README.md modified

[rsem.git] / SingleQModel.h

diff --git a/SingleQModel.h b/SingleQModel.h
index 92d8890c60958f370155b379d018ca80c06fc319..dff9c4691153911a3d060b9d063a4856f4628b77 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();
 
@@ -377,7 +378,7 @@ 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 +466,6 @@ void SingleQModel::calcMW() {
   memset(mw, 0, sizeof(double) * (M + 1));
   mw[0] = 1.0;
 
-
   probF = ori->getProb(0);
   probR = ori->getProb(1);