Package org.snpsift

Class SnpSiftCmdTsTv

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

public class SnpSiftCmdTsTv extends SnpSift
Calculate Ts/Tv rations per sample (transitions vs transversions)
Author:
pablocingolani
  • Field Details

  • Constructor Details

    • SnpSiftCmdTsTv

      public SnpSiftCmdTsTv()
    • SnpSiftCmdTsTv

      public SnpSiftCmdTsTv(String[] args)
  • Method Details

    • error

      public void error(Throwable e, String message)
      Show an error (if not 'quiet' mode)
      Overrides:
      error in class SnpSift
    • 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()
      Analyze the file
      Specified by:
      run in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      run in class SnpSift
    • usage

      public void usage(String errMsg)
      Show usage and exit
      Specified by:
      usage in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      usage in class SnpSift