+ if (isPaired && notgood) general_assert((b->core.flag & 0x0004) && (b2->core.flag & 0x0004), cstrtos(bam1_qname(b)) + "'s two mates are not all marked as unalignable!");
if (!notgood) {
// for collapsing
if (isPaired) {
assert(b->core.tid == b2->core.tid);
if (!notgood) {
// for collapsing
if (isPaired) {
assert(b->core.tid == b2->core.tid);
+ general_assert(b->core.tid == b2->core.tid, cstrtos(bam1_qname(b)) + "'s two mates are aligned to two different transcripts!");
if ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)) {
bam1_t *tmp = b; b = b2; b2 = tmp;
}
if ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)) {