From 848977678def2b118eec66e487f6000c3f137029 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 29 Dec 2010 22:06:19 +0000 Subject: [PATCH] No reason to convert the GLs to a String for formatting when they're just going to be converted to PLs later. That was 5% of the UG runtime... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4913 348d0f76-0448-11de-a6fe-93d51630548a --- .../genotyper/UnifiedGenotyperEngine.java | 2 +- .../UnifiedGenotyperIntegrationTest.java | 32 +++++++++---------- 2 files changed, 17 insertions(+), 17 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index aa1f7a480..39dc944f9 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -208,7 +208,7 @@ public class UnifiedGenotyperEngine { HashMap attributes = new HashMap(); GenotypeLikelihoods likelihoods = new GenotypeLikelihoods(GL.getLikelihoods(), VCFConstants.GENOTYPE_LIKELIHOODS_KEY); attributes.put(VCFConstants.DEPTH_KEY, GL.getDepth()); - attributes.put(likelihoods.getKey(), likelihoods.getAsString()); + attributes.put(likelihoods.getKey(), likelihoods); genotypes.put(GL.getSample(), new Genotype(GL.getSample(), noCall, Genotype.NO_NEG_LOG_10PERROR, null, attributes, false)); } 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 442e950cd..9380bb06f 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -25,7 +25,7 @@ public class public void testMultiSamplePilot1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1, - Arrays.asList("c4c75b08bb49fa404403c01198269133")); + Arrays.asList("e90af2265bdbfc1c336c7e1484b86a4a")); executeTest("testMultiSamplePilot1", spec); } @@ -33,7 +33,7 @@ public class public void testMultiSamplePilot2() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1, - Arrays.asList("17cea9547213f3fbdd28a8e8c5971564")); + Arrays.asList("9ef1405f3ddf4a9894d12718cc6041a1")); executeTest("testMultiSamplePilot2", spec); } @@ -41,7 +41,7 @@ public class public void testSingleSamplePilot2() { 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("43f7691454678e5ff529a1e21ce1c0e6")); + Arrays.asList("88a095d59e3210955dd066e54cfff6cd")); executeTest("testSingleSamplePilot2", spec); } @@ -51,7 +51,7 @@ public class // // -------------------------------------------------------------------------------------------------------------- - private final static String COMPRESSED_OUTPUT_MD5 = "bb2e7c10d69d526a298947b292d17620"; + private final static String COMPRESSED_OUTPUT_MD5 = "f213174bc3f6890dbe72628763be75d0"; @Test public void testCompressedOutput() { @@ -78,7 +78,7 @@ public class @Test public void testParallelization() { - String md5 = "9a4b3035ba16959d5b553ab70b791751"; + String md5 = "4c88572ec014cd0b256b76cb5fac41df"; 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, @@ -105,12 +105,12 @@ public class @Test public void testParameter() { HashMap e = new HashMap(); - e.put( "-genotype", "01f3d6d0e18267bfb7dc0331d4cb798d" ); - e.put( "-all_bases", "a2ff7f6c232e9210607e0c918da4bc61" ); - e.put( "--min_base_quality_score 26", "3af28da44a4bcfa7385797795ea8fed1" ); - e.put( "--min_mapping_quality_score 26", "8a61e97afa50571ce21cd39e72aa840f" ); - e.put( "--max_mismatches_in_40bp_window 5", "29f53ab510c8d65b75436f1fc41a9321" ); - e.put( "--p_nonref_model GRID_SEARCH", "00593066022525ed9e3bad2c009a7d2a" ); + e.put( "-genotype", "9d24c57250ec66905a157975c27f7094" ); + e.put( "-all_bases", "6bd860e4de6a4f013693a49556ccfd02" ); + e.put( "--min_base_quality_score 26", "94de36ab7021e767f14903b7fd0cf80e" ); + e.put( "--min_mapping_quality_score 26", "a86e9cdc629f0957658f8d570014f45b" ); + e.put( "--max_mismatches_in_40bp_window 5", "4cf60eeff7f25d8e778c72deb7e14cc2" ); + e.put( "--p_nonref_model GRID_SEARCH", "eda1afbdb42c9c5d6fc07a321020071a" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -124,12 +124,12 @@ public class public void testConfidence() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1, - Arrays.asList("00593066022525ed9e3bad2c009a7d2a")); + Arrays.asList("eda1afbdb42c9c5d6fc07a321020071a")); executeTest("testConfidence1", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1, - Arrays.asList("d32899eb5817ad451a84a69a16edfe67")); + Arrays.asList("8daa14278976555e64c582c4e44b9b8e")); executeTest("testConfidence2", spec2); } @@ -141,8 +141,8 @@ public class @Test public void testHeterozyosity() { HashMap e = new HashMap(); - e.put( 0.01, "76c75d43c19086a30f99098305d108eb" ); - e.put( 1.0 / 1850, "12aee2a5aab5c604b02eee07b9ad0c15" ); + e.put( 0.01, "3679786112b414546a464c94c900174e" ); + e.put( 1.0 / 1850, "efa1cb09fa72dd4bd6dbdf6c0fa0f038" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -165,7 +165,7 @@ public class " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("bde6ecc6ca31cbfc4d08ca65887ed842")); + Arrays.asList("037e7c0d56e88b4d85f326bf27ad9f1c")); executeTest(String.format("testMultiTechnologies"), spec); }