- if (!isValid) { printf("\nOne of paired-end read %s's alignment does not have two mates adjacent to each other!\n", qname.c_str()); continue; }
+ if (!isValid) { printf("\nOne of paired-end read %s's alignment does not have two mates adjacent to each other! If you're running covert-sam-for-rsem now, this might mean the read contains duplicate alignments.\n", qname.c_str()); continue; }