100 lines
3.2 KiB
Java
Executable File
100 lines
3.2 KiB
Java
Executable File
package org.broadinstitute.sting.gatk;
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import org.broadinstitute.sting.utils.cmdLine.*;
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import java.util.List;
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import java.util.ArrayList;
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import net.sf.samtools.SAMFileReader;
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/**
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*
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* User: aaron
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* Date: May 8, 2009
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* Time: 10:50:58 AM
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*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*
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*/
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/**
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* @author aaron
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* @version 1.0
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* @date May 8, 2009
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* <p/>
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* Class CommandLineGATK
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* <p/>
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* We run command line GATK programs using this class. It gets the command line args, parses them, and hands the
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* gatk all the parsed out information. Pretty much anything dealing with the underlying system should go here,
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* the gatk engine should deal with any data related information.
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*/
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public class CommandLineGATK extends CommandLineExecutable {
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// our genome analysis engine
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private GenomeAnalysisEngine GATKEngine = null;
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@Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
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private String analysisName = null;
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@Argument(fullName = "plugin_path", doc = "Which path will the GATK search for plugin walkers.", required = false)
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private String pluginPath = null;
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// our argument collection, the collection of command line args we accept
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@ArgumentCollection
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private GATKArgumentCollection argCollection = new GATKArgumentCollection();
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/**
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* Get pleasing info about the GATK.
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* @return A list of Strings that contain pleasant info about the GATK.
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*/
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@Override
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protected List<String> getApplicationHeader() {
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List<String> header = new ArrayList<String>();
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header.add("The Genome Analysis Toolkit (GATK)");
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header.add("Copyright (c) 2009 The Broad Institute");
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header.add("Please view our documentation at http://www.broadinstitute.org/gsa/wiki");
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header.add("For support, email gsadevelopers@broadinstitute.org");
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header.add("");
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return header;
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}
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/**
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* Lazy load the GATK engine. This current CANNOT happen until after the command-line arguments are populated.
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* TODO: Make this chain of events more explicit. Perhaps an abstract initialize method after clp arguments are parsed?
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* @return The GATK engine that will power the requested traversal.
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*/
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@Override
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protected GenomeAnalysisEngine getGATKEngine() {
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if( GATKEngine == null )
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GATKEngine = new GenomeAnalysisEngine( pluginPath );
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return GATKEngine;
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}
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@Override
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protected String getAnalysisName() {
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return analysisName;
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}
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@Override
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protected GATKArgumentCollection getArgumentCollection() {
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return argCollection;
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}
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/** Required main method implementation. */
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public static void main(String[] argv) {
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try {
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CommandLineGATK instance = new CommandLineGATK();
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start(instance, argv);
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} catch (Exception e) {
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exitSystemWithError(e);
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}
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}
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}
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