From db43e3f1abb1c690115fb65c3259815e81c0389d Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 13 Jun 2011 18:52:14 +0000
Subject: [PATCH] Fixing an apparent parenthesis matching problem

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5986 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/variantrecalibration/VariantDataManager.java     | 5 ++++-
 .../walkers/variantrecalibration/VariantRecalibrator.java    | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 3c80dcf05..2aaa4c04b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -240,7 +240,10 @@ public class VariantDataManager {
         datum.consensusCount = 0;
         for( final TrainingSet trainingSet : trainingSets ) {
             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.atTruthSite = datum.atTruthSite || trainingSet.isTruth;
                     datum.atTrainingSite = datum.atTrainingSite || trainingSet.isTraining;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index aee8101d0..4eb3f7639 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -196,7 +196,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     public static boolean checkRecalibrationMode( final VariantContext vc, final VariantRecalibratorArgumentCollection.Mode mode ) {
         return mode == VariantRecalibratorArgumentCollection.Mode.BOTH ||
                 (mode == VariantRecalibratorArgumentCollection.Mode.SNP && vc.isSNP()) ||
-	    (mode == VariantRecalibratorArgumentCollection.Mode.INDEL && (vc.isIndel() || vc.isMixed()));
+	            (mode == VariantRecalibratorArgumentCollection.Mode.INDEL && (vc.isIndel() || vc.isMixed()));
     }
 
     //---------------------------------------------------------------------------------------------------------------