public static void setupParser(Subparsers subParsers) {
BiFunction<String[], Namespace, AnnotatePositionCommand> handler = (argv, args) -> {
try {
return new AnnotatePositionCommand(argv, args);
} catch (CommandLineParsingException e) {
throw new UncheckedJannovarException("Could not parse command line", e);
}
};
Subparser subParser = subParsers.addParser("annotate-pos", true)
.help("annotate genomic changes given on the command line").setDefault("cmd", handler);
subParser.description("Perform annotation of genomic changes given on the command line");
ArgumentGroup requiredGroup = subParser.addArgumentGroup("Required arguments");
requiredGroup.addArgument("-d", "--database").help("Path to database .ser file").required(true);
requiredGroup.addArgument("-c", "--genomic-change").help("Genomic change to annotate, you can give multiple ones")
.action(Arguments.append()).required(true);
subParser.epilog("Example: java -jar Jannovar.jar annotate-pos -d hg19_refseq.ser -c 'chr1:12345C>A'");
JannovarAnnotationOptions.setupParser(subParser);
}