From 80d92e0c636a58b9cfc948ab42f650a54955ba6d Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 12 Oct 2012 13:50:10 -0400
Subject: [PATCH] Allowing the GATK to have non-required outputs

Modified the SAMFileWriterArgumentTypeDescriptor to accept output bam files that are null if they're not required (in the @Output annotation).

This change enables the nWayOut parameter for the IndeRealigner and ReduceReads to operate optionally while maintaining the original single way out.

[#DEV-10 transition:31 resolution:1]
---
 .../SAMFileWriterArgumentTypeDescriptor.java  | 36 +++++++++----------
 .../gatk/walkers/indels/IndelRealigner.java   |  4 +--
 .../indels/IndelRealignerIntegrationTest.java | 10 ++++++
 3 files changed, 27 insertions(+), 23 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
index 8566f6c63..dcf2704f5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
@@ -124,32 +124,28 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
 
         // This parser has been passed a null filename and the GATK is not responsible for creating a type default for the object;
         // therefore, the user must have failed to specify a type default
-        if(writerFileName == null) {
-            if(!source.isRequired())
-                throw new MissingArgumentValueException(bamArgumentDefinition);
-            if(generateMD5)
+        if(writerFileName == null && generateMD5)
                 throw new ArgumentException("MD5 generation specified, but no output file specified.  If md5 generation is desired, please specify a BAM output file and an md5 file will be written alongside.");
-        }
 
         // Create the stub and set parameters.
-        SAMFileWriterStub stub;
-        if ( writerFileName != null )
+        SAMFileWriterStub stub = null;      // stub = new SAMFileWriterStub(engine, defaultOutputStream);
+
+        if ( writerFileName != null ) {
             stub = new SAMFileWriterStub(engine, new File(writerFileName));
-        else
-            stub = new SAMFileWriterStub(engine, defaultOutputStream);
 
-        if ( compressionLevel != null )
-            stub.setCompressionLevel(compressionLevel);
-        if ( indexOnTheFly )
-            stub.setIndexOnTheFly(indexOnTheFly);
-        if ( generateMD5 )
-            stub.setGenerateMD5(generateMD5);
-        if ( simplifyBAM )
-            stub.setSimplifyBAM(simplifyBAM);
+            if ( compressionLevel != null )
+                stub.setCompressionLevel(compressionLevel);
+            if ( indexOnTheFly )
+                stub.setIndexOnTheFly(indexOnTheFly);
+            if ( generateMD5 )
+                stub.setGenerateMD5(generateMD5);
+            if ( simplifyBAM )
+                stub.setSimplifyBAM(simplifyBAM);
 
-        // WARNING: Side effects required by engine!
-        parsingEngine.addTags(stub,getArgumentTags(matches));
-        engine.addOutput(stub);
+            // WARNING: Side effects required by engine!
+            parsingEngine.addTags(stub,getArgumentTags(matches));
+            engine.addOutput(stub);
+        }
 
         return stub;
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 76d8d85c2..998894fbf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -370,8 +370,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
         currentInterval = intervals.hasNext() ? intervals.next() : null;
 
-        writerToUse = writer;
-
         if ( N_WAY_OUT != null ) {
             boolean createIndex =  true;
 
@@ -383,9 +381,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         createIndex, generateMD5s,createProgramRecord(),KEEP_ALL_PG_RECORDS);
             }
         }   else {
-
             // set up the output writer
             setupWriter(getToolkit().getSAMFileHeader());
+            writerToUse = writer;
         }
         manager = new ConstrainedMateFixingManager(writerToUse, getToolkit().getGenomeLocParser(), MAX_ISIZE_FOR_MOVEMENT, MAX_POS_MOVE_ALLOWED, MAX_RECORDS_IN_MEMORY);
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index 040845828..9b464cfec 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -113,4 +113,14 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
             executeTest(String.format("realigner [%s]", entry.getKey()), spec);
         }
     }
+
+    @Test
+    public void testNWayOut() {
+        WalkerTestSpec spec1 = new WalkerTestSpec(
+                baseCommandPrefix + " -nWayOut .clean.bam ",
+                1,
+                Arrays.asList("d41d8cd98f00b204e9800998ecf8427e"));
+        executeTest("test realigner nWayOut", spec1);
+    }
+
 }