rsem v1.1.12, add a script to extract transcript-to-gene-map info from Trinity output

[rsem.git] / PairedEndQModel.h

diff --git a/PairedEndQModel.h b/PairedEndQModel.h
index e328779b6675a3579aa221c32f490b99648053e4..64e486b66b98d19fafc98bce67ef0a5bd85131ad 100644 (file)
--- a/PairedEndQModel.h
+++ b/PairedEndQModel.h
@@ -61,12 +61,12 @@ public:
                mw = NULL;
 
                if (isMaster) {
-                       ori = new Orientation(params.probF);
                        if (!estRSPD) rspd = new RSPD(estRSPD);
                        qd = new QualDist();
                        mld = new LenDist(params.mate_minL, params.mate_maxL);
                }
 
+               ori = new Orientation(params.probF);
                gld = new LenDist(params.minL, params.maxL);
                if (estRSPD) rspd = new RSPD(estRSPD, params.B);
                qpro = new QProfile();
@@ -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);
@@ -311,15 +309,19 @@ void PairedEndQModel::read(const char* inpF) {
        qpro->read(fi);
        nqpro->read(fi);
 
-       if (fscanf(fi, "%d", &M) == 1) {
-         mw = new double[M + 1];
-         for (int i = 0; i <= M; i++) fscanf(fi, "%lf", &mw[i]);
+       if (fscanf(fi, "%d", &val) == 1) {
+               if (M == 0) M = val;
+               if (M == val) {
+                       mw = new double[M + 1];
+                       for (int i = 0; i <= M; i++) assert(fscanf(fi, "%lf", &mw[i]) == 1);
+               }
        }
 
+
        fclose(fi);
 }
 
-//Only master node can call
+//Only master node can call. Only be called at EM.cpp
 void PairedEndQModel::write(const char* outF) {
        FILE *fo = fopen(outF, "w");
 
@@ -335,7 +337,7 @@ void PairedEndQModel::write(const char* outF) {
        nqpro->write(fo);
 
        if (mw != NULL) {
-         fprintf(fo, "%d\n", M);
+         fprintf(fo, "\n%d\n", M);
          for (int i = 0; i < M; i++) {
            fprintf(fo, "%.15g ", mw[i]);
          }
@@ -401,9 +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));