de.charite.compbio.jannovar.Jannovar Maven / Gradle / Ivy

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package de.charite.compbio.jannovar;

import de.charite.compbio.jannovar.cmd.JannovarCommand;
import de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions;
import de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions;
import de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions;
import de.charite.compbio.jannovar.cmd.db_list.JannovarDBListOptions;
import de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions;
import de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions;
import de.charite.compbio.jannovar.cmd.rest_server.RestServerOptions;
import de.charite.compbio.jannovar.cmd.statistics.JannovarGatherStatisticsOptions;
import java.util.function.BiFunction;

import de.charite.compbio.jannovar.cmd.vardb_annotate.vardb_import.JannovarVardbAnnotateOptions;
import de.charite.compbio.jannovar.cmd.vardb_import.JannovarVardbImportOptions;
import de.charite.compbio.jannovar.cmd.vardb_list.JannovarVardbListOptions;
import net.sourceforge.argparse4j.ArgumentParsers;
import net.sourceforge.argparse4j.impl.Arguments;
import net.sourceforge.argparse4j.inf.ArgumentParser;
import net.sourceforge.argparse4j.inf.ArgumentParserException;
import net.sourceforge.argparse4j.inf.Namespace;
import net.sourceforge.argparse4j.inf.Subparsers;

/**
 * This is the driver class for a program called Jannovar.
 *
 * @author Peter N Robinson
 * @author Marten Jaeger
 * @author Max Schubach
 * @author Manuel Holtgrewe
 */
public final class Jannovar {

	public static void main(String argv[]) {
		// Setup command line parser
		ArgumentParser parser = ArgumentParsers.newArgumentParser("jannovar-cli");
		parser.version(getVersion());
		parser.addArgument("--version").help("Show Jannovar version").action(Arguments.version());
		parser.description(
			"Jannovar CLI performs a series of VCF annotation tasks, including predicted "
				+ "molecular impact of variants and annotation of compatible Mendelian inheritance.");
		Subparsers subParsers = parser.addSubparsers();
		JannovarAnnotatePosOptions.setupParser(subParsers);
		JannovarAnnotateCSVOptions.setupParser(subParsers);
		JannovarAnnotateVCFOptions.setupParser(subParsers);
		JannovarDBListOptions.setupParser(subParsers);
		JannovarDownloadOptions.setupParser(subParsers);
		JannovarGatherStatisticsOptions.setupParser(subParsers);
		JannovarVardbImportOptions.setupParser(subParsers);
		JannovarVardbListOptions.setupParser(subParsers);
		JannovarVardbAnnotateOptions.setupParser(subParsers);
		RestServerOptions.setupParser(subParsers);
		ProjectTranscriptToChromosomeOptions.setupParser(subParsers);
		parser.defaultHelp(true);
		parser.epilog("You can find out more at http://jannovar.rtfd.org");

		// Parse command line arguments
		Namespace args = null;
		try {
			args = parser.parseArgs(argv);
		} catch (ArgumentParserException e) {
			parser.handleError(e);
			System.exit(1);
		}

		BiFunction factory = args.get("cmd");
		JannovarCommand cmd = factory.apply(argv, args);
		if (cmd == null) {
			System.exit(1);
		}

		// Execute the command.
		try {
			cmd.run();
		} catch (JannovarException e) {
			System.err.println("ERROR: " + e.getMessage());
			e.printStackTrace();
			System.exit(1);
		}
	}

	public static String getVersion() {
		return Jannovar.class.getPackage().getSpecificationVersion();
	}
}