Normalized Read Fraction(nrf) are eliminated from outputs and posterior mean counts...

[rsem.git] / EM.cpp

diff --git a/EM.cpp b/EM.cpp
index 00cb8527afe966771b61408debe86a74ad0294a1..e381b470e002be865e2bdb8a30adb3f6f510ec07 100644 (file)
--- a/EM.cpp
+++ b/EM.cpp
@@ -315,21 +315,13 @@ void writeResults(ModelType& model, double* counts) {
        fprintf(fo, "%.15g\n", theta[M]);
        fclose(fo);
 
-
-       //calculate normalized read fraction
-       double *nrf = new double[M + 1];
-       memset(nrf, 0, sizeof(double) * (M + 1));
-       denom = 1.0 - theta[0];
-       if (denom <= 0) { fprintf(stderr, "No alignable reads?!\n"); exit(-1); }
-       for (int i = 1; i <= M; i++) nrf[i] = theta[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) {
+         if (eel[i] >= EPSILON) {
            tau[i] = theta[i] / eel[i];
            denom += tau[i];
          }   
@@ -348,8 +340,6 @@ void writeResults(ModelType& model, double* counts) {
        }
        for (int i = 1; i <= M; i++)
                fprintf(fo, "%.2f%c", counts[i], (i < M ? '\t' : '\n'));
-       for (int i = 1; i <= M; i++)
-               fprintf(fo, "%.15g%c", nrf[i], (i < M ? '\t' : '\n'));
        for (int i = 1; i <= M; i++)
                fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
        for (int i = 1; i <= M; i++) {
@@ -371,12 +361,6 @@ void writeResults(ModelType& model, double* counts) {
                for (int j = b; j < e; j++) sumC += counts[j];
                fprintf(fo, "%.2f%c", sumC, (i < m - 1 ? '\t' : '\n'));
        }
-       for (int i = 0; i < m; i++) {
-               double sumN = 0.0; // sum of normalized read fraction
-               int b = gi.spAt(i), e = gi.spAt(i + 1);
-               for (int j = b; j < e; j++) sumN += nrf[j];
-               fprintf(fo, "%.15g%c", sumN, (i < m - 1 ? '\t' : '\n'));
-       }
        for (int i = 0; i < m; i++) {
                double sumT = 0.0; // sum of tau values
                int b = gi.spAt(i), e = gi.spAt(i + 1);
@@ -391,7 +375,6 @@ void writeResults(ModelType& model, double* counts) {
        }
        fclose(fo);
 
-       delete[] nrf;
        delete[] tau;
 
        if (verbose) { printf("Expression Results are written!\n"); }
@@ -472,7 +455,6 @@ void EM() {
        pthread_attr_init(&attr);
        pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
 
-
        ROUND = 0;
        do {
                ++ROUND;