cnt += 2;
if (verbose && cnt % 1000000 == 0) { printf("%d alignment lines are loaded!\n", cnt); }
- if (!((b->core.flag & 0x0002) && (b2->core.flag & 0x0002))) continue;
+ if ((b->core.flag & 0x0004) || (b2->core.flag & 0x0004)) continue;
//swap if b is mate 2
if (b->core.flag & 0x0080) {