- 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);
+ }