a bug in simulation.cpp is fixed.

diff --git a/simulation.cpp b/simulation.cpp
index 5b1e7320dec60e69c2cae1cbb64ffa6cc55ccc44..19f2b928b247f4557b24414f80d9eeda029743da 100644 (file)
--- a/simulation.cpp
+++ b/simulation.cpp
@@ -157,30 +157,18 @@ void writeResFiles(char* outFN) {
        FILE *fo;
        double denom;
 
-       //calculate normalized read fraction
-       double *nrf = new double[M + 1];
-       memset(nrf, 0, sizeof(double) * (M + 1));
-       denom = 0.0;
-       for (int i = 1; i <= M; i++)
-         if (eel[i] > EPSILON) {
-           nrf[i] = counts[i];
-           denom += nrf[i];
-         }
-         else {
-           if (counts[i] > EPSILON) { printf("Warning: An isoform which EEL is less than %.6g gets sampled!\n", MINEEL); }
-         }
-       assert(denom > 0.0);
-       for (int i = 1; i <= M; i++) nrf[i] /= denom;
-
        //calculate tau values
        double *tau = new double[M + 1];
        memset(tau, 0, sizeof(double) * (M + 1));
        denom = 0.0;
        for (int i = 1; i <= M; i++) 
-         if (eel[i] > EPSILON) {
-           tau[i] = nrf[i] / eel[i];
-           denom += tau[i];
-         }   
+               if (eel[i] > EPSILON) {
+                       tau[i] = counts[i] / eel[i];
+                       denom += tau[i];
+               }
+               else {
+                   if (counts[i] > EPSILON) { printf("Warning: An isoform which EEL is less than %.6g gets sampled!\n", MINEEL); }
+               }
        assert(denom > 0.0);
        for (int i = 1; i <= M; i++) tau[i] /= denom;
 
@@ -189,7 +177,7 @@ void writeResFiles(char* outFN) {
        fo = fopen(isoResF, "w");
        for (int i = 1; i <= M; i++) {
                const Transcript& transcript = transcripts.getTranscriptAt(i);
-               fprintf(fo, "%s\t%.2f\t%.15g\t%.15g", transcript.getTranscriptID().c_str(), counts[i], nrf[i], tau[i]);
+               fprintf(fo, "%s\t%.2f\t%.15g", transcript.getTranscriptID().c_str(), counts[i], tau[i]);
                
                if (transcript.getLeft() != "") { fprintf(fo, "\t%s", transcript.getLeft().c_str()); }
                fprintf(fo, "\n");
@@ -200,22 +188,20 @@ void writeResFiles(char* outFN) {
        sprintf(geneResF, "%s.sim.genes.results", outFN);
        fo = fopen(geneResF, "w");
        for (int i = 0; i < m; i++) {
-         double sum_c = 0.0, sum_nrf = 0.0, sum_tau = 0.0;
+         double sum_c = 0.0, sum_tau = 0.0;
                int b = gi.spAt(i), e = gi.spAt(i + 1);
                for (int j = b; j < e; j++) {
                        sum_c += counts[j];
-                       sum_nrf += nrf[j];
                        sum_tau += tau[j];
                }
                const string& gene_id = transcripts.getTranscriptAt(b).getGeneID();
-               fprintf(fo, "%s\t%.2f\t%.15g\t%.15g\t", gene_id.c_str(), sum_c, sum_nrf, sum_tau);
+               fprintf(fo, "%s\t%.2f\t%.15g\t", gene_id.c_str(), sum_c, sum_tau);
                for (int j = b; j < e; j++) {
                        fprintf(fo, "%s%c", transcripts.getTranscriptAt(j).getTranscriptID().c_str(), (j < e - 1 ? ',' : '\n'));
                }
        }
        fclose(fo);
 
-       delete[] nrf;
        delete[] tau;
 }