X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=SingleQModel.h;h=5d4191a809d39c454e1bfea7805b12f5fde990c0;hb=791b978145b0d22865ee350db9d58072bb99d816;hp=92d8890c60958f370155b379d018ca80c06fc319;hpb=a95154919f950f86de9104b2b9dcf1f0c7e83387;p=rsem.git

diff --git a/SingleQModel.h b/SingleQModel.h
index 92d8890..5d4191a 100644
--- 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();
 
@@ -282,9 +283,12 @@ void SingleQModel::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);
-				qd->update(read.getQScore());
-				if (i == 0) { nqpro->updateC(read.getReadSeq(), read.getQScore()); }
+				if (!read.isLowQuality()) {
+				  mld != NULL ? mld->update(read.getReadLength(), 1.0) : gld->update(read.getReadLength(), 1.0);
+				  qd->update(read.getQScore());
+				  if (i == 0) { nqpro->updateC(read.getReadSeq(), read.getQScore()); }
+				}
+				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); }
@@ -333,12 +337,12 @@ void SingleQModel::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);
 	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);
@@ -348,15 +352,18 @@ 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++) 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 SingleQModel::write(const char* outF) {
 	FILE *fo = fopen(outF, "w");
 
@@ -377,7 +384,7 @@ 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]);
 	  }
@@ -439,9 +446,8 @@ bool SingleQModel::simulate(int rid, SingleReadQ& read, int& sid) {
 		}
 	}
 
-	std::ostringstream stdout;
-	stdout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos;
-	name = stdout.str();
+	strout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos;
+	name = strout.str();
 
 	read = SingleReadQ(name, readseq, qual);
 
@@ -465,7 +471,6 @@ void SingleQModel::calcMW() {
   memset(mw, 0, sizeof(double) * (M + 1));
   mw[0] = 1.0;
 
-
   probF = ori->getProb(0);
   probR = ori->getProb(1);