X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=PairedEndModel.h;h=c011ceea16d53757384e320ae7196251eea7b956;hb=791b978145b0d22865ee350db9d58072bb99d816;hp=e73c03dd779aec9574a20bcb314c3db0eb1d2975;hpb=1794b68d34625b39404d5aba9e72646805b710ce;p=rsem.git

diff --git a/PairedEndModel.h b/PairedEndModel.h
index e73c03d..c011cee 100644
--- a/PairedEndModel.h
+++ b/PairedEndModel.h
@@ -59,11 +59,11 @@ public:
 		mw = NULL;
 
 		if (isMaster) {
-			ori = new Orientation(params.probF);
 			if (!estRSPD) rspd = new RSPD(estRSPD);
 			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);
 		pro = new Profile(params.maxL);
@@ -236,14 +236,19 @@ void PairedEndModel::estimateFromReads(const char* readFN) {
     		while (reader.next(read)) {
     			SingleRead mate1 = read.getMate1();
     			SingleRead mate2 = read.getMate2();
-
-    			mld->update(mate1.getReadLength(), 1.0);
-    			mld->update(mate2.getReadLength(), 1.0);
-
-    			if (i == 0) {
-    				npro->updateC(mate1.getReadSeq());
-    				npro->updateC(mate2.getReadSeq());
-    			}
+			
+			if (!read.isLowQuality()) {
+			  mld->update(mate1.getReadLength(), 1.0);
+			  mld->update(mate2.getReadLength(), 1.0);
+			  
+			  if (i == 0) {
+			    npro->updateC(mate1.getReadSeq());
+			    npro->updateC(mate2.getReadSeq());
+			  }
+			}
+			else if (verbose && (mate1.getReadLength() < OLEN || mate2.getReadLength() < OLEN)) { 
+			  printf("Warning: Read %s is ignored due to at least one of the mates' length < %d!\n", read.getName().c_str(), OLEN);
+			}
 
     			++cnt;
     			if (verbose && cnt % 1000000 == 0) { printf("%d READS PROCESSED\n", cnt); }
@@ -288,7 +293,7 @@ void PairedEndModel::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);
@@ -298,15 +303,18 @@ void PairedEndModel::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 master node can call. Only be called at EM.cpp
 void PairedEndModel::write(const char* outF) {
 	FILE *fo = fopen(outF, "w");
 
@@ -382,9 +390,8 @@ bool PairedEndModel::simulate(int rid, PairedEndRead& read, int& sid) {
 		readseq2 = pro->simulate(sampler, mateL2, m2pos, m2dir, ref);
 	}
 
-	std::ostringstream stdout;
-	stdout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos<<"_"<<insertL;
-	name = stdout.str();
+	strout<<rid<<"_"<<dir<<"_"<<sid<<"_"<<pos<<"_"<<insertL;
+	name = strout.str();
 
 	read = PairedEndRead(SingleRead(name + "/1", readseq1), SingleRead(name + "/2", readseq2));