initial check-in of an easy way to create command line tools based on the GATK

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@970 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -0,0 +1,192 @@
+package org.broadinstitute.sting.gatk;
+
+import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
+import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
+import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.gatk.walkers.Walker;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.List;
+import java.util.ArrayList;
+
+
+/*
+ * Copyright (c) 2009 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+/**
+ * @author aaron
+ *         <p/>
+ *         Generate a executable class for the SomaticCoverageWalker
+ */
+public abstract class CommandLineExecutable extends CommandLineProgram {
+
+    // our argument collection, the collection of command line args we accept
+    protected GATKArgumentCollection argCollection = new GATKArgumentCollection();
+
+    /** the type of analysis to run - switch to the type of analysis */
+    private String analysisName = "SomaticCoverageWalker";
+
+    // our walker manager
+    private WalkerManager walkerManager = null;
+
+    // our genome analysis engine
+    private GenomeAnalysisEngine GATKEngine = null;
+
+    public String pluginPathName = null;
+
+    // get the analysis name
+    protected abstract String getAnalysisName();
+
+    // override select arguments
+    protected abstract void overrideArguments();
+
+    /**
+     * this is the function that the inheriting class can expect to have called
+     * when the command line system has initialized.
+     *
+     * @return the return code to exit the program with
+     */
+    protected int execute() {
+
+        // create the walker
+        Walker<?, ?> mWalker = null;
+        try {
+            mWalker = walkerManager.createWalkerByName(analysisName);
+        } catch (InstantiationException ex) {
+            throw new RuntimeException("Unable to instantiate walker.", ex);
+        }
+        catch (IllegalAccessException ex) {
+            throw new RuntimeException("Unable to access walker", ex);
+        }
+
+        // load the arguments into the walkers
+        loadArgumentsIntoObject(argCollection);
+        loadArgumentsIntoObject(mWalker);
+
+        // process any arguments that need a second pass
+        processArguments(argCollection);
+
+        // set the analysis name in the argument collection
+        this.argCollection.analysisName = this.analysisName;
+        try {
+            GATKEngine = new GenomeAnalysisEngine(argCollection, mWalker);
+        }
+        catch (ArgumentException ex) {
+            // Rethrow argument exceptions.  Let the command-line argument do what it's designed to do.
+            throw ex;
+        }
+        catch (StingException exp) {
+            System.err.println("Caught StingException. It's message is " + exp.getMessage());
+            exp.printStackTrace();
+            return -1;
+        }
+        return 0;
+    }
+
+    /**
+     * GATK can add arguments dynamically based on analysis type.
+     *
+     * @return true
+     */
+    @Override
+    protected boolean canAddArgumentsDynamically() {
+        return true;
+    }
+
+    /**
+     * GATK provides the walker as an argument source.  As a side-effect, initializes the walker variable.
+     *
+     * @return List of walkers to load dynamically.
+     */
+    @Override
+    protected Class[] getArgumentSources() {
+        // get the analysis name from the overriding class
+        analysisName = this.getAnalysisName();
+        
+        // get any argument overrides they want to present
+        overrideArguments();
+        // No walker info?  No plugins.
+        if (analysisName == null) return new Class[]{};
+
+        walkerManager = new WalkerManager(pluginPathName);
+
+        if (!walkerManager.doesWalkerExist(analysisName))
+            throw new IllegalArgumentException("Invalid analysis name");
+
+        return new Class[]{walkerManager.getWalkerClassByName(analysisName)};
+    }
+
+
+    /**
+     * Preprocess the arguments before submitting them to the GATK engine.
+     *
+     * @param argCollection Collection of arguments to preprocess.
+     */
+    private void processArguments( GATKArgumentCollection argCollection ) {
+        argCollection.samFiles = unpackReads(argCollection.samFiles);
+    }
+
+    /**
+     * Unpack the files to be processed, given a list of files.  That list of files can
+     * itself contain lists of other files to be read.
+     *
+     * @param inputFiles
+     *
+     * @return
+     */
+    private List<File> unpackReads( List<File> inputFiles ) {
+        List<File> unpackedReads = new ArrayList<File>();
+        for (File inputFile : inputFiles) {
+            if (inputFile.getName().endsWith(".list")) {
+                try {
+                    for (String fileName : new xReadLines(inputFile))
+                        unpackedReads.add(new File(fileName));
+                }
+                catch (FileNotFoundException ex) {
+                    throw new StingException("Unable to find file while unpacking reads", ex);
+                }
+            } else
+                unpackedReads.add(inputFile);
+        }
+        return unpackedReads;
+    }
+
+    @Override
+    protected String getArgumentSourceName( Class argumentSource ) {
+        return WalkerManager.getWalkerName((Class<Walker>) argumentSource);
+    }
+
+    public GATKArgumentCollection getArgCollection() {
+        return argCollection;
+    }
+
+    public void setArgCollection( GATKArgumentCollection argCollection ) {
+        this.argCollection = argCollection;
+    }
+
+
+}

java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java

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+package org.broadinstitute.sting.playground.somaticcoverage;
+
+import org.broadinstitute.sting.gatk.CommandLineExecutable;
+import org.broadinstitute.sting.gatk.GATKArgumentCollection;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+
+import java.io.File;
+import java.util.List;
+import java.util.ArrayList;
+
+
+/*
+ * Copyright (c) 2009 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+/**
+ * @author aaron
+ *
+ *
+ * a executable command line for the Somatic Coverage Walker.
+ */
+public class SomaticCoverageTool extends CommandLineExecutable {
+
+    // the two sam/bam files, one for cancer, one for normal
+    @Argument(fullName = "bam_files", shortName = "I", doc = "The bam files, one for the tumor one for the normal", required = true)
+    public List<File> samFiles = new ArrayList<File>();
+
+
+    /** Required main method implementation. */
+    public static void main( String[] argv ) {
+        try {
+            SomaticCoverageTool instance = new SomaticCoverageTool();
+            start(instance, argv);
+        } catch (Exception e) {
+            exitSystemWithError(e);
+        }
+    }
+
+    /**
+     * a required method, returns the analysis name.  This is usually the walker
+     * name with 'Walker' stripped off.
+     *
+     * @return the name of the analysis we're running
+     */
+    protected String getAnalysisName() {
+        return "SomaticCoverage";
+    }
+
+    /** override any arguments we see fit. */
+    protected void overrideArguments() {
+        this.argCollection = GATKArgumentCollection.unmarshal("SomaticCoverage.xml");
+        this.argCollection.intervals = "CancerIntervals.interval";
+        this.argCollection.samFiles = samFiles;
+    }
+}