From 6ad8943ca07bc9b89edc8cfb70123c4966f003df Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 9 Sep 2011 09:45:24 -0400
Subject: [PATCH] CompOverlap no longer keeps track of the number of comp sites
 since it wasn't (and cannot) keeping track of them correctly.

---
 .../gatk/walkers/varianteval/evaluators/CompOverlap.java    | 6 +-----
 .../walkers/varianteval/VariantEvalIntegrationTest.java     | 6 +++---
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
index 5ccacac37..9facb11b5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
@@ -22,9 +22,6 @@ public class CompOverlap extends VariantEvaluator implements StandardEval {
     @DataPoint(description = "number of eval SNP sites")
     long nEvalVariants = 0;
 
-    @DataPoint(description = "number of comp SNP sites")
-    long nCompVariants = 0;
-
     @DataPoint(description = "number of eval sites outside of comp sites")
     long novelSites = 0;
 
@@ -76,9 +73,8 @@ public class CompOverlap extends VariantEvaluator implements StandardEval {
 
     public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         boolean evalIsGood = eval != null && eval.isPolymorphic();
-        boolean compIsGood = comp != null && comp.isNotFiltered() && (eval == null || comp.getType() == eval.getType());
+        boolean compIsGood = comp != null && comp.isNotFiltered();
 
-        if (compIsGood) nCompVariants++;           // count the number of comp events
         if (evalIsGood) nEvalVariants++;           // count the number of eval events
 
         if (compIsGood && evalIsGood) {
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 699c8fac7..f94c20ff6 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
@@ -291,7 +291,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     @Test
     public void testCompOverlap() {
         String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals --comp:comphapmap " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf --eval " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("462d4784dd55294ef9d5118217b157a5"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("009ecc8376a20dce81ff5299ef6bfecb"));
         executeTestParallel("testCompOverlap",spec);
     }
 
@@ -332,13 +332,13 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                            " -noST -noEV -ST Novelty -EV CompOverlap" +
                            " -o %s";
 
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("a3c2177849cb00fdff99574cff7f0e4f"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("0b81d97f843ec4a1a4222d1f9949bfca"));
         executeTestParallel("testMultipleCompTracks",spec);
     }
 
     @Test
     public void testPerSampleAndSubsettedSampleHaveSameResults() {
-        String md5 = "dab415cc76846e18fcf8c78f2b2ee033";
+        String md5 = "b0565ac61b2860248e4abd478a177b5e";
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 buildCommandLine(