Class SnpEffCmdTranslocationsReport

  • All Implemented Interfaces:
    CommandLine

    public class SnpEffCmdTranslocationsReport
    extends SnpEff
    Create an SVG representation of a Marker
    • Field Detail

      • DEFAULT_REPORT_HTML_FILE

        public static final java.lang.String DEFAULT_REPORT_HTML_FILE
        See Also:
        Constant Field Values
    • Constructor Detail

      • SnpEffCmdTranslocationsReport

        public SnpEffCmdTranslocationsReport()
    • Method Detail

      • 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()
        Description copied from class: SnpEff
        Run according to command line options
        Specified by:
        run in interface CommandLine
        Overrides:
        run in class SnpEff
      • setOnlyOneTranscript

        public void setOnlyOneTranscript​(boolean onlyOneTranscript)
      • setVcfFileName

        public void setVcfFileName​(java.lang.String vcfFileName)
      • 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