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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
This commit is contained in:
depristo 2010-10-08 20:22:12 +00:00
parent 38a67fed63
commit 116309b3c3
2 changed files with 27 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
View File

@ -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() ) {

25
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -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