Class SnpEffCmdCount

  • All Implemented Interfaces:
    CommandLine

    public class SnpEffCmdCount
    extends SnpEff
    Count reads from a BAM file given a list of intervals
    Author:
    pablocingolani
    • Constructor Detail

      • SnpEffCmdCount

        public SnpEffCmdCount()
    • Method Detail

      • parseArgs

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