new FlaggedOption("input-file", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 'i', "input-file", "File containing the input sequences."),
new FlaggedOption("sequence", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 's', "sequence",
"Optionally, pass a single sequence as a string. Place it between quotes, with space-separated symbols.") });
final JSAPResult jsapResult = jsap.parse(args);
if (jsap.messagePrinted())
return;
if (jsapResult.getBoolean("verbose")) {
logger.setLevel(Level.DEBUG);
}