiftOver. (UCSC format)")
        public File CHAIN
      • LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS

        public static final int LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS
        See Also:
        Constant Field Values
    • Constructor Detail

      • LiftOverHaplotypeMap

        public LiftOverHaplotypeMap()
    • Method Detail

      • 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.