More test cases for UG integration test. We currently fail doing multi-threaded gzip output, FYI

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4472 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java

@@ -60,7 +60,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
             throw new UserException.CouldNotCreateOutputFile(file, "Unable to open target output stream", ex);
         }
 
-        return new StandardVCFWriter(file, this.stream);
+        return new StandardVCFWriter(file, this.stream, ! stub.isCompressed());
     }
 
 
@@ -117,6 +117,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
 //    }
     public void mergeInto(VCFWriterStorage target) {
         try {
+            System.out.printf("merging %s%n", file);
             BasicFeatureSource<VariantContext> source = BasicFeatureSource.getFeatureSource(file.getAbsolutePath(), new VCFCodec());
             
             for ( VariantContext vc : source.iterator() ) {

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -45,6 +45,31 @@ public class
         executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
     }
 
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // testing compressed output
+    //
+    // --------------------------------------------------------------------------------------------------------------
+
+    private final static String COMPRESSED_OUTPUT_MD5 = "dfbdccf53668b95e3490c198cbad77e8";
+
+    @Test
+    public void testCompressedOutput() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
+                Arrays.asList("gz"), Arrays.asList(COMPRESSED_OUTPUT_MD5));
+        executeTest("testCompressedOutput", spec);
+    }
+
+    // todo -- fixme
+//    @Test
+//    public void testCompressedOutputParallel() {
+//        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+//                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000 -nt 4", 1,
+//                Arrays.asList("gz"), Arrays.asList(COMPRESSED_OUTPUT_MD5));
+//        executeTest("testCompressedOutput-nt4", spec);
+//    }
+
     // --------------------------------------------------------------------------------------------------------------
     //
     // testing parallelization