Updated exact-match tests.

broadinstitute · Mar 7, 2022 · 9eb886c · 9eb886c
1 parent 45ef091
commit 9eb886c
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Showing 16 changed files with 40 additions and 39 deletions.
diff --git a/.../org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibratorIntegrationTest.java b/.../org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibratorIntegrationTest.java
@@ -356,7 +356,7 @@ public void testBothAggregateRecalMode() throws IOException {
         spec.executeTest("testBothRecalMode", this);
     }
 
-    private final String tmpDir = "/home/slee/test"; //createTempDir(this.getTestedClassName()).getAbsolutePath();
+    private final String tmpDir = createTempDir(this.getTestedClassName()).getAbsolutePath();
     private final String modelReportFilename = tmpDir + "/snpSampledModel.report";
     private final String modelReportRecal = getLargeVQSRTestDataDir() + "expected/snpSampledRecal.vcf";
     private final String modelReportTranches = getLargeVQSRTestDataDir() + "expected/snpSampledTranches.txt";
@@ -497,6 +497,7 @@ public void testVariantRecalibratorSNPscattered(final String[] params) throws IO
     }
 
     //One of the Gaussians has a covariance matrix with a determinant of zero, (can be confirmed that the entries of sigma for the row and column with the index of the constant annotation are zero) which leads to all +Inf LODs if we don't throw
+    //This convergence failure was fixed in https://github.com/broadinstitute/gatk/pull/7709
     @Test(expectedExceptions = {UserException.VQSRPositiveModelFailure.class}, enabled = false)
     public void testAnnotationsWithNoVarianceSpecified() throws IOException {
         // use an ArrayList - ArgumentBuilder tokenizes using the "=" in the resource args

diff --git a/src/test/resources/large/VQSR/bothRecal.vcf b/src/test/resources/large/VQSR/bothRecal.vcf
diff --git a/src/test/resources/large/VQSR/bothRecalWithAggregate.vcf b/src/test/resources/large/VQSR/bothRecalWithAggregate.vcf
diff --git a/src/test/resources/large/VQSR/expected/SNPAlternateTranches.txt b/src/test/resources/large/VQSR/expected/SNPAlternateTranches.txt
diff --git a/src/test/resources/large/VQSR/expected/SNPDefaultTranches.txt b/src/test/resources/large/VQSR/expected/SNPDefaultTranches.txt
diff --git a/src/test/resources/large/VQSR/expected/bothTranches.txt b/src/test/resources/large/VQSR/expected/bothTranches.txt
diff --git a/src/test/resources/large/VQSR/expected/bothTranchesWithAggregate.txt b/src/test/resources/large/VQSR/expected/bothTranchesWithAggregate.txt
diff --git a/src/test/resources/large/VQSR/expected/expected.AS.recal.vcf b/src/test/resources/large/VQSR/expected/expected.AS.recal.vcf
diff --git a/src/test/resources/large/VQSR/expected/indelTranches.txt b/src/test/resources/large/VQSR/expected/indelTranches.txt
diff --git a/src/test/resources/large/VQSR/expected/snpSampledRecal.vcf b/src/test/resources/large/VQSR/expected/snpSampledRecal.vcf
diff --git a/src/test/resources/large/VQSR/expected/snpSampledTranches.txt b/src/test/resources/large/VQSR/expected/snpSampledTranches.txt
diff --git a/src/test/resources/large/VQSR/indelRecal.vcf b/src/test/resources/large/VQSR/indelRecal.vcf
diff --git a/src/test/resources/large/VQSR/snpRecal.vcf b/src/test/resources/large/VQSR/snpRecal.vcf
diff --git a/src/test/resources/large/VQSR/snpTranches.scattered.txt b/src/test/resources/large/VQSR/snpTranches.scattered.txt
diff --git a/...resources/org/broadinstitute/hellbender/tools/walkers/VQSR/expected.AS.alternate.tranches b/...resources/org/broadinstitute/hellbender/tools/walkers/VQSR/expected.AS.alternate.tranches
@@ -1,15 +1,15 @@
 # Variant quality score tranches file
 # Version number 5
 targetTruthSensitivity,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName,model,accessibleTruthSites,callsAtTruthSites,truthSensitivity
-90.00,0,2507,0.0000,3.2205,-1.4017,VQSRTrancheSNP0.00to90.00,SNP,2786,2507,0.8999
-97.00,0,2702,0.0000,3.2351,-2.1306,VQSRTrancheSNP90.00to97.00,SNP,2786,2702,0.9698
-98.00,0,2730,0.0000,3.2457,-2.4533,VQSRTrancheSNP97.00to98.00,SNP,2786,2730,0.9799
-99.00,0,2758,0.0000,3.2496,-3.2164,VQSRTrancheSNP98.00to99.00,SNP,2786,2758,0.9899
-99.30,0,2766,0.0000,3.2488,-4.0653,VQSRTrancheSNP99.00to99.30,SNP,2786,2766,0.9928
-99.40,0,2769,0.0000,3.2469,-5.1648,VQSRTrancheSNP99.30to99.40,SNP,2786,2769,0.9939
-99.50,0,2772,0.0000,3.2450,-5.9262,VQSRTrancheSNP99.40to99.50,SNP,2786,2772,0.9950
-99.60,0,2774,0.0000,3.2416,-6.5841,VQSRTrancheSNP99.50to99.60,SNP,2786,2774,0.9957
-99.80,0,2780,0.0000,3.2314,-58913.3494,VQSRTrancheSNP99.60to99.80,SNP,2786,2780,0.9978
-99.90,0,2783,0.0000,3.2295,-59210.6252,VQSRTrancheSNP99.80to99.90,SNP,2786,2783,0.9989
-100.00,0,2786,0.0000,3.2340,-Infinity,VQSRTrancheSNP99.90to100.00,SNP,2786,2786,1.0000
-99.95,0,2786,0.0000,3.2340,-Infinity,VQSRTrancheSNP100.00to99.95,SNP,2786,2786,1.0000
+90.00,0,2507,0.0000,3.2134,935.3268,VQSRTrancheSNP0.00to90.00,SNP,2786,2507,0.8999
+97.00,0,2702,0.0000,3.2484,758.5107,VQSRTrancheSNP90.00to97.00,SNP,2786,2702,0.9698
+98.00,0,2730,0.0000,3.2523,710.0883,VQSRTrancheSNP97.00to98.00,SNP,2786,2730,0.9799
+99.00,0,2758,0.0000,3.2562,626.3145,VQSRTrancheSNP98.00to99.00,SNP,2786,2758,0.9899
+99.30,0,2766,0.0000,3.2423,573.6691,VQSRTrancheSNP99.00to99.30,SNP,2786,2766,0.9928
+99.40,0,2769,0.0000,3.2469,511.3402,VQSRTrancheSNP99.30to99.40,SNP,2786,2769,0.9939
+99.50,0,2772,0.0000,3.2515,342.2903,VQSRTrancheSNP99.40to99.50,SNP,2786,2772,0.9950
+99.60,0,2774,0.0000,3.2481,250.6941,VQSRTrancheSNP99.50to99.60,SNP,2786,2774,0.9957
+99.80,0,2780,0.0000,3.2314,-5.7548,VQSRTrancheSNP99.60to99.80,SNP,2786,2780,0.9978
+99.90,0,2783,0.0000,3.2295,-12.9282,VQSRTrancheSNP99.80to99.90,SNP,2786,2783,0.9989
+99.95,0,2784,0.0000,3.2310,-22753.7269,VQSRTrancheSNP99.90to99.95,SNP,2786,2784,0.9993
+100.00,0,2786,0.0000,3.2340,-39326.4087,VQSRTrancheSNP99.95to100.00,SNP,2786,2786,1.0000
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VQSR/expected.AS.tranches b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VQSR/expected.AS.tranches
@@ -1,7 +1,7 @@
 # Variant quality score tranches file
 # Version number 5
 targetTruthSensitivity,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName,model,accessibleTruthSites,callsAtTruthSites,truthSensitivity
-90.00,0,2507,0.0000,3.2205,-1.4017,VQSRTrancheSNP0.00to90.00,SNP,2786,2507,0.8999
-99.00,0,2758,0.0000,3.2496,-3.2164,VQSRTrancheSNP90.00to99.00,SNP,2786,2758,0.9899
-99.90,0,2783,0.0000,3.2295,-59210.6252,VQSRTrancheSNP99.00to99.90,SNP,2786,2783,0.9989
-100.00,0,2786,0.0000,3.2340,-Infinity,VQSRTrancheSNP99.90to100.00,SNP,2786,2786,1.0000
+90.00,0,2507,0.0000,3.2134,935.3268,VQSRTrancheSNP0.00to90.00,SNP,2786,2507,0.8999
+99.00,0,2758,0.0000,3.2562,626.3145,VQSRTrancheSNP90.00to99.00,SNP,2786,2758,0.9899
+99.90,0,2783,0.0000,3.2295,-12.9282,VQSRTrancheSNP99.00to99.90,SNP,2786,2783,0.9989
+100.00,0,2786,0.0000,3.2340,-39326.4087,VQSRTrancheSNP99.90to100.00,SNP,2786,2786,1.0000