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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
This commit is contained in:
chartl 2009-10-02 20:03:31 +00:00
parent 7fc4472e6d
commit 88d0890cc3
1 changed files with 4 additions and 2 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -112,6 +112,7 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
// //
// Add new analyses here! // Add new analyses here!
// //
analyses.add(new PooledGenotypeConcordance(pathToHapmapPoolFile));
analyses.add(new VariantCounter()); analyses.add(new VariantCounter());
analyses.add(new VariantDBCoverage(knownSNPDBName)); analyses.add(new VariantDBCoverage(knownSNPDBName));
analyses.add(new GenotypeConcordance(genotypeChipName)); analyses.add(new GenotypeConcordance(genotypeChipName));
@ -130,8 +131,9 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
VariantAnalysis analysis = iter.next(); VariantAnalysis analysis = iter.next();
boolean disableForGenotyping = evalContainsGenotypes && ! (analysis instanceof GenotypeAnalysis); boolean disableForGenotyping = evalContainsGenotypes && ! (analysis instanceof GenotypeAnalysis);
boolean disableForPopulation = ! evalContainsGenotypes && ! (analysis instanceof PopulationAnalysis); boolean disableForPopulation = ! evalContainsGenotypes && ! (analysis instanceof PopulationAnalysis);
boolean disable = disableForGenotyping | disableForPopulation; boolean disableForPools = pathToHapmapPoolFile == null;
String causeName = disableForGenotyping ? "population" : (disableForPopulation ? "genotype" : null); boolean disable = disableForGenotyping | disableForPopulation | disableForPools;
String causeName = disableForGenotyping ? "population" : (disableForPopulation ? "genotype" : ( disableForPools ? "pool" : null ));
if ( disable ) { if ( disable ) {
logger.info(String.format("Disabling %s-only analysis %s in set %s", causeName, analysis, setName)); logger.info(String.format("Disabling %s-only analysis %s in set %s", causeName, analysis, setName));
iter.remove(); iter.remove();