Package org.snpsift

Class SnpSiftCmdVcfCheck

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdVcfCheck
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdVcfCheck extends SnpSift
Check VCF files (run some simple checks)
Author:
pcingola
  • Constructor Details

    • SnpSiftCmdVcfCheck

      public SnpSiftCmdVcfCheck()
    • SnpSiftCmdVcfCheck

      public SnpSiftCmdVcfCheck(String[] args)
  • Method Details

    • parseArgs

      public void parseArgs(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 the whole VCF file
      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 -