Package org.snpsift

Class SnpSiftCmdRemoveReferenceGenotypes

  • All Implemented Interfaces:
    org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

    public class SnpSiftCmdRemoveReferenceGenotypes
    extends SnpSift
    Removes reference genotypes. I.e. replaces the genotype string by the MISSING string ('.') if the genotype is just homozygous reference (e.g. '0/0')
    Author:
    pablocingolani
    • Constructor Detail

      • SnpSiftCmdRemoveReferenceGenotypes

        public SnpSiftCmdRemoveReferenceGenotypes()
      • SnpSiftCmdRemoveReferenceGenotypes

        public SnpSiftCmdRemoveReferenceGenotypes​(java.lang.String[] args)
    • Method Detail

      • parseArgs

        public void parseArgs​(java.lang.String[] args)
        Description copied from class: SnpSift
        Parse command line arguments
        Specified by:
        parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        parseArgs in class SnpSift
      • run

        public boolean run()
        Analyze the file
        Specified by:
        run in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        run in class SnpSift
      • usage

        public void usage​(java.lang.String errMsg)
        Show usage and exit
        Specified by:
        usage in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        usage in class SnpSift