Class SnpEffCmdGenes2Bed

java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
All Implemented Interfaces:
CommandLine
public class SnpEffCmdGenes2Bed extends SnpEff
Simple test program
Author:
pcingola

  • Constructor Details

    • SnpEffCmdGenes2Bed

      public SnpEffCmdGenes2Bed()

  • Method Details

    • main

      public static void main(String[] args)

    • parseArgs

      public void parseArgs(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(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