Class SnpSiftCmdCaseControlSummary

java.lang.Object
org.snpsift.SnpSift
org.snpsift.caseControl.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 Details

    • formatVersion

      public static org.snpeff.vcf.EffFormatVersion formatVersion

    • CaseControl

      public static Boolean[] CaseControl

  • Constructor Details

    • SnpSiftCmdCaseControlSummary

      public SnpSiftCmdCaseControlSummary()

    • SnpSiftCmdCaseControlSummary

      public SnpSiftCmdCaseControlSummary(String[] args)

  • Method Details

    • parseArgs

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