From d5ab00244995582f3fb8b8173d2bf5f350db0a5c Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 8 Jan 2010 06:02:01 +0000 Subject: [PATCH] Curiously, it seems I never set the default base quality used by the Genotyper to 10. It's done now. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2546 348d0f76-0448-11de-a6fe-93d51630548a --- .../genotyper/UnifiedArgumentCollection.java | 2 +- .../UnifiedGenotyperIntegrationTest.java | 38 +++++++++---------- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 806e1ebc9..bd774783c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -73,7 +73,7 @@ public class UnifiedArgumentCollection { public double CONFIDENCE_THRESHOLD = 0.0; @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false) - public int MIN_BASE_QUALTY_SCORE = 20; + public int MIN_BASE_QUALTY_SCORE = 10; @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false) public int MIN_MAPPING_QUALTY_SCORE = 10; 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 d5e0bcea5..fec835294 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -22,7 +22,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1PointEM() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1, - Arrays.asList("706efd396f3ac5e3addff73c15d1ec87")); + Arrays.asList("b7ea2739f9190ea6c5c63ffd1150454e")); executeTest("testMultiSamplePilot1 - Point Estimate EM", spec); } @@ -30,7 +30,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot2PointEM() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1, - Arrays.asList("917d9ede2b2bccbcc41c6b7534788fa2")); + Arrays.asList("b200b56b0f6363105b23417f459ec4dc")); executeTest("testMultiSamplePilot2 - Point Estimate EM", spec); } @@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testPooled1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1, - Arrays.asList("48b3719bf39705983876276b8da2642f")); + Arrays.asList("1fc421c8e5ccba7ba2f803fc17c27565")); executeTest("testPooled1", spec); } @@ -56,7 +56,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("057493e22a64cf5c78619707464cedbe")); + Arrays.asList("0078a4e6611cbfc7225f52209b87c4aa")); executeTest("testMultiSamplePilot1 - Joint Estimate", spec); } @@ -64,7 +64,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("05f32f8ba686260b79c98c661a01e8f8")); + Arrays.asList("9c862cf36124710648d6d8b83882c603")); executeTest("testMultiSamplePilot2 - Joint Estimate", spec); } @@ -72,7 +72,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testSingleSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("5fcc0ecff04d408d33ce5fdc0a8d8b89")); + Arrays.asList("4f6aeda8903be49344353b79ee7763b4")); executeTest("testSingleSamplePilot2 - Joint Estimate", spec); } @@ -85,7 +85,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testParallelization() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,400,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 -nt 4", 1, - Arrays.asList("b0e221e54f8ff9c6355654510acb7153")); + Arrays.asList("dbaff01edcfc8d83efa937f5887b26c2")); executeTest("test parallelization", spec); } @@ -98,11 +98,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testParameter() { HashMap e = new HashMap(); - e.put( "-genotype", "d82b53aad30005330203a7ca07ce83d5" ); - e.put( "-all_bases", "563566eaa2c621e88080149512d368b6" ); + e.put( "-genotype", "c6abe711dade515e72b671d7e0d6e724" ); + e.put( "-all_bases", "d9705e4c89f333f3fa6e771716db57e4" ); e.put( "--min_base_quality_score 26", "015509aca82954b89d7dc83134f2103e" ); - e.put( "--min_mapping_quality_score 26", "ba7fe92be077750225c762981ead4b0d" ); - e.put( "--max_mismatches_in_40bp_window 5", "abecda3de7b195d6d0f7ff97bc624b5f" ); + e.put( "--min_mapping_quality_score 26", "a3926d2d24f9b4b4d772243a50ebdd59" ); + e.put( "--max_mismatches_in_40bp_window 5", "ab592c8d0996d9bc4bb6685eaf874883" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -116,7 +116,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testConfidence() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10 ", 1, - Arrays.asList("c434515cae99d2da5a353f0b0866af81")); + Arrays.asList("15af52b80e2be8e8d2d489c3f86bdadc")); executeTest("testConfidence", spec); } @@ -129,8 +129,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOtherFormat() { HashMap e = new HashMap(); - e.put( "GLF", "2dabd6313cbf65564933187511bf823e" ); - e.put( "GELI_BINARY", "e0af9777893c4b872b9ad867f0a2758c" ); + e.put( "GLF", "cc1782d734e0a02fef00900a6db0e550" ); + e.put( "GELI_BINARY", "764a0fed1b3cf089230fd91f3be9c2df" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -152,8 +152,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testHeterozyosity() { HashMap e = new HashMap(); - e.put( 0.01, "0556dc160a18eeaf1a7303d5c1e1ce46" ); - e.put( 1.0 / 1850, "0556dc160a18eeaf1a7303d5c1e1ce46" ); + e.put( 0.01, "ee390f91867e8729b96220115e56ddb3" ); + e.put( 1.0 / 1850, "f96ad0ed71449bdb16b0c5561303a05a" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -172,8 +172,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOtherBaseCallModel() { HashMap e = new HashMap(); - e.put( "one_state", "78c4cfdd9ef21650709de5355178449a" ); - e.put( "three_state", "8ae5cebc06d520b1277b2f71265dd7e0" ); + e.put( "one_state", "bcc983210b576d9fd228a67c5b9f372a" ); + e.put( "three_state", "2db3a5f3d46e13e2f44c34fbb7e7936f" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -200,7 +200,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -gm JOINT_ESTIMATE" + " -vf GELI", 1, - Arrays.asList("1eabfec6a377992edb847d84608ab562")); + Arrays.asList("f09ac61858c2633e5d1326fcf098b36d")); executeTest(String.format("testMultiTechnologies"), spec); }