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chhylp123
2020-12-29 09:15:44 -05:00
parent 5d506e82c9
commit c545fd84c7
4 changed files with 169 additions and 98 deletions
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Overlaps.cpp
+32 -75
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@@ -10981,71 +10981,7 @@ void set_pre_uid(buf_t* b, hc_links* link, ma_ug_t *ug)
}
void collect_reverse_unitigs_back(buf_t* b_0, buf_t* b_1, hc_links* link, ma_ug_t *ug)
{
uint32_t k, m;
uint64_t d = (uint64_t)-1;
set_pre_uid(b_0, link, ug);
set_pre_uid(b_1, link, ug);
for (k = 0; k < b_0->b.n; k++)
{
for (m = 0; m < b_1->b.n; m++)
{
if(b_0->b.a[k] == b_1->b.a[m]) continue;
push_hc_edge(&(link->a.a[b_0->b.a[k]]), b_1->b.a[m], 1, 1, &d);
push_hc_edge(&(link->a.a[b_1->b.a[m]]), b_0->b.a[k], 1, 1, &d);
}
}
}
void collect_reverse_unitigs_back(buf_t* b_0, uint32_t b_0_uLen, buf_t* b_1, uint32_t b_1_uLen, hc_links* link, ma_ug_t *ug)
{
uint32_t b_0_i, b_0_i_l, b_0_k, b_1_i, b_1_i_l, b_1_k, pre_0, pre_1, rId_0, rId_1;
uint64_t d = (uint64_t)-1;
ma_utg_t* u_b_0 = NULL;
ma_utg_t* u_b_1 = NULL;
if(b_0->b.n == 0 || b_1->b.n == 0) return;
if(b_0_uLen == 0 || b_1_uLen == 0) return;
for (b_0_i = b_0_i_l = 0, pre_0 = (uint32_t)-1; b_0_i < b_0->b.n; b_0_i++)
{
u_b_0 = &(ug->u.a[b_0->b.a[b_0_i]>>1]);
if(u_b_0->n == 0) continue;
for (b_0_k = 0; b_0_k < u_b_0->n; b_0_k++)
{
rId_0 = u_b_0->a[b_0_k]>>33;
if(link->u_idx[rId_0] == (uint32_t)-1) continue;
if(pre_0 == link->u_idx[rId_0]) continue;
pre_0 = link->u_idx[rId_0];
b_0_i_l++;
if(b_0_i_l > b_0_uLen) return;
for (b_1_i = b_1_i_l = 0, pre_1 = (uint32_t)-1; b_1_i < b_1->b.n; b_1_i++)
{
u_b_1 = &(ug->u.a[b_1->b.a[b_1_i]>>1]);
if(u_b_1->n == 0) continue;
for (b_1_k = 0; b_1_k < u_b_1->n; b_1_k++)
{
rId_1 = u_b_1->a[b_1_k]>>33;
if(link->u_idx[rId_1] == (uint32_t)-1) continue;
if(pre_1 == link->u_idx[rId_1]) continue;
pre_1 = link->u_idx[rId_1];
b_1_i_l++;
if(b_1_i_l > b_1_uLen) goto b_1_i_end;
push_hc_edge(&(link->a.a[pre_0]), pre_1, 1, 1, &d);
push_hc_edge(&(link->a.a[pre_1]), pre_0, 1, 1, &d);
}
}
b_1_i_end:;
}
}
}
inline uint64_t get_utg_len(buf_t* b, ma_ug_t *ug, asg_t *read_sg, uint64_t* len_thre, uint64_t* occ)
inline uint64_t get_utg_len(buf_t* b, ma_ug_t *ug, asg_t *read_sg, uint64_t ignore_end, uint64_t* len_thre, uint64_t* occ)
{
if(len_thre && occ)(*occ) = (uint64_t)-1;
uint32_t ori, uid, v, nv, l, k, idx;
@@ -11085,7 +11021,7 @@ inline uint64_t get_utg_len(buf_t* b, ma_ug_t *ug, asg_t *read_sg, uint64_t* len
}
if(k == nv) fprintf(stderr, "ERROR\n");
len += l;
if(len_thre && occ && len >= (*len_thre) && (*occ) != (uint64_t)-1)
if(len_thre && occ && len >= (*len_thre))
{
(*occ) = idx - 1;
return len;
@@ -11120,7 +11056,7 @@ inline uint64_t get_utg_len(buf_t* b, ma_ug_t *ug, asg_t *read_sg, uint64_t* len
}
if(k == nv) fprintf(stderr, "ERROR\n");
len += l;
if(len_thre && occ && len >= (*len_thre) && (*occ) != (uint64_t)-1)
if(len_thre && occ && len >= (*len_thre))
{
(*occ) = idx - 1;
return len;
@@ -11130,33 +11066,38 @@ inline uint64_t get_utg_len(buf_t* b, ma_ug_t *ug, asg_t *read_sg, uint64_t* len
}
}
if(p_v != (uint32_t)-1)
if(ignore_end == 0 && p_v != (uint32_t)-1)
{
len += read_sg->seq[p_v>>1].len;
if(len_thre && occ && len >= (*len_thre) && (*occ) != (uint64_t)-1)
if(len_thre && occ && len >= (*len_thre))
{
(*occ) = idx - 1;
return len;
}
}
if(len_thre && occ)
{
(*occ) = idx;
}
return len;
}
void collect_reverse_unitigs(buf_t* b_0, buf_t* b_1, hc_links* link, ma_ug_t *ug, asg_t *read_sg)
{
uint32_t b_0_i, b_0_k, b_1_i, b_1_k, pre_0, pre_1, rId_0, rId_1, ori_0, ori_1;
uint64_t d = (uint64_t)-1, len_0, len_1, thre_0, thre_1;
uint64_t d = RC_1, len_0, len_1, thre_0, thre_1;
ma_utg_t* u_b_0 = NULL;
ma_utg_t* u_b_1 = NULL;
if(b_0->b.n == 0 || b_1->b.n == 0) return;
len_0 = get_utg_len(b_0, ug, read_sg, NULL, NULL);
len_1 = get_utg_len(b_1, ug, read_sg, NULL, NULL);
len_0 = get_utg_len(b_0, ug, read_sg, 1, NULL, NULL);
len_1 = get_utg_len(b_1, ug, read_sg, 1, NULL, NULL);
len_0 = MIN(len_0, len_1);
get_utg_len(b_0, ug, read_sg, &len_0, &thre_0);
get_utg_len(b_1, ug, read_sg, &len_0, &thre_1);
get_utg_len(b_0, ug, read_sg, 0, &len_0, &thre_0);
get_utg_len(b_1, ug, read_sg, 0, &len_0, &thre_1);
for (b_0_i = len_0 = 0, pre_0 = (uint32_t)-1; b_0_i < b_0->b.n; b_0_i++)
@@ -11202,9 +11143,25 @@ void collect_reverse_unitigs(buf_t* b_0, buf_t* b_1, hc_links* link, ma_ug_t *ug
if(pre_1 == link->u_idx[rId_1]) continue;
pre_1 = link->u_idx[rId_1];
push_hc_edge(&(link->a.a[pre_0]), pre_1, 1, 1, &d);
push_hc_edge(&(link->a.a[pre_1]), pre_0, 1, 1, &d);
// if(pre_0 == 5 || pre_1 == 5)
// {
// fprintf(stderr, "\npre_0: utg%.6ul, len_0: %lu, thre_0: %lu, pre_1: utg%.6ul, len_1: %lu, thre_1: %lu\n",
// (int)(pre_0+1), len_0, thre_0, (int)(pre_1+1), len_1, thre_1);
// uint32_t xxx_i;
// for (xxx_i = 0; xxx_i < b_0->b.n; xxx_i++)
// {
// fprintf(stderr,"+: utg%.6ul\n", (int)((b_0->b.a[xxx_i]>>1)+1));
// }
// for (xxx_i = 0; xxx_i < b_1->b.n; xxx_i++)
// {
// fprintf(stderr,"-: utg%.6ul\n", (int)((b_1->b.a[xxx_i]>>1)+1));
// }
// }
}
}