From 7060e01a8e0bcbd20d98f6601c48705ed939be74 Mon Sep 17 00:00:00 2001
From: Chris Hartl <chartl@broadinstitute.org>
Date: Tue, 22 Jan 2013 15:14:41 -0500
Subject: [PATCH] Fix for broken unit test plus some minor changes to comments.
 Unit tests were broken by my pulling the site status utility function into
 the enum. Thankfully the unit tests caught my silly duplication of a line.

---
 .../gatk/walkers/variantutils/ConcordanceMetrics.java      | 2 +-
 .../gatk/walkers/variantutils/GenotypeConcordance.java     | 5 +++--
 .../walkers/variantutils/ConcordanceMetricsUnitTest.java   | 7 ++++++-
 3 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
index 8a87c9957..9d5495351 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
@@ -299,7 +299,7 @@ public class ConcordanceMetrics {
                 return EVAL_ONLY;
 
             boolean evalSubsetTruth = VariantContextUtils.allelesAreSubset(eval,truth);
-            boolean truthSubsetEval = VariantContextUtils.allelesAreSubset(eval,truth);
+            boolean truthSubsetEval = VariantContextUtils.allelesAreSubset(truth,eval);
 
             if ( evalSubsetTruth && truthSubsetEval )
                 return ALLELES_MATCH;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
index e8965dfc8..6902f864e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
@@ -168,8 +168,9 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
      * Eval: 20   4000     A     C
      * Eval: 20   4000     A    AC
      * Comp: 20   4000     A     C
-     * So for each eval, loop through the comps. If the eval alleles (non-emptily) intersect the comp alleles, pair them up and remove
-     * that comp records. Continue until we're out of evals or comps. This is n^2, but should rarely actually happen.
+     * So for each eval, loop through the comps. If the types match, or for mixed types if eval alleles (non-emptily)
+     * intersect the comp alleles, pair them up and remove that comp records.
+     * Continue until we're out of evals or comps. This is n^2, but should rarely actually happen.
      *
      * The remaining unpaired records get paird with an empty contexts. So in the example above we'd get a list of:
      *  1 - (20,4000,A/C  |  20,4000,A/C)
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
index 6db44efd5..0fff41d52 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
@@ -190,7 +190,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
     }
 
     @Test(enabled=true)
-    public void testMismatchingAllele() {
+    public void testMismatchingAlleleInAlleleSubset() {
         Pair<VariantContext,VariantContext> data = getData2();
         VariantContext eval = data.getFirst();
         VariantContext truth = data.getSecond();
@@ -709,8 +709,13 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
 
         List<Pair<VariantContext,VariantContext>> data = getData7();
 
+        int idx = 0;
+        int[] expecNotMatch = new int[]{0,0,0,0,0,1,1};
         for ( Pair<VariantContext,VariantContext> varPair : data ) {
             metrics.update(varPair.getFirst(),varPair.getSecond());
+            Assert.assertEquals(metrics.getOverallSiteConcordance().get(ConcordanceMetrics.SiteConcordanceType.ALLELES_DO_NOT_MATCH),expecNotMatch[idx]);
+            logger.info(idx);
+            idx++;
         }
 
         Assert.assertEquals(metrics.getOverallSiteConcordance().get(ConcordanceMetrics.SiteConcordanceType.ALLELES_DO_NOT_MATCH),1);