Class SnpSiftCmdCaseControlSummary

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

    public class SnpSiftCmdCaseControlSummary
    extends SnpSift
    Summarize a VCF annotated file
    Author:
    pcingola
    • Field Detail

      • formatVersion

        public static org.snpeff.vcf.EffFormatVersion formatVersion
      • CaseControl

        public static java.lang.Boolean[] CaseControl
    • Constructor Detail

      • SnpSiftCmdCaseControlSummary

        public SnpSiftCmdCaseControlSummary()
      • SnpSiftCmdCaseControlSummary

        public SnpSiftCmdCaseControlSummary​(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()
        Run summary
        Specified by:
        run in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        run in class SnpSift
      • usage

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