rsem v1.1.13, speed up EM by only updating model parameters for first 10 iterations...

[rsem.git] / SingleQModel.h

diff --git a/SingleQModel.h b/SingleQModel.h
index f32b747ad298d2bcc94f109083025a3c4277dac0..5d4191a809d39c454e1bfea7805b12f5fde990c0 100644 (file)
--- 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);