Class SnpEffCmdGsa

  • All Implemented Interfaces:
    CommandLine

    public class SnpEffCmdGsa
    extends SnpEff
    Command line: Gene-Sets Analysis Perform gene set analysys
    Author:
    pcingola
    • Field Detail

      • READ_INPUT_SHOW_EVERY

        public static int READ_INPUT_SHOW_EVERY
      • MAX_WARNS

        public static int MAX_WARNS
    • Constructor Detail

      • SnpEffCmdGsa

        public SnpEffCmdGsa()
    • Method Detail

      • config

        protected void config()
        Read config file, load & build database
      • parseArgs

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

        public boolean run()
        Run command
        Specified by:
        run in interface CommandLine
        Overrides:
        run in class SnpEff
      • runAnalisis

        protected boolean runAnalisis()
        Run command
      • runAnalisisRand

        protected boolean runAnalisisRand()
        Run enrichment analysis using random scores
      • runCommands

        protected boolean runCommands()
        Read "command" lines from file. Loads database only once to save time
        Returns:
      • usage

        public void usage​(java.lang.String message)
        Show usage and exit
        Specified by:
        usage in interface CommandLine
        Overrides:
        usage in class SnpEff