checked in a sample xml file used to store the defaults for the SomaticCoverage tool, and added it to the SomaticCoverage.jar in build.sml. Also added a inputStream marshalling method to the GATKArgumentCollection.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@979 348d0f76-0448-11de-a6fe-93d51630548a

build.xml

@@ -103,9 +103,12 @@
     
         <jar jarfile="dist/SomaticCoverage.jar" whenmanifestonly="skip">
           <fileset dir="build">
-            <include name="**/*.class"/>
+            <include name="**/somaticcoverage/*.class"/>
-            <exclude name="**/utils/**"/>
+            <include name="**/walkers/SomaticCoverageWalker.class"/>
-            <exclude name="**/gatk/**"/>
+            
+          </fileset>
+          <fileset dir="java">
+            <include name="**/somaticcoverage/*.xml"/>
           </fileset>
             <manifest>
             <attribute name="Main-Class" value="org.broadinstitute.sting.playground.somaticcoverage.SomaticCoverageTool" />

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

@@ -8,6 +8,7 @@ import org.simpleframework.xml.stream.Format;
 import org.simpleframework.xml.stream.HyphenStyle;
 
 import java.io.File;
+import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -33,11 +34,6 @@ import java.util.Map;
 /**
  * @author aaron
  * @version 1.0
- * @date May 7, 2009
- * <p/>
- * Class ArgumentObject
- * <p/>
- * Encapsolute the massively large list of possible parameters we take in the Genome Analysis tool
  */
 @Root
 public class GATKArgumentCollection {
@@ -181,10 +177,28 @@ public class GATKArgumentCollection {
         }
     }
 
+    /**
+     * unmashall the object from a configuration file
+     *
+     * @param file the inputstream to marshal from
+     */
+    public static GATKArgumentCollection unmarshal( InputStream file ) {
+        Serializer serializer = new Persister(new Format(new HyphenStyle()));
+        try {
+            GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, file);
+            return example;
+        } catch (Exception e) {
+            throw new StingException("Failed to marshal the data to file " + file.toString(), e);
+        }
+    }
+
+
     /**
      * test equality between two arg collections.  This function defines the statement:
      * "not fun to write"
+     *
      * @param other the other collection
+     *
      * @return true if they're equal
      */
     public boolean equals( GATKArgumentCollection other ) {

java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverage.xml

@@ -0,0 +1,34 @@
+<!--
+  ~ 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.
+  -->
+
+<GATK-argument-collection>
+   <strictness-level>strict</strictness-level>
+   <intervals>/seq/references/HybSelOligos/whole_exome_refseq_coding/whole_exome_refseq_coding.targets.interval_list</intervals>
+   <reference-file>/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta</reference-file>
+   <enabled-threaded-IO>true</enabled-threaded-IO>
+   <unsafe>false</unsafe>
+   <disable-threading>false</disable-threading>
+   <number-of-threads>1</number-of-threads>
+</GATK-argument-collection>

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

@@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.GATKArgumentCollection;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.List;
 import java.util.ArrayList;
 
@@ -69,8 +70,11 @@ public class SomaticCoverageTool extends CommandLineExecutable {
 
     /** override any arguments we see fit. */
     protected void overrideArguments() {
-        this.argCollection = GATKArgumentCollection.unmarshal("SomaticCoverage.xml");
+        try {
-        this.argCollection.intervals = "CancerIntervals.list";
+            this.argCollection = GATKArgumentCollection.unmarshal(this.getClass().getResource("/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverage.xml").openStream());
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
         this.argCollection.samFiles = samFiles;
     }
 }