From 2ded0277628e97e0363b8af051580a87786f0459 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 7 Sep 2011 16:09:24 -0400 Subject: [PATCH] Removed dysfunctional tranches support from VariantEval --- .../walkers/varianteval/VariantEvalWalker.java | 18 ------------------ .../VariantEvalIntegrationTest.java | 2 +- 2 files changed, 1 insertion(+), 19 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index 65e3d3e5a..0d09b7033 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -149,9 +149,6 @@ public class VariantEvalWalker extends RodWalker implements Tr @Argument(shortName="mvq", fullName="mendelianViolationQualThreshold", doc="Minimum genotype QUAL score for each trio member required to accept a site as a violation", required=false) protected double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 50; - @Argument(fullName="tranchesFile", shortName="tf", doc="The input tranches file describing where to cut the data", required=false) - private String TRANCHE_FILENAME = null; - @Argument(fullName="ancestralAlignments", shortName="aa", doc="Fasta file with ancestral alleles", required=false) private File ancestralAlignmentsFile = null; @@ -226,16 +223,6 @@ public class VariantEvalWalker extends RodWalker implements Tr } sampleNamesForStratification.add(ALL_SAMPLE_NAME); - // Add select expressions for anything in the tranches file - if ( TRANCHE_FILENAME != null ) { - // we are going to build a few select names automatically from the tranches file - for ( Tranche t : Tranche.readTranches(new File(TRANCHE_FILENAME)) ) { - logger.info("Adding select for all variant above the pCut of : " + t); - SELECT_EXPS.add(String.format(VariantRecalibrator.VQS_LOD_KEY + " >= %.2f", t.minVQSLod)); - SELECT_NAMES.add(String.format("TS-%.2f", t.ts)); - } - } - // Initialize select expressions for (VariantContextUtils.JexlVCMatchExp jexl : VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS)) { SortableJexlVCMatchExp sjexl = new SortableJexlVCMatchExp(jexl.name, jexl.exp); @@ -245,18 +232,13 @@ public class VariantEvalWalker extends RodWalker implements Tr // Initialize the set of stratifications and evaluations to use stratificationObjects = variantEvalUtils.initializeStratificationObjects(this, NO_STANDARD_STRATIFICATIONS, STRATIFICATIONS_TO_USE); Set> evaluationObjects = variantEvalUtils.initializeEvaluationObjects(NO_STANDARD_MODULES, MODULES_TO_USE); - boolean usingJEXL = false; for ( VariantStratifier vs : getStratificationObjects() ) { if ( vs.getClass().getSimpleName().equals("Filter") ) byFilterIsEnabled = true; else if ( vs.getClass().getSimpleName().equals("Sample") ) perSampleIsEnabled = true; - usingJEXL = usingJEXL || vs.getClass().equals(JexlExpression.class); } - if ( TRANCHE_FILENAME != null && ! usingJEXL ) - throw new UserException.BadArgumentValue("tf", "Requires the JexlExpression ST to enabled"); - // Initialize the evaluation contexts evaluationContexts = variantEvalUtils.initializeEvaluationContexts(stratificationObjects, evaluationObjects, null, null); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 7b6d13223..6c4393d6a 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -261,7 +261,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { return String.format("%s -select '%s' -selectName %s", cmd, select, name); } - @Test + @Test(enabled = false) // no longer supported in the GATK public void testTranches() { String extraArgs = "-T VariantEval -R "+ hg18Reference +" --eval " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt"; WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("6af2b9959aa1778a5b712536de453952"));