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Fixing an apparent parenthesis matching problem 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5986 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-06-13 18:52:14 +00:00
parent 52f930d708
commit db43e3f1ab
2 changed files with 5 additions and 2 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
View File

@ -240,7 +240,10 @@ public class VariantDataManager {
datum.consensusCount = 0; datum.consensusCount = 0;
for( final TrainingSet trainingSet : trainingSets ) { for( final TrainingSet trainingSet : trainingSets ) {
for( final VariantContext trainVC : tracker.getVariantContexts( ref, trainingSet.name, null, context.getLocation(), false, false ) ) { for( final VariantContext trainVC : tracker.getVariantContexts( ref, trainingSet.name, null, context.getLocation(), false, false ) ) {
if( trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() && ((evalVC.isSNP() && trainVC.isSNP())) || ((evalVC.isIndel()||evalVC.isMixed()) && (trainVC.isIndel()||trainVC.isMixed())) && (TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphic()) ) { if( trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() &&
((evalVC.isSNP() && trainVC.isSNP()) || ((evalVC.isIndel()||evalVC.isMixed()) && (trainVC.isIndel()||trainVC.isMixed()))) &&
(TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphic()) ) {
datum.isKnown = datum.isKnown || trainingSet.isKnown; datum.isKnown = datum.isKnown || trainingSet.isKnown;
datum.atTruthSite = datum.atTruthSite || trainingSet.isTruth; datum.atTruthSite = datum.atTruthSite || trainingSet.isTruth;
datum.atTrainingSite = datum.atTrainingSite || trainingSet.isTraining; datum.atTrainingSite = datum.atTrainingSite || trainingSet.isTraining;

2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
View File

@ -196,7 +196,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
public static boolean checkRecalibrationMode( final VariantContext vc, final VariantRecalibratorArgumentCollection.Mode mode ) { public static boolean checkRecalibrationMode( final VariantContext vc, final VariantRecalibratorArgumentCollection.Mode mode ) {
return mode == VariantRecalibratorArgumentCollection.Mode.BOTH || return mode == VariantRecalibratorArgumentCollection.Mode.BOTH ||
(mode == VariantRecalibratorArgumentCollection.Mode.SNP && vc.isSNP()) || (mode == VariantRecalibratorArgumentCollection.Mode.SNP && vc.isSNP()) ||
(mode == VariantRecalibratorArgumentCollection.Mode.INDEL && (vc.isIndel() || vc.isMixed())); (mode == VariantRecalibratorArgumentCollection.Mode.INDEL && (vc.isIndel() || vc.isMixed()));
} }
//--------------------------------------------------------------------------------------------------------------- //---------------------------------------------------------------------------------------------------------------