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Merge branch 'master' into layout 

Conflicts:
	main.c
This commit is contained in:
Heng Li 2014-04-14 16:05:08 -04:00
parent 6d4a6debdc 836d464239
commit a38b065642
1 changed files with 6 additions and 2 deletions
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8
bntseq.c
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@ -397,12 +397,16 @@ uint8_t *bns_fetch_seq(const bntseq_t *bns, const uint8_t *pac, int64_t *beg, in
far_end = far_beg + bns->anns[*rid].len; far_end = far_beg + bns->anns[*rid].len;
if (is_rev) { // flip to the reverse strand if (is_rev) { // flip to the reverse strand
int64_t tmp = far_beg; int64_t tmp = far_beg;
far_beg = (bns->l_pac<<1) - 1 - far_end; far_beg = (bns->l_pac<<1) - far_end;
far_end = (bns->l_pac<<1) - 1 - tmp; far_end = (bns->l_pac<<1) - tmp;
} }
*beg = *beg > far_beg? *beg : far_beg; *beg = *beg > far_beg? *beg : far_beg;
*end = *end < far_end? *end : far_end; *end = *end < far_end? *end : far_end;
seq = bns_get_seq(bns->l_pac, pac, *beg, *end, &len); seq = bns_get_seq(bns->l_pac, pac, *beg, *end, &len);
if (seq == 0 || *end - *beg != len) {
fprintf(stderr, "[E::%s] begin=%ld, mid=%ld, end=%ld, len=%ld, seq=%p, rid=%d, far_beg=%ld, far_end=%ld\n",
__func__, (long)*beg, (long)mid, (long)*end, (long)len, seq, *rid, (long)far_beg, (long)far_end);
}
assert(seq && *end - *beg == len); // assertion failure should never happen assert(seq && *end - *beg == len); // assertion failure should never happen
return seq; return seq;
} }