Style edits to rsem-plot-model

[rsem.git] / SingleQModel.h

diff --git a/SingleQModel.h b/SingleQModel.h
index 92d8890c60958f370155b379d018ca80c06fc319..d2c8ca1fdb67f8075e699db44f097c5502c12419 100644 (file)
--- a/SingleQModel.h
+++ b/SingleQModel.h
@@ -63,7 +63,6 @@ public:
                mw = NULL;
 
                if (isMaster) {
-                       ori = new Orientation(params.probF);
                        gld = new LenDist(params.minL, params.maxL);                    
                        if (mean >= EPSILON) {
                                mld = new LenDist(params.mate_minL, params.mate_maxL);
@@ -72,6 +71,7 @@ public:
                        qd = new QualDist();
                }
 
+               ori = new Orientation(params.probF);
                if (estRSPD) { rspd = new RSPD(estRSPD, params.B); }
                qpro = new QProfile();
                nqpro = new NoiseQProfile();
@@ -158,7 +158,8 @@ public:
        void update(const SingleReadQ& read, const SingleHit& hit, double frac) {
                if (read.isLowQuality() || frac < EPSILON) return;
 
-               RefSeq& ref = refs->getRef(hit.getSid());
+               const RefSeq& ref = refs->getRef(hit.getSid());
+
                int dir = hit.getDir();
                int pos = hit.getPos();
 
@@ -348,15 +349,18 @@ void SingleQModel::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 SingleQModel::write(const char* outF) {
        FILE *fo = fopen(outF, "w");
 
@@ -377,7 +381,7 @@ void SingleQModel::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]);
          }
@@ -465,7 +469,6 @@ void SingleQModel::calcMW() {
   memset(mw, 0, sizeof(double) * (M + 1));
   mw[0] = 1.0;
 
-
   probF = ori->getProb(0);
   probR = ori->getProb(1);