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done second alignment

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chhylp123
2022-10-09 16:59:54 -04:00
parent 2443e63ef5
commit 1d0562ebd1
5 changed files with 421 additions and 30 deletions
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Correct.cpp
+43 -3
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@@ -14973,6 +14973,8 @@ uint64_t query_gen_gov_idx(asg64_v *ovidx, uint64_t v, uint64_t w)
///[s, e)
uint64_t gen_region_phase(overlap_region* ol, uint64_t *id_a, uint64_t id_n, uint64_t s, uint64_t e, uint64_t dp, ul_ov_t *c_idx, uint64_t *buf, asg64_v *ovidx)
{
#define id_mm ((uint64_t)0x7fffffffffffffff)
#define id_set ((uint64_t)0x8000000000000000)
if(!id_n) return id_n;
uint64_t k, m, mn, q[2], buf_n, rm_n, i; int64_t err, msc, msc_k, msc_n;
overlap_region *z; ul_ov_t *p;
@@ -15031,14 +15033,47 @@ uint64_t gen_region_phase(overlap_region* ol, uint64_t *id_a, uint64_t id_n, uin
buf[k] = ovlp_id((c_idx[(uint32_t)buf[k]]));
// if(k < mn) fprintf(stderr, "d::bst::[M::%s::utg%.6dl]\n", __func__, (int32_t)ol[buf[k]].y_id+1);
}
for (k = 0; k < mn; k++) {
if(buf[k]&id_set) continue;
for (i = 0; i < k; i++) {
if(query_gen_gov_idx(ovidx, buf[k]&id_mm, buf[i]&id_mm)) break;
}
if(i < k) {
if(!(buf[k]&id_set)) {
ol[buf[k]&id_mm].overlapLen -= e - s;
ol[buf[k]&id_mm].align_length -= e - s;
}
buf[k] |= id_set;
if(!(buf[i]&id_set)) {
ol[buf[i]&id_mm].overlapLen -= e - s;
ol[buf[i]&id_mm].align_length -= e - s;
}
buf[i] |= id_set;
}
}
for (k = mn; k < buf_n; k++) {
z = &(ol[buf[k]]);
z = &(ol[buf[k]&id_mm]);
z->align_length -= e - s;
for (i = 0; i < mn; i++) {
if(query_gen_gov_idx(ovidx, buf[k], buf[i])) break;
if(query_gen_gov_idx(ovidx, buf[k]&id_mm, buf[i]&id_mm)) break;
}
if(i < mn) {
z->align_length += e - s;
if(!(buf[k]&id_set)) {
ol[buf[k]&id_mm].overlapLen -= e - s;
ol[buf[k]&id_mm].align_length -= e - s;
}
buf[k] |= id_set;
if(!(buf[i]&id_set)) {
ol[buf[i]&id_mm].overlapLen -= e - s;
ol[buf[i]&id_mm].align_length -= e - s;
}
buf[i] |= id_set;
// fprintf(stderr, "i::bst::[M::%s::utg%.6dl]\n", __func__, (int32_t)ol[buf[k]].y_id+1);
}
}
@@ -15328,7 +15363,12 @@ void region_phase(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t
}
///hap->length
// for (k = 0; k < on; k++) {
// z = &(ol->list[k]);
// if(z->align_length == z->overlapLen) {///prefer alignments without any trans hit
// z->align_length = z->overlapLen = z->x_pos_e+1-z->x_pos_s;
// }
// }
}
void ul_gap_filling_adv(overlap_region_alloc* ol, Candidates_list *cl, kv_ul_ov_t *aln, uint64_t wl,