diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java index b4c6d8fe1..960207647 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java @@ -89,13 +89,15 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp public List done() { List s = new ArrayList(); s.add(String.format("name %s", dbName)); - s.add(String.format("\t\tCALLED_REF\tCALLED_VAR_HET\tCALLED_VAR_HOM\tNO_CALL\t\t\tTOTALS")); + s.add(String.format("\t\tCALLED_REF\tCALLED_VAR_HET\tCALLED_VAR_HOM\tNO_CALL\t\t\tTOTALS\tDISCOVERY_ACCURACY\tGENOTYPE_ACCURACY")); for (int i=0; i < 4; i++) { StringBuffer sb = new StringBuffer(); sb.append(TRUTH_NAMES[i] + "\t"); for (int j=0; j < 4; j++) sb.append(table[i][j] +" (" + cellPercent(table[i][j], truth_totals[i]) + ")\t\t"); sb.append(truth_totals[i]); + if ( i == TRUTH_VAR_HET || i == TRUTH_VAR_HOM ) + sb.append("\t"+cellPercent(table[i][CALL_VAR_HET]+table[i][CALL_VAR_HOM], truth_totals[i]) + "\t\t\t" + cellPercent(table[i][i], truth_totals[i])); s.add(sb.toString()); } s.add("\n"); @@ -115,7 +117,10 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp s.add(TRUTH_NAMES[i]+"_"+CALL_NAMES[j]+"_PERCENT_OF_TRUTH "+cellPercent(table[i][j], truth_totals[i])); s.add(TRUTH_NAMES[i]+"_"+CALL_NAMES[j]+"_PERCENT_OF_CALLS "+cellPercent(table[i][j], calls_totals[j])); } - } + if ( i == TRUTH_VAR_HET || i == TRUTH_VAR_HOM ) { + s.add(TRUTH_NAMES[i]+"_DISCOVERY_ACCURACY "+cellPercent(table[i][CALL_VAR_HET]+table[i][CALL_VAR_HOM], truth_totals[i])); + s.add(TRUTH_NAMES[i]+"_GENOTYPE_ACCURACY "+cellPercent(table[i][i], truth_totals[i])); + } } return s; }