// both mates are mapped
if (!(b->core.flag & 0x0004) && !(b2->core.flag & 0x0004)) {
isValid = (b->core.tid == b2->core.tid) && (b->core.pos == b2->core.mpos) && (b2->core.pos == b->core.mpos);
- 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; }
}
readlen = ((b->core.flag & 0x0040) ? (uint64_t(b->core.l_qseq) << 32) + b2->core.l_qseq : (uint64_t(b2->core.l_qseq) << 32) + b->core.l_qseq);