From 88d0890cc3d618b2e7a0981341a9306f009fbddb Mon Sep 17 00:00:00 2001 From: chartl Date: Fri, 2 Oct 2009 20:03:31 +0000 Subject: [PATCH] Made PooledGenotypeConcordance a standard test in VariantEval git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1759 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/varianteval/VariantEvalWalker.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java index 91b82807e..5be4d8157 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java @@ -112,6 +112,7 @@ public class VariantEvalWalker extends RefWalker { // // Add new analyses here! // + analyses.add(new PooledGenotypeConcordance(pathToHapmapPoolFile)); analyses.add(new VariantCounter()); analyses.add(new VariantDBCoverage(knownSNPDBName)); analyses.add(new GenotypeConcordance(genotypeChipName)); @@ -130,8 +131,9 @@ public class VariantEvalWalker extends RefWalker { VariantAnalysis analysis = iter.next(); boolean disableForGenotyping = evalContainsGenotypes && ! (analysis instanceof GenotypeAnalysis); boolean disableForPopulation = ! evalContainsGenotypes && ! (analysis instanceof PopulationAnalysis); - boolean disable = disableForGenotyping | disableForPopulation; - String causeName = disableForGenotyping ? "population" : (disableForPopulation ? "genotype" : null); + boolean disableForPools = pathToHapmapPoolFile == null; + boolean disable = disableForGenotyping | disableForPopulation | disableForPools; + String causeName = disableForGenotyping ? "population" : (disableForPopulation ? "genotype" : ( disableForPools ? "pool" : null )); if ( disable ) { logger.info(String.format("Disabling %s-only analysis %s in set %s", causeName, analysis, setName)); iter.remove();