- Added poly(A) tails to 'reference_name.transcripts.fa' so that the RSEM generated...

[rsem.git] / EM.cpp

diff --git a/EM.cpp b/EM.cpp
index fdc75cce046eb533755b4f99a669d48cf8e13c7b..59783f3089b5a96c7ea67db0113f9b558818d861 100644 (file)
--- a/EM.cpp
+++ b/EM.cpp
@@ -336,7 +336,7 @@ void calcExpressionValues(const vector<double>& theta, const vector<double>& eel
            frac[i] = theta[i];
            denom += frac[i];
          }
-       general_assert(denom > 0, "No alignable reads?!");
+       general_assert(denom >= EPSILON, "No alignable reads?!");
        for (int i = 1; i <= M; i++) frac[i] /= denom;
   
        //calculate FPKM
@@ -384,18 +384,18 @@ void writeResults(ModelType& model, double* counts) {
                }
 
                if (gene_tpm[i] < EPSILON) {
-                 double frac = 1.0 / (e - b);
-                 for (int j = b; j < e; j++) {
-                   glens[i] += tlens[j] * frac;
-                   gene_eels[i] += eel[j] * frac;
-                 } 
+                       double frac = 1.0 / (e - b);
+                       for (int j = b; j < e; j++) {
+                               glens[i] += tlens[j] * frac;
+                               gene_eels[i] += eel[j] * frac;
+                       }
                }
                else {
-                 for (int j = b; j < e; j++) {
-                   isopct[j] = tpm[j] / gene_tpm[i];
-                   glens[i] += tlens[j] * isopct[j];
-                   gene_eels[i] += eel[j] * isopct[j];
-                 }
+                       for (int j = b; j < e; j++) {
+                               isopct[j] = tpm[j] / gene_tpm[i];
+                               glens[i] += tlens[j] * isopct[j];
+                               gene_eels[i] += eel[j] * isopct[j];
+                       }
                }
        }