Refactored wiggle code and added rsem-bam2readdepth program

[rsem.git] / PairedEndModel.h

diff --git a/PairedEndModel.h b/PairedEndModel.h
index e73c03dd779aec9574a20bcb314c3db0eb1d2975..6e0f1a4fb385f7dbc53f904c85c95508f7f933a8 100644 (file)
--- a/PairedEndModel.h
+++ b/PairedEndModel.h
@@ -59,11 +59,11 @@ public:
                mw = NULL;
 
                if (isMaster) {
-                       ori = new Orientation(params.probF);
                        if (!estRSPD) rspd = new RSPD(estRSPD);
                        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);
                pro = new Profile(params.maxL);
@@ -298,15 +298,18 @@ void PairedEndModel::read(const char* inpF) {
        pro->read(fi);
        npro->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 PairedEndModel::write(const char* outF) {
        FILE *fo = fopen(outF, "w");