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Cosmetic changes (comments and variable names) to GenotypeConcordance and ConcordanceMetrics to address reviewer comments.

This commit is contained in:
Chris Hartl 2013-05-08 17:25:14 -04:00
parent 6ff74deac7
commit d3c9910af6
2 changed files with 4 additions and 4 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
View File

@ -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);
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
View File

@ -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());