xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-25 04:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

adjusted chain sc

Browse Source
This commit is contained in:
chhylp123
2022-10-09 18:14:07 -04:00
parent 1d0562ebd1
commit 3d65bef9de
3 changed files with 31 additions and 21 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Correct.cpp
+22 -16
View File
@@ -14970,13 +14970,15 @@ uint64_t query_gen_gov_idx(asg64_v *ovidx, uint64_t v, uint64_t w)
return 0;
}
// #define id_mm ((uint64_t)0x7fffffffffffffff)
#define id_set ((uint64_t)0x8000000000000000)
#define id_get(a) ((uint32_t)(a))
#define err_get(a) (((a)&((uint64_t)0x7fffffffffffffff))>>32)
///[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;
uint64_t k, m, mn, q[2], buf_n, rm_n, i, oid; int64_t err, msc, msc_k, msc_n;
overlap_region *z; ul_ov_t *p;
for (k = buf_n = rm_n = 0; k < id_n; k++) {
p = &(c_idx[id_a[k]]);
@@ -15030,25 +15032,26 @@ uint64_t gen_region_phase(overlap_region* ol, uint64_t *id_a, uint64_t id_n, uin
}
// fprintf(stderr, "[M::%s] buf_n::%ld, msc_n::%ld, mn::%lu\n", __func__, buf_n, msc_n, mn);
for (k = 0; k < buf_n; k++) {
buf[k] = ovlp_id((c_idx[(uint32_t)buf[k]]));
oid = ovlp_id((c_idx[(uint32_t)buf[k]]));
buf[k] >>= 32; buf[k] <<= 32; buf[k] |= oid;
// 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(query_gen_gov_idx(ovidx, id_get(buf[k]), id_get(buf[i]))) 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;
ol[id_get(buf[k])].overlapLen -= e - s;
ol[id_get(buf[k])].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;
ol[id_get(buf[i])].overlapLen -= e - s;
ol[id_get(buf[i])].align_length -= e - s;
}
buf[i] |= id_set;
}
@@ -15057,24 +15060,27 @@ uint64_t gen_region_phase(overlap_region* ol, uint64_t *id_a, uint64_t id_n, uin
for (k = mn; k < buf_n; k++) {
z = &(ol[buf[k]&id_mm]);
z = &(ol[id_get(buf[k])]);
z->align_length -= e - s;
for (i = 0; i < mn; i++) {
if(query_gen_gov_idx(ovidx, buf[k]&id_mm, buf[i]&id_mm)) break;
if(query_gen_gov_idx(ovidx, id_get(buf[k]), id_get(buf[i]))) 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;
ol[id_get(buf[k])].overlapLen -= e - s;
ol[id_get(buf[k])].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;
ol[id_get(buf[i])].overlapLen -= e - s;
ol[id_get(buf[i])].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);
} else {
assert(err_get(buf[i]) > (uint64_t)msc);
z->non_homopolymer_errors += err_get(buf[i])-msc;
}
}
}
@@ -15287,7 +15293,7 @@ void region_phase(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t
kv_resize(ul_ov_t, *c_idx, ol->length);
for (k = idx->n = c_idx->n = 0; k < on; k++) {
z = &(ol->list[k]); zwn = z->w_list.n;
z->align_length = z->overlapLen = z->x_pos_e+1-z->x_pos_s;
z->align_length = z->overlapLen = z->x_pos_e+1-z->x_pos_s; z->non_homopolymer_errors = 0;
if(!zwn) continue;
q[0] = q[1] = t[0] = t[1] = w[0] = w[1] = INT32_MIN;
for (i = 0; i < zwn; i++) {