From cd61ef7169bfcaf9a7500395581ccdea27227b1f Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 8 Apr 2011 03:07:39 +0000 Subject: [PATCH] Re-enabling multi-threaded integration tests. To make this work, downsampling and annotations are disabled for this test so that we don't have randomization issues for it based on which shards get executed first. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5597 348d0f76-0448-11de-a6fe-93d51630548a --- .../UnifiedGenotyperIntegrationTest.java | 39 ++++--------------- 1 file changed, 8 insertions(+), 31 deletions(-) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 5c613b847..18103f690 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -100,26 +100,29 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - @Test (enabled = false) + @Test public void testParallelization() { - String md5 = "7e51ad5e76b8440cbf26373df83a8f41"; + + // Note that we need to turn off any randomization for this to work, so no downsampling and no annotations + + String md5 = "f56fdf5c6a2db85031a3cece37e12a56"; WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( - baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1, + baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1, Arrays.asList(md5)); executeTest("test parallelization (single thread)", spec1); GenomeAnalysisEngine.resetRandomGenerator(); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( - baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 2", 1, + baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 2", 1, Arrays.asList(md5)); executeTest("test parallelization (2 threads)", spec2); GenomeAnalysisEngine.resetRandomGenerator(); WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( - baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 4", 1, + baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 4", 1, Arrays.asList(md5)); executeTest("test parallelization (4 threads)", spec3); } @@ -279,32 +282,6 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest(String.format("test indel calling, multiple technologies"), spec); } - // Indel parallelization - //@Test - - // todo - test fails because for some reason when including -nt we get "PASS" instead of . in filter fields - public void testIndelParallelization() { - String md5 = "599220ba0cc5d8a32e4952fca85fd080"; - - WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( - baseCommand + " -I " + validationDataLocation + - "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -glm INDEL -o %s -L 1:10,000,000-10,100,000", 1, - Arrays.asList(md5)); - executeTest("test indel caller parallelization (single thread)", spec1); - - WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( - baseCommand + " -I " + validationDataLocation + - "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -glm INDEL -o %s -L 1:10,000,000-10,100,000 -nt 2", 1, - Arrays.asList(md5)); - executeTest("test indel caller parallelization (2 threads)", spec2); - - WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( - baseCommand + " -I " + validationDataLocation + - "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -glm INDEL -o %s -L 1:10,000,000-10,100,000 -nt 4", 1, - Arrays.asList(md5)); - executeTest("test indel caller parallelization (4 threads)", spec3); - } - // todo - feature not yet fully working with indels //@Test public void testWithIndelAllelesPassedIn() {