Class SnpEffCmdGenes2Bed

  • All Implemented Interfaces:
    CommandLine

    public class SnpEffCmdGenes2Bed
    extends SnpEff
    Simple test program
    Author:
    pcingola
    • Constructor Detail

      • SnpEffCmdGenes2Bed

        public SnpEffCmdGenes2Bed()
    • Method Detail

      • main

        public static void main​(java.lang.String[] args)
      • parseArgs

        public void parseArgs​(java.lang.String[] args)
        Description copied from class: SnpEff
        Parse command line arguments
        Specified by:
        parseArgs in interface CommandLine
        Overrides:
        parseArgs in class SnpEff
      • run

        public boolean run()
        Description copied from class: SnpEff
        Run according to command line options
        Specified by:
        run in interface CommandLine
        Overrides:
        run in class SnpEff
      • showGenes

        public void showGenes()
        Show genes in BED format
      • usage

        public void usage​(java.lang.String message)
        Description copied from class: SnpEff
        Show 'usage' message and exit with an error code '-1'
        Specified by:
        usage in interface CommandLine
        Overrides:
        usage in class SnpEff