Refactored wiggle code and added rsem-bam2readdepth program

[rsem.git] / PairedEndQModel.h

diff --git a/PairedEndQModel.h b/PairedEndQModel.h
index e328779b6675a3579aa221c32f490b99648053e4..2b899c57fa6061e0974e56083da03f580766351d 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();
@@ -311,15 +311,19 @@ 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++) fscanf(fi, "%lf", &mw[i]);
+               }
        }
 
+
        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 +339,7 @@ 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]);
          }