X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=SingleModel.h;h=97ffd29c8ce9b7d499d99979bf0d51546cb17ab7;hb=791b978145b0d22865ee350db9d58072bb99d816;hp=532f79cd2c126c79199b1072508642394e083445;hpb=1794b68d34625b39404d5aba9e72646805b710ce;p=rsem.git

diff --git a/SingleModel.h b/SingleModel.h
index 532f79c..97ffd29 100644
--- a/SingleModel.h
+++ b/SingleModel.h
@@ -61,7 +61,6 @@ 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);
@@ -69,6 +68,7 @@ public:
 			if (!estRSPD) { rspd = new RSPD(estRSPD); }
 		}
 
+		ori = new Orientation(params.probF);
 		if (estRSPD) { rspd = new RSPD(estRSPD, params.B); }
 		pro = new Profile(params.maxL);
 		npro = new NoiseProfile();
@@ -273,8 +273,11 @@ void SingleModel::estimateFromReads(const char* readFN) {
 
 			int cnt = 0;
 			while (reader.next(read)) {
-				mld != NULL ? mld->update(read.getReadLength(), 1.0) : gld->update(read.getReadLength(), 1.0);
-				if (i == 0) { npro->updateC(read.getReadSeq()); }
+				if (!read.isLowQuality()) {
+				  mld != NULL ? mld->update(read.getReadLength(), 1.0) : gld->update(read.getReadLength(), 1.0);
+				  if (i == 0) { npro->updateC(read.getReadSeq()); }
+				}
+				else if (verbose && read.getReadLength() < OLEN) { printf("Warning: Read %s is ignored due to read length < %d!\n", read.getName().c_str(), OLEN); }
 
 				++cnt;
 				if (verbose && cnt % 1000000 == 0) { printf("%d READS PROCESSED\n", cnt); }
@@ -315,17 +318,18 @@ void SingleModel::collect(const SingleModel& o) {
 	npro->collect(*(o.npro));
 }
 
+//Only master node can call
 void SingleModel::read(const char* inpF) {
 	int val;
 	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);
 	gld->read(fi);
-	fscanf(fi, "%d", &val);
+	assert(fscanf(fi, "%d", &val) == 1);
 	if (val > 0) {
 		if (mld == NULL) mld = new LenDist();
 		mld->read(fi);
@@ -334,14 +338,18 @@ void SingleModel::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++) assert(fscanf(fi, "%lf", &mw[i]) == 1);
+		}
 	}
 
 	fclose(fi);
 }
 
+//Only master node can call. Only be called at EM.cpp
 void SingleModel::write(const char* outF) {
 	FILE *fo = fopen(outF, "w");
 
@@ -418,9 +426,8 @@ bool SingleModel::simulate(int rid, SingleRead& read, int& sid) {
 		}
 	}
 
-	std::ostringstream stdout;
-	stdout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos;
-	name = stdout.str();
+	strout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos;
+	name = strout.str();
 
 	read = SingleRead(name, readseq);
 
@@ -437,7 +444,7 @@ void SingleModel::finishSimulation() {
 
 void SingleModel::calcMW() {
   double probF, probR;
-  
+
   assert(seedLen >= OLEN && (mld == NULL ? gld->getMinL() : mld->getMinL()) >= seedLen);
   
   memset(mw, 0, sizeof(double) * (M + 1));