Temporary fix for Eric's problems with SOLiD reads: make sure the command-line argument system takes the --validation-strictness command-line argument into account when creating SAMFileReaders.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1183 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -4,16 +4,15 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.xReadLines;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
-import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
+import org.broadinstitute.sting.utils.cmdLine.*;
 
 import java.io.FileNotFoundException;
 import java.io.File;
 import java.util.List;
 import java.util.ArrayList;
 
+import net.sf.samtools.SAMFileReader;
+
 /**
  *
  * User: aaron
@@ -148,6 +147,24 @@ public class CommandLineGATK extends CommandLineProgram {
         this.argCollection = argCollection;
     }
 
+    /**
+     * Get a custom factory for instantiating specialty GATK arguments.
+     * @return An instance of the command-line argument of the specified type.
+     */
+    @Override
+    protected ArgumentFactory getCustomArgumentFactory() {
+        return new ArgumentFactory() {
+            public Object createArgument( Class type, String repr ) {
+                if (type == SAMFileReader.class) {
+                    SAMFileReader samFileReader = new SAMFileReader(new File(repr),true);
+                    samFileReader.setValidationStringency(GenomeAnalysisEngine.getValidationStringency(argCollection));
+                    return samFileReader;
+                }
+                return null;
+            }
+        };
+    }
+
 
     /**
      * Preprocess the arguments before submitting them to the GATK engine.

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

@@ -125,7 +125,7 @@ public class GenomeAnalysisEngine {
         }
 
         // Determine the validation stringency.  Default to ValidationStringency.STRICT.
-        ValidationStringency strictness = getValidationStringency();
+        ValidationStringency strictness = getValidationStringency(argCollection);
 
         logger.info("Strictness is " + strictness);
 
@@ -219,7 +219,7 @@ public class GenomeAnalysisEngine {
      */
     private Reads extractSourceInfoFromArguments( GATKArgumentCollection argCollection ) {
         return new Reads( argCollection.samFiles,
-                          getValidationStringency(),
+                          getValidationStringency(argCollection),
                           argCollection.downsampleFraction,
                           argCollection.downsampleCoverage,
                           !argCollection.unsafe,
@@ -264,10 +264,10 @@ public class GenomeAnalysisEngine {
 
     /**
      * Default to ValidationStringency.STRICT.
-     *
+     * TODO: Store ValidationStringency as pre-parsed enum in GATKArgumentCollection.
      * @return the validation stringency
      */
-    private ValidationStringency getValidationStringency() {
+    public static ValidationStringency getValidationStringency( GATKArgumentCollection argCollection ) {
         ValidationStringency strictness = ValidationStringency.SILENT;
         try {
             strictness = Enum.valueOf(ValidationStringency.class, argCollection.strictnessLevel.toUpperCase().trim());

java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentFactory.java

@@ -0,0 +1,40 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.utils.cmdLine;
+
+/**
+ * Provides a service whereby the application can provide a mechanism
+ * for creating specialty arguments.
+ * @version 0.1
+ */
+public abstract class ArgumentFactory {
+    /**
+     * Create an instance of a specified type of argument.
+     * @param type The type of the argument to create.
+     * @param repr A String representation of the argument.
+     * @return
+     */
+    public abstract Object createArgument(Class type, String repr);
+}

java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java

@@ -142,6 +142,14 @@ public abstract class CommandLineProgram {
      */
     protected abstract int execute();
 
+    /**
+     * Retrieves a factory for custom creation of command-line arguments, specified by the
+     * subclass.
+     * @return
+     */
+    protected ArgumentFactory getCustomArgumentFactory() {
+        return null;
+    }
 
     /**
      * This function is called to start processing the command line, and kick
@@ -160,7 +168,7 @@ public abstract class CommandLineProgram {
             PatternLayout layout = new PatternLayout();
 
             // setup the parser
-            ParsingEngine parser = clp.parser = new ParsingEngine();
+            ParsingEngine parser = clp.parser = new ParsingEngine( clp.getCustomArgumentFactory() );
             parser.addArgumentSource( clp.getClass() );
 
             // process the args

java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java

@@ -53,6 +53,13 @@ public class ParsingEngine {
      */
     ArgumentMatches argumentMatches = null;
 
+    /**
+     * Stores a custom argument factory for building out arguments of which only
+     * subclasses of CommandLineProgram should be aware.
+     */
+    ArgumentFactory customArgumentFactory = null;
+
+
     /**
      * Techniques for parsing and for argument lookup.
      */
@@ -63,7 +70,8 @@ public class ParsingEngine {
      */
     protected static Logger logger = Logger.getLogger(ParsingEngine.class);
 
-    public ParsingEngine() {
+    public ParsingEngine( ArgumentFactory customArgumentFactory ) {
+        this.customArgumentFactory = customArgumentFactory;
         parsingMethods.add( ParsingMethod.FullNameParsingMethod );
         parsingMethods.add( ParsingMethod.ShortNameParsingMethod );
     }
@@ -423,10 +431,13 @@ public class ParsingEngine {
      * @return parsed form of String.
      */
     private Object constructSingleElement(Field f, Class type, String str) {
-        // lets go through the types we support
-        if (type == SAMFileReader.class) {
-            return new SAMFileReader(new File(str),true);
+        if( customArgumentFactory != null ) {
+            Object instance = customArgumentFactory.createArgument(type, str);
+            if( instance != null )
+                return instance;
         }
+
+        // lets go through the types we support
         if (type == Boolean.TYPE) {
             boolean b = false;
             if (str.toLowerCase().equals("true")) {