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 960207647..526c78ac1 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 @@ -89,17 +89,20 @@ 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\tDISCOVERY_ACCURACY\tGENOTYPE_ACCURACY")); + s.add(String.format("\t\tCALLED_REF\tCALLED_VAR_HET\tCALLED_VAR_HOM\tNO_CALL\t\t\tTOTALS\tTRUE_GENOTYPE_CONCORDANCE\tGENOTYPE_SENSITIVITY")); 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])); + if ( i == TRUTH_VAR_HET || i == TRUTH_VAR_HOM ) { + sb.append("\t"+cellPercent(table[i][i], table[i][CALL_REF]+table[i][CALL_VAR_HET]+table[i][CALL_VAR_HOM]) + "\t\t\t"); + sb.append(cellPercent(truth_totals[i]-table[i][NO_CALL], truth_totals[i])); + } s.add(sb.toString()); } + s.add("VARIANT_SENSITIVITY: " + cellPercent(table[TRUTH_VAR_HET][CALL_VAR_HET]+table[TRUTH_VAR_HET][CALL_VAR_HOM]+table[TRUTH_VAR_HOM][CALL_VAR_HET]+table[TRUTH_VAR_HOM][CALL_VAR_HOM], truth_totals[TRUTH_VAR_HET]+truth_totals[TRUTH_VAR_HOM])); s.add("\n"); s.add(String.format("\t\tCALLED_REF\tCALLED_VAR_HET\tCALLED_VAR_HOM\tNO_CALL")); for (int i=0; i < 4; i++) { @@ -118,8 +121,8 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp 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])); + s.add(TRUTH_NAMES[i]+"_TRUE_GENOTYPE_CONCORDANCE "+cellPercent(table[i][i], table[i][CALL_REF]+table[i][CALL_VAR_HET]+table[i][CALL_VAR_HOM])); + s.add(TRUTH_NAMES[i]+"_GENOTYPE_SENSITIVITY "+cellPercent(truth_totals[i]-table[i][NO_CALL], truth_totals[i])); } } return s; }