Class SnpSiftCmdHwe

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

    public class SnpSiftCmdHwe
    extends SnpSift
    Calculate Hardy-Weinberg equilibrium and goodness of fit for each entry in a VCF file
    Author:
    pablocingolani
    • Constructor Detail

      • SnpSiftCmdHwe

        public SnpSiftCmdHwe()
      • SnpSiftCmdHwe

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

      • main

        public static void main​(java.lang.String[] args)
        Main
      • 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()
        Analyze the file (run multi-thread mode)
        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