Package org.snpsift

Class 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
    • Constructor Detail

      • SnpSiftCmdTsTv

        public SnpSiftCmdTsTv()
      • SnpSiftCmdTsTv

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

      • error

        public void error​(java.lang.Throwable e,
                          java.lang.String message)
        Show an error (if not 'quiet' mode)
        Overrides:
        error 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
        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