From d3c9910af6606d67a59cec09a004d6d42f7d3a6c Mon Sep 17 00:00:00 2001
From: Chris Hartl <chartl@broadinstitue.org>
Date: Wed, 8 May 2013 17:25:14 -0400
Subject: [PATCH] Cosmetic changes (comments and variable names) to
 GenotypeConcordance and ConcordanceMetrics to address reviewer comments.

---
 .../sting/gatk/walkers/variantutils/ConcordanceMetrics.java | 2 +-
 .../gatk/walkers/variantutils/GenotypeConcordance.java      | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
index 005acf27b..848261d73 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
@@ -168,7 +168,7 @@ public class ConcordanceMetrics {
         total += concordanceCounts[GenotypeType.HET.ordinal()][GenotypeType.HOM_VAR.ordinal()];
         total += concordanceCounts[GenotypeType.HOM_VAR.ordinal()][GenotypeType.HOM_REF.ordinal()];
         total += concordanceCounts[GenotypeType.HOM_VAR.ordinal()][GenotypeType.HET.ordinal()];
-        // NRD is by definition incorrec/total = 1.0-correct/total
+        // OGC is by definition correct/total
         // note: if there are no observations (so the ratio is NaN), set this to 100%
         return total == 0 ? 1.0 : ( (double) correct)/( (double) total);
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
index dd9e822c8..10397d718 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
@@ -272,7 +272,7 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
         GATKReportTable concordanceCounts = new GATKReportTable("GenotypeConcordance_Counts","Per-sample concordance tables: comparison counts",2+GenotypeType.values().length*GenotypeType.values().length);
         GATKReportTable concordanceEvalProportions = new GATKReportTable("GenotypeConcordance_EvalProportions", "Per-sample concordance tables: proportions of genotypes called in eval",2+GenotypeType.values().length*GenotypeType.values().length);
         GATKReportTable concordanceCompProportions = new GATKReportTable("GenotypeConcordance_CompProportions", "Per-sample concordance tables: proportions of genotypes called in comp",2+GenotypeType.values().length*GenotypeType.values().length);
-        GATKReportTable concordanceSummary = new GATKReportTable("GenotypeConcordance_Summary","Per-sample summary statistics: NRS and NRD",2);
+        GATKReportTable concordanceSummary = new GATKReportTable("GenotypeConcordance_Summary","Per-sample summary statistics: NRS, NRD, and OGC",2);
         GATKReportTable siteConcordance = new GATKReportTable("SiteConcordance_Summary","Site-level summary statistics",ConcordanceMetrics.SiteConcordanceType.values().length);
         if ( moltenize ) {
             concordanceCompProportions.addColumn("Sample","%s");
@@ -379,8 +379,8 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
             for ( Map.Entry<String,Double> nrdEntry : metrics.getPerSampleNRD().entrySet() ) {
                 concordanceSummary.set(nrdEntry.getKey(),"Non-Reference_Discrepancy",nrdEntry.getValue());
             }
-            for ( Map.Entry<String,Double> nrdEntry : metrics.getPerSampleOGC().entrySet() ) {
-                concordanceSummary.set(nrdEntry.getKey(),"Overall_Genotype_Concordance",nrdEntry.getValue());
+            for ( Map.Entry<String,Double> ogcEntry : metrics.getPerSampleOGC().entrySet() ) {
+                concordanceSummary.set(ogcEntry.getKey(),"Overall_Genotype_Concordance",ogcEntry.getValue());
             }
             concordanceSummary.set("ALL_NRS_NRD","Sample","ALL");
             concordanceSummary.set("ALL_NRS_NRD","Non-Reference_Sensitivity",metrics.getOverallNRS());