Class SnpEffCmdBuild

  • All Implemented Interfaces:
    CommandLine

    public class SnpEffCmdBuild
    extends SnpEff
    Command line program: Build database
    Author:
    pcingola
    • Constructor Detail

      • SnpEffCmdBuild

        public SnpEffCmdBuild()
    • Method Detail

      • fileExists

        protected boolean fileExists​(java.lang.String path)
        Does either 'path' or 'path'+'.gz' exist?
      • guessGenesFormat

        protected SnpEff.GeneDatabaseFormat guessGenesFormat()
        Try to guess database format by checking which file type is present
      • 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()
        Build database
        Specified by:
        run in interface CommandLine
        Overrides:
        run in class SnpEff
      • setCheckNumOk

        public void setCheckNumOk​(boolean checkNumOk)
      • setStoreAlignments

        public void setStoreAlignments​(boolean storeAlignments)
      • usage

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