for ( GenotypeType evalType : GenotypeType.values() ) {
for ( GenotypeType compType : GenotypeType.values() ) {
String rowKey = String.format("%s_%s_%s",entry.getKey(),evalType.toString(),compType.toString());
concordanceCounts.set(rowKey,"Sample",entry.getKey());
concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString());
concordanceCounts.set(rowKey,"Comp_Genotype",compType.toString());
int count = table.get(evalType, compType);
concordanceCounts.set(rowKey,"Count",count);
if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) {
concordanceEvalProportions.set(rowKey,"Sample",entry.getKey());
concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString());
concordanceEvalProportions.set(rowKey,"Comp_Genotype",compType.toString());
concordanceEvalProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
concordanceCompProportions.set(rowKey,"Eval_Genotype",evalType.toString());
concordanceCompProportions.set(rowKey,"Comp_Genotype",compType.toString());
concordanceCompProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
for ( GenotypeType evalType : GenotypeType.values() ) {
for ( GenotypeType compType : GenotypeType.values() ) {
String rowKey = String.format("%s_%s_%s",sampleKey,evalType.toString(),compType.toString());
concordanceCounts.set(rowKey,"Sample",sampleKey);
concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString());
concordanceCounts.set(rowKey,"Comp_Genotype",compType.toString());
int count = table.get(evalType, compType);
concordanceCounts.set(rowKey,"Count",count);
if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) {
concordanceEvalProportions.set(rowKey,"Sample",sampleKey);
concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString());