X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=PairedEndQModel.h;h=64e486b66b98d19fafc98bce67ef0a5bd85131ad;hb=bf13409ebd15750dc9be1f92a622188d81ae634d;hp=e328779b6675a3579aa221c32f490b99648053e4;hpb=a95154919f950f86de9104b2b9dcf1f0c7e83387;p=rsem.git

diff --git a/PairedEndQModel.h b/PairedEndQModel.h
index e328779..64e486b 100644
--- 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));