Fixed a bug in perl scripts for printing error messages

[rsem.git] / simulation.cpp

diff --git a/simulation.cpp b/simulation.cpp
index 5b1e7320dec60e69c2cae1cbb64ffa6cc55ccc44..97cee6ee610fc1f6f37202b1e5c9715e95cec2e1 100644 (file)
--- a/simulation.cpp
+++ b/simulation.cpp
@@ -31,7 +31,7 @@
 
 using namespace std;
 
-int N;
+READ_INT_TYPE N;
 int model_type, M, m;
 
 Refs refs;
@@ -138,49 +138,37 @@ void simulate(char* modelF, char* resultsF) {
        fin.close();
        for (int i = 1; i <= M; i++) theta[i] = theta[i] / denom * (1.0 - theta[0]);
        
-       int tmp2140 = 0;
+       READ_INT_TYPE resimulation_count = 0;
 
        //simulating...
        model.startSimulation(&sampler, theta);
-       for (int i = 0; i < N; i++) {
-         while (!model.simulate(i, read, sid)) { ++tmp2140; }//;
+       for (READ_INT_TYPE i = 0; i < N; i++) {
+               while (!model.simulate(i, read, sid)) { ++resimulation_count; }
                read.write(n_os, os);
                ++counts[sid];
-               if ((i + 1) % 1000000 == 0 && verbose) printf("GEN %d\n", i + 1);
+               if ((i + 1) % 1000000 == 0 && verbose) cout<<"GEN "<< i + 1<< endl;
        }
        model.finishSimulation();
 
-       printf("Total number of resimulation is %d\n", tmp2140);
+       cout<< "Total number of resimulation is "<< resimulation_count<< endl;
 }
 
 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;
 }
 
@@ -251,7 +237,7 @@ int main(int argc, char* argv[]) {
        //read model type from modelF
        fi = fopen(argv[2], "r");
        if (fi == NULL) { fprintf(stderr, "Cannot open %s! It may not exist.\n", argv[2]); exit(-1); }
-       fscanf(fi, "%d", &model_type);
+       assert(fscanf(fi, "%d", &model_type) == 1);
        fclose(fi);
 
        theta = new double[M + 1];