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

[rsem.git] / PairedEndQModel.h

diff --git a/PairedEndQModel.h b/PairedEndQModel.h
index 64e486b66b98d19fafc98bce67ef0a5bd85131ad..cbc5475588d19996154d892cc99af336b75ddbde 100644 (file)
--- a/PairedEndQModel.h
+++ b/PairedEndQModel.h
@@ -243,16 +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); }