}
VirtualProteinMergerRunner virtualProteinMergerRunner = new VirtualProteinMergerRunner(
searchResultsPaths, translationTableFile, genomeFile,
chromosomeDir, outputWriter, confidenceScore);
virtualProteinMergerRunner.run();
} catch (ParseException pe) {
System.err.println("Version = " + VERSION);
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("virtual_protein_merger", options, true);
System.exit(1);