X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=SingleQModel.h;fp=SingleQModel.h;h=5d4191a809d39c454e1bfea7805b12f5fde990c0;hb=86e650e9577999a7ba00ab454d1f6bf674b0ea70;hp=f32b747ad298d2bcc94f109083025a3c4277dac0;hpb=5b867894f164d9fa3fbc1a8e659b34890b977716;p=rsem.git

diff --git a/SingleQModel.h b/SingleQModel.h
index f32b747..5d4191a 100644
--- a/SingleQModel.h
+++ b/SingleQModel.h
@@ -283,9 +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); }
@@ -339,7 +342,7 @@ void SingleQModel::read(const char* inpF) {
 
 	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);