Package org.snpeff.snpEffect.commandLine

Interface CommandLine

All Known Subinterfaces:
VcfAnnotator
All Known Implementing Classes:
FastqSplit, SnpEff, SnpEffCmdAcat, SnpEffCmdBuild, SnpEffCmdBuildNextProt, SnpEffCmdCds, SnpEffCmdClosest, SnpEffCmdCount, SnpEffCmdDatabases, SnpEffCmdDownload, SnpEffCmdDump, SnpEffCmdEff, SnpEffCmdGenes2Bed, SnpEffCmdGsa, SnpEffCmdLen, SnpEffCmdPdb, SnpEffCmdProtein, SnpEffCmdSeq, SnpEffCmdShow, SnpEffCmdSpliceAnalysis, SnpEffCmdTranslocationsReport, VcfAnnotatorChain
public interface CommandLine
Command line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }
Author:
pcingola

  • Method Summary

    Modifier and Type
    Method
    Description
    String[]
    getArgs()
     
    void
    parseArgs(String[] args)
    Parse command line arguments
    boolean
    run()
    Run the command
    void
    usage(String message)
    Show 'usage' message and exit with an error code '-1'

  • Method Details

    • getArgs

      String[] getArgs()

    • parseArgs

      void parseArgs(String[] args)
      Parse command line arguments

    • run

      boolean run()
      Run the command

    • usage

      void usage(String message)
      Show 'usage' message and exit with an error code '-1'