Class SnpEffCmdDatabases

  • All Implemented Interfaces:
    CommandLine

    public class SnpEffCmdDatabases
    extends SnpEff
    Show all databases configures in snpEff.config Create an HTML 'download' table based on the config file Also creates a list of genome for Galaxy menu
    Author:
    pablocingolani
    • Constructor Detail

      • SnpEffCmdDatabases

        public SnpEffCmdDatabases()
    • Method Detail

      • 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
      • 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