add computing auc

gtfcuff/gtfcuff.cc

@@ -286,7 +286,6 @@ int gtfcuff::match_correct(int refsize, int mcorrect)
 	return 0;
 }
 
-
 int gtfcuff::match_sensitivity(int refsize, double sensitivity)
 {
 	if(items.size() == 0) return 0;
@@ -376,6 +375,42 @@ int gtfcuff::roc_quant(const string &qfile, double min_tpm, double max_tpm)
 	return 0;
 }
 
+int gtfcuff::auc(int refsize)
+{
+	if(items.size() == 0) return 0;
+
+	sort(items.begin(), items.end(), cuffitem_cmp_coverage);
+
+	int correct = 0;
+	for(int i = 0; i < items.size(); i++) if(items[i].code == '=') correct++;
+
+	int correct0 = correct;
+	double sen0 = correct * 100.0 / refsize;
+	double pre0 = correct * 100.0 / items.size();
+	double auc = sen0 * pre0;
+	for(int i = 0; i < items.size() - 1; i++)
+	{
+		if(items[i].code == '=') correct--;
+
+		double sen = correct * 100.0 / refsize;
+		double pre = correct * 100.0 / (items.size() - i - 1);
+
+		double area = (sen + sen0) * 0.5 * (pre - pre0);
+		auc += area;
+
+		pre0 = pre;
+		sen0 = sen;
+
+		//printf("reference = %d prediction = %lu correct = %d sensitivity = %.2lf precision = %.2lf | area = %.5lf, auc = %.5lf | coverage = %.3lf, length = %d\n",
+		//		refsize, items.size() - i, correct, sen, pre, area, auc, items[i].coverage, items[i].length);
+	}
+
+	printf("reference = %d prediction = %lu correct = %d sensitivity = %.2lf precision = %.2lf auc = %.3lf\n",
+		refsize, items.size(), correct0, correct0 * 100.0 / refsize, correct0 * 100.0 / items.size(), auc);
+
+	return 0;
+}
+
 int gtfcuff::acc(int refsize)
 {
 	if(items.size() == 0) return 0;

gtfcuff/gtfcuff.h

@@ -35,6 +35,7 @@ class gtfcuff
 	int build_quant_index();
 
 	int roc(int refsize);
+	int auc(int refsize);
 	int acc(int refsize);
 	int compute_single_accuracy();
 	int match_precision(int refsize, double precision);

gtfcuff/main.cc

@@ -16,6 +16,7 @@ int main(int argc, const char **argv)
 	{
 		cout<<"usage: " <<endl;
 		cout<<"       " <<argv[0] << " roc <cuff.tmap> <ref-size>"<<endl;
+		cout<<"       " <<argv[0] << " auc <cuff.tmap> <ref-size>"<<endl;
 		cout<<"       " <<argv[0] << " acc <cuff.tmap> <ref-size>"<<endl;
 		cout<<"       " <<argv[0] << " acc-single <cuff.tmap>"<<endl;
 		cout<<"       " <<argv[0] << " roc-trunc <cuff.tmap> <ref-size> <min-coverage> <max-coverage>"<<endl;
@@ -32,6 +33,13 @@ int main(int argc, const char **argv)
 		return 0;
 	}
 
+	if(string(argv[1]) == "auc")
+	{
+		assert(argc == 4);
+		gtfcuff cuff(argv[2]);
+		cuff.auc(atoi(argv[3]));
+	}
+
 	if(string(argv[1]) == "roc")
 	{
 		assert(argc == 4);