Re-add the plugin path.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1271 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk;
 import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentFactory;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.xReadLines;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -42,17 +43,22 @@ import net.sf.samtools.SAMFileReader;
 
 /**
  * @author aaron
- *         <p/>
- *         Generate a executable class for the SomaticCoverageWalker
  */
 public abstract class CommandLineExecutable extends CommandLineProgram {
 
-    // our genome analysis engine
+    /**
-    private GenomeAnalysisEngine GATKEngine = new GenomeAnalysisEngine();
+     * Get an instance of the GATK engine.
+     * @return The GATK engine that will power the requested traversal.
+     */
+    protected abstract GenomeAnalysisEngine getGATKEngine();
 
     // get the analysis name
     protected abstract String getAnalysisName();
 
+    /**
+     * Gets the GATK argument bundle.
+     * @return A structure consisting of whatever arguments should be used to initialize the GATK engine.
+     */
     protected abstract GATKArgumentCollection getArgumentCollection();
 
     // override select arguments
@@ -65,10 +71,11 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      * @return the return code to exit the program with
      */
     protected int execute() {
-        Walker<?,?> mWalker = GATKEngine.getWalkerByName(getAnalysisName());
+        GenomeAnalysisEngine GATKEngine = getGATKEngine();
-
         GATKArgumentCollection arguments = getArgumentCollection();
 
+        Walker<?,?> mWalker = GATKEngine.getWalkerByName(getAnalysisName());
+
         // load the arguments into the walkers
         loadArgumentsIntoObject(arguments);
         loadArgumentsIntoObject(mWalker);
@@ -101,7 +108,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
     protected Class[] getArgumentSources() {
         // No walker info?  No plugins.
         if (getAnalysisName() == null) return new Class[] {};
-        return new Class[] { GATKEngine.getWalkerByName(getAnalysisName()).getClass() };
+        return new Class[] { getGATKEngine().getWalkerByName(getAnalysisName()).getClass() };
     }
 
     @Override

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

@@ -36,13 +36,18 @@ import net.sf.samtools.SAMFileReader;
  * the gatk engine should  deal with any data related information.
  */
 public class CommandLineGATK extends CommandLineExecutable {
+    // our genome analysis engine
+    private GenomeAnalysisEngine GATKEngine = null;
 
     @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
-    public String analysisName = null;
+    private String analysisName = null;
+
+    @Argument(fullName = "plugin_path", doc = "Which path will the GATK search for plugin walkers.", required = false)
+    private String pluginPath = null;            
 
     // our argument collection, the collection of command line args we accept
     @ArgumentCollection
-    protected GATKArgumentCollection argCollection = new GATKArgumentCollection();    
+    private GATKArgumentCollection argCollection = new GATKArgumentCollection();    
 
     /**
      * Get pleasing info about the GATK.
@@ -59,6 +64,19 @@ public class CommandLineGATK extends CommandLineExecutable {
         return header;
     }
 
+    /**
+     * Lazy load the GATK engine.  This current CANNOT happen until after the command-line arguments are populated.
+     * TODO: Make this chain of events more explicit.  Perhaps an abstract initialize method after clp arguments are parsed?
+     * @return The GATK engine that will power the requested traversal.
+     */
+    @Override
+    protected GenomeAnalysisEngine getGATKEngine() {
+        if( GATKEngine == null )
+            GATKEngine = new GenomeAnalysisEngine( pluginPath );
+        return GATKEngine;
+    }
+
+
     @Override
     protected String getAnalysisName() {
         return analysisName;

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

@@ -63,9 +63,6 @@ public class GenomeAnalysisEngine {
     /** our walker manager */
     private final WalkerManager walkerManager;
 
-    /** plugin path for the walker manager. */
-    public final String pluginPathName = null;
-
     /**
      * our constructor, where all the work is done
      * <p/>
@@ -73,7 +70,7 @@ public class GenomeAnalysisEngine {
      * new MicroScheduler class we'll be able to delete that function.
      *
      */
-    public GenomeAnalysisEngine() {
+    public GenomeAnalysisEngine( String pluginPathName ) {
         // make sure our instance variable points to this analysis engine
         instance = this;
         walkerManager = new WalkerManager(pluginPathName);

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

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.somaticcoverage;
 
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.GATKArgumentCollection;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.io.File;
@@ -42,6 +43,8 @@ import java.util.ArrayList;
  * a executable command line for the Somatic Coverage Walker.
  */
 public class SomaticCoverageTool extends CommandLineExecutable {    
+    // our genome analysis engine
+    private GenomeAnalysisEngine GATKEngine = null;
 
     // the two sam/bam files, one for cancer, one for normal
     @Argument(fullName = "bam_file", shortName = "I", doc = "The bam files, one for the tumor one for the normal", required = true)
@@ -57,6 +60,14 @@ public class SomaticCoverageTool extends CommandLineExecutable {
         }
     }
 
+    @Override
+    protected GenomeAnalysisEngine getGATKEngine() {
+        if( GATKEngine == null )
+            GATKEngine = new GenomeAnalysisEngine( null );
+        return GATKEngine;
+    }
+
+
     /**
      * a required method, returns the analysis name.  This is usually the walker
      * name with 'Walker' stripped off.