X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=PairedEndQModel.h;h=cbc5475588d19996154d892cc99af336b75ddbde;hb=1bcc1302290b4ae654b0362aae770fcf5c767cb7;hp=5437eb4c0051974b501829aa6ad68c6f69072ac3;hpb=a97cc1d4f0111f7fe523227412a2147f7a763d56;p=rsem.git

diff --git a/PairedEndQModel.h b/PairedEndQModel.h
index 5437eb4..cbc5475 100644
--- a/PairedEndQModel.h
+++ b/PairedEndQModel.h
@@ -199,8 +199,6 @@ public:
 	}
 
 	int getModelType() const { return model_type; }
-
-	bool simulate(int, PairedEndReadQ&, SingleReadQ&, int&);
  
 private:
 	static const int model_type = 3;
@@ -245,16 +243,21 @@ void PairedEndQModel::estimateFromReads(const char* readFN) {
     			SingleReadQ mate1 = read.getMate1();
     			SingleReadQ mate2 = read.getMate2();
 
-    			mld->update(mate1.getReadLength(), 1.0);
-    			mld->update(mate2.getReadLength(), 1.0);
-
-    			qd->update(mate1.getQScore());
-    			qd->update(mate2.getQScore());
-
-    			if (i == 0) {
-    				nqpro->updateC(mate1.getReadSeq(), mate1.getQScore());
-    				nqpro->updateC(mate2.getReadSeq(), mate2.getQScore());
-    			}
+			if (!read.isLowQuality()) {
+			  mld->update(mate1.getReadLength(), 1.0);
+			  mld->update(mate2.getReadLength(), 1.0);
+
+			  qd->update(mate1.getQScore());
+			  qd->update(mate2.getQScore());
+			  
+			  if (i == 0) {
+			    nqpro->updateC(mate1.getReadSeq(), mate1.getQScore());
+			    nqpro->updateC(mate2.getReadSeq(), mate2.getQScore());
+			  }
+			}
+			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); }
@@ -300,7 +303,7 @@ 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 +314,19 @@ 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");
 
@@ -401,9 +408,8 @@ 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));