rsem v1.1.11, allow spaces appear in field seqname and attributes gene_id, transcript...

[rsem.git] / PairedEndQModel.h

diff --git a/PairedEndQModel.h b/PairedEndQModel.h
index 2b899c57fa6061e0974e56083da03f580766351d..64e486b66b98d19fafc98bce67ef0a5bd85131ad 100644 (file)
--- a/PairedEndQModel.h
+++ b/PairedEndQModel.h
@@ -199,8 +199,6 @@ public:
        }
 
        int getModelType() const { return model_type; }
-
-       bool simulate(int, PairedEndReadQ&, SingleReadQ&, int&);
  
 private:
        static const int model_type = 3;
@@ -300,7 +298,7 @@ void PairedEndQModel::read(const char* inpF) {
        FILE *fi = fopen(inpF, "r");
        if (fi == NULL) { fprintf(stderr, "Cannot open %s! It may not exist.\n", inpF); exit(-1); }
 
-       fscanf(fi, "%d", &val);
+       assert(fscanf(fi, "%d", &val) == 1);
        assert(val == model_type);
 
        ori->read(fi);
@@ -315,7 +313,7 @@ void PairedEndQModel::read(const char* inpF) {
                if (M == 0) M = val;
                if (M == val) {
                        mw = new double[M + 1];
-                       for (int i = 0; i <= M; i++) fscanf(fi, "%lf", &mw[i]);
+                       for (int i = 0; i <= M; i++) assert(fscanf(fi, "%lf", &mw[i]) == 1);
                }
        }
 
@@ -405,9 +403,8 @@ bool PairedEndQModel::simulate(int rid, PairedEndReadQ& read, int& sid) {
                readseq2 = qpro->simulate(sampler, mateL2, m2pos, m2dir, qual2, ref);
        }
 
-       std::ostringstream stdout;
-       stdout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos<<"_"<<insertL;
-       name = stdout.str();
+       strout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos<<"_"<<insertL;
+       name = strout.str();
 
        read = PairedEndReadQ(SingleReadQ(name + "/1", readseq1, qual1), SingleReadQ(name + "/2", readseq2, qual2));