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

[rsem.git] / SingleModel.h

diff --git a/SingleModel.h b/SingleModel.h
index bdf920ff271c133c749214244604fa319eac80c4..97ffd29c8ce9b7d499d99979bf0d51546cb17ab7 100644 (file)
--- a/SingleModel.h
+++ b/SingleModel.h
@@ -273,8 +273,11 @@ void SingleModel::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);
-                               if (i == 0) { npro->updateC(read.getReadSeq()); }
+                               if (!read.isLowQuality()) {
+                                 mld != NULL ? mld->update(read.getReadLength(), 1.0) : gld->update(read.getReadLength(), 1.0);
+                                 if (i == 0) { npro->updateC(read.getReadSeq()); }
+                               }
+                               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); }
@@ -441,7 +444,7 @@ void SingleModel::finishSimulation() {
 
 void SingleModel::calcMW() {
   double probF, probR;
-  
+
   assert(seedLen >= OLEN && (mld == NULL ? gld->getMinL() : mld->getMinL()) >= seedLen);
   
   memset(mw, 0, sizeof(double) * (M + 1));