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 nrdEntry : metrics.getPerSampleNRD().entrySet() ) { concordanceSummary.set(nrdEntry.getKey(),"Non-Reference_Discrepancy",nrdEntry.getValue()); } - for ( Map.Entry nrdEntry : metrics.getPerSampleOGC().entrySet() ) { - concordanceSummary.set(nrdEntry.getKey(),"Overall_Genotype_Concordance",nrdEntry.getValue()); + for ( Map.Entry 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());