Merge branch 'unstable' of github.com:broadinstitute/cmi-gatk into unstable

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java

@@ -181,15 +181,6 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
     @Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "", required = false)
     private double minIndelProportionToTriggerVariant = 0.05;
 
-    /**
-     * Minimum proportion of indels in a site to trigger a variant region. Anything below this will be
-     * considered consensus.
-     */
-    @Argument(fullName = "contigs", shortName = "ctg", doc = "", required = false)
-    private int nContigs = 2;
-
-
-
     /**
      * Downsamples the coverage of a variable region approximately (guarantees the minimum to be equal to this).
      * A value of 0 turns downsampling off.
@@ -197,6 +188,14 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
     @Argument(fullName = "downsample_coverage", shortName = "ds", doc = "", required = false)
     private int downsampleCoverage = 250;
 
+    /**
+     * Number of chromossomes in the sample (this is used for the polyploid consensus compression). Only
+     * tested for humans (or organisms with n=2). Use at your own risk!
+     */
+    @Hidden
+    @Argument(fullName = "contigs", shortName = "ctg", doc = "", required = false)
+    private int nContigs = 2;
+
     @Hidden
     @Argument(fullName = "", shortName = "dl", doc = "", required = false)
     private int debugLevel = 0;

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(writerFileName == null && generateMD5)
-            if(!source.isRequired())
-                throw new MissingArgumentValueException(bamArgumentDefinition);
-            if(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;
+        SAMFileWriterStub stub = null;      // stub = new SAMFileWriterStub(engine, defaultOutputStream);
-        if ( writerFileName != null )
+
+        if ( writerFileName != null ) {
             stub = new SAMFileWriterStub(engine, new File(writerFileName));
-        else
-            stub = new SAMFileWriterStub(engine, defaultOutputStream);
 
-        if ( compressionLevel != null )
+            if ( compressionLevel != null )
-            stub.setCompressionLevel(compressionLevel);
+                stub.setCompressionLevel(compressionLevel);
-        if ( indexOnTheFly )
+            if ( indexOnTheFly )
-            stub.setIndexOnTheFly(indexOnTheFly);
+                stub.setIndexOnTheFly(indexOnTheFly);
-        if ( generateMD5 )
+            if ( generateMD5 )
-            stub.setGenerateMD5(generateMD5);
+                stub.setGenerateMD5(generateMD5);
-        if ( simplifyBAM )
+            if ( simplifyBAM )
-            stub.setSimplifyBAM(simplifyBAM);
+                stub.setSimplifyBAM(simplifyBAM);
 
-        // WARNING: Side effects required by engine!
+            // WARNING: Side effects required by engine!
-        parsingEngine.addTags(stub,getArgumentTags(matches));
+            parsingEngine.addTags(stub,getArgumentTags(matches));
-        engine.addOutput(stub);
+            engine.addOutput(stub);
+        }
 
         return stub;
     }

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);
 

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);
+    }
+
 }