if (!notgood) {
- assert((b->core.tid == b2->core.tid) && (b->core.flag & 0x0040) && (b2->core.flag & 0x0080)); // for collapsing
+ if (isPaired) assert((b->core.tid == b2->core.tid) && (b->core.flag & 0x0040) && (b2->core.flag & 0x0080)); // for collapsing
const Transcript& transcript = transcripts.getTranscriptViaEid(b->core.tid + 1);