Package org.snpsift

Class SnpSiftCmdGt

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

    public class SnpSiftCmdGt
    extends SnpSift
    Add genotype information to INFO fields
    Author:
    pcingola
    • Field Detail

      • SHOW_EVERY

        public static int SHOW_EVERY
    • Constructor Detail

      • SnpSiftCmdGt

        public SnpSiftCmdGt()
      • SnpSiftCmdGt

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

      • getOutput

        public java.lang.String getOutput()
        Overrides:
        getOutput in class SnpSift
      • headers

        protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()
        Description copied from class: SnpSift
        Headers to add
        Overrides:
        headers in class SnpSift
      • parseArgs

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

        public boolean run()
        Process a VCF entry and return a string (tab separated values)
        Specified by:
        run in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        run in class SnpSift
      • usage

        public void usage​(java.lang.String msg)
        Description copied from class: SnpSift
        Show usage message
        Specified by:
        usage in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        usage in class SnpSift