xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-27 07:38:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

resolve conflict

Browse Source
This commit is contained in:
chhylp123
2020-11-16 01:44:12 -05:00
parent ab073aa1fc
commit d87314a07e
3 changed files with 129 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files
CommandLines.cpp
+9 -4
View File
@@ -27,6 +27,7 @@ static ko_longopt_t long_options[] = {
{ "lowQ", ko_required_argument, 312 },
{ "h1", ko_required_argument, 313 },
{ "h2", ko_required_argument, 314 },
{ "enzyme", ko_required_argument, 315 },
{ 0, 0, 0 }
};
@@ -101,6 +102,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->required_read_name = NULL;
asm_opt->hic_files[0] = NULL;
asm_opt->hic_files[1] = NULL;
asm_opt->hic_enzymes = NULL;
asm_opt->thread_num = 1;
asm_opt->k_mer_length = 51;
asm_opt->hic_mer_length = 31;
@@ -139,14 +141,13 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->recover_atg_cov_max = INT_MAX;
asm_opt->hom_global_coverage = -1;
asm_opt->bed_inconsist_rate = 70;
asm_opt->bub_mer_length = 3;
}
void destory_opt(hifiasm_opt_t* asm_opt)
{
if(asm_opt->read_file_names != NULL)
{
free(asm_opt->read_file_names);
}
if(asm_opt->read_file_names != NULL) free(asm_opt->read_file_names);
if(asm_opt->hic_enzymes != NULL) free(asm_opt->hic_enzymes);
}
void ha_opt_reset_to_round(hifiasm_opt_t* asm_opt, int round)
@@ -401,6 +402,10 @@ void get_queries(int argc, char *argv[], ketopt_t* opt, hifiasm_opt_t* asm_opt)
}
}
void get_hic_enzymes(char *argv, hifiasm_opt_t* asm_opt)
{
///strtok
}
int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
{
CommandLines.h
+2
View File
@@ -31,10 +31,12 @@ typedef struct {
char *fn_bin_list[2];
char *extract_list;
char *hic_files[2];
char **hic_enzymes;
int extract_iter;
int thread_num;
int k_mer_length;
int hic_mer_length;
int bub_mer_length;
int mz_win;
int bf_shift;
double high_factor; // coverage cutoff set to high_factor*hom_cov
hic.cpp
+118 -1
View File
@@ -60,9 +60,11 @@ typedef struct{
kvec_t(uint8_t) rGraphSet;
kvec_t(uint8_t) rGraphVis;
kvec_t(uint8_t) utgVis;
kvec_t(uint8_t) bmerVis;
kdq_t(uint64_t) *q;
kvec_t(uint64_t) parent;
uint64_t uID_mode, uID_shift, n, src, dest;
int p_mer, a_mer, b_mer;
} min_cut_t;
typedef struct {
@@ -1445,6 +1447,8 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub)
{
bub->index[(a[v]>>1)] = i;
}
bub->index[(beg>>1)] = bub->index[(sink>>1)] = (uint32_t)-1;
}
///free(bub->index); bub->index = NULL;
@@ -1859,8 +1863,10 @@ void init_min_cut_t(min_cut_t* x, hc_links* link, const bubble_type* bub, const
x->n = utg_num;
kv_malloc(x->rGraphSet, utg_num); x->rGraphSet.n = utg_num;
///must utg_num<<1)
kv_malloc(x->rGraphVis, utg_num); x->rGraphVis.n = utg_num;
kv_malloc(x->utgVis, utg_num); x->utgVis.n = utg_num;
kv_malloc(x->bmerVis, utg_num); x->bmerVis.n = utg_num;
kv_malloc(x->order, utg_num); x->order.n = utg_num;
kv_malloc(x->parent, utg_num); x->parent.n = utg_num;
///uresolved BUGs, if use kv_resize segfault; if use kv_malloc, work?????
@@ -1881,6 +1887,7 @@ void init_min_cut_t(min_cut_t* x, hc_links* link, const bubble_type* bub, const
x->rGraphSet.a[i] = 0;
x->rGraphVis.a[i] = 0;
x->utgVis.a[i] = 0;
x->bmerVis.a[i] = 0;
x->parent.a[i] = (uint64_t)-1;
///uresolved BUGs, if use kv_resize segfault; if use kv_malloc, work?????
@@ -1906,6 +1913,7 @@ void init_min_cut_t(min_cut_t* x, hc_links* link, const bubble_type* bub, const
x->q = kdq_init(uint64_t);
radix_sort_hc64(x->order.a, x->order.a + x->order.n);
x->b_mer = asm_opt.bub_mer_length;
///fprintf(stderr, "[M::%s]\n", __func__);
///exit(0);
}
@@ -1917,6 +1925,7 @@ void destory_min_cut_t(min_cut_t* x)
kv_destroy(x->rGraphSet);
kv_destroy(x->rGraphVis);
kv_destroy(x->utgVis);
kv_destroy(x->bmerVis);
uint64_t i;
for (i = 0; i < x->rGraph.m; i++)
{
@@ -1931,12 +1940,13 @@ void reset_min_cut_t(min_cut_t* x, hc_links* link)
///no need to reset parent[] and q
uint64_t i, j;
///important to have this line
x->parent.n = x->order.n = x->rGraph.n = x->rGraphVis.n = x->rGraphSet.n = link->a.n;
x->bmerVis.n = x->parent.n = x->order.n = x->rGraph.n = x->rGraphVis.n = x->rGraphSet.n = link->a.n;
kdq_clear(x->q);
for (i = 0; i < x->rGraphSet.n; i++)
{
x->rGraphVis.a[i] = 0;
///x->bmerVis.a[i] = 0;
///important to have this line
x->rGraph.a[i].n = link->a.a[i].e.n;
@@ -1955,6 +1965,7 @@ uint64_t add_mul_convex(min_cut_t* x, uint64_t* a, uint64_t n)
if(n == 1) return a[0];
kv_push(uint8_t, x->rGraphSet, 0);
kv_push(uint8_t, x->rGraphVis, 0);
kv_push(uint8_t, x->bmerVis, 0);
kv_push(uint64_t, x->parent, 0);
kv_resize(hc_edge_warp, x->rGraph, x->rGraph.n+1);
kv_init(x->rGraph.a[x->rGraph.n]);
@@ -2021,6 +2032,7 @@ uint64_t bfs_flow(uint64_t src, uint64_t dest, min_cut_t* x, kvec_t_u64_warp* bu
if(x->rGraph.a[v].a[i].weight == 0) continue;
u = x->rGraph.a[v].a[i].uID;
if(x->rGraphVis.a[u]) continue;
if(!x->bmerVis.a[u]) continue;
///x->parent.a[u] = v;
x->parent.a[u] = x->rGraph.a[v].a[i].weight;
@@ -2125,6 +2137,7 @@ void graph_cut(uint64_t src, uint64_t dest, min_cut_t* x)
if(x->rGraph.a[i].a[j].del) continue;
u = x->rGraph.a[i].a[j].uID;
if(x->rGraphVis.a[u]) continue;
if(!x->bmerVis.a[u]) continue;
/*******************************for debug************************************/
fprintf(stderr, "utg%.6lul\tutg%.6lul\t%d\n", v+1, u+1, x->rGraph.a[i].a[j].weight);
/*******************************for debug************************************/
@@ -2252,6 +2265,106 @@ uint64_t src, uint64_t dest, uint64_t utg_thres, int weight_thres)
return 1;
}
uint64_t inline set_dv(uint64_t v, uint64_t dis)
{
dis <<= 32; dis |= v;
return dis;
}
uint64_t select_bmer(uint32_t src, uint64_t k, const bubble_type* bub, min_cut_t* x)
{
uint32_t beg, sink, n, *a;
uint32_t v, d, u, i, nv, b_mer_d, j;
asg_t *sg = bub->ug->g;
uint64_t *p = NULL;
asg_arc_t *av = NULL;
memset(x->rGraphVis.a, 0, x->rGraphVis.n);
kdq_push(uint64_t, x->q, set_dv(src , 0));
b_mer_d = 0;
x->rGraphVis.a[src] = 1;
x->bmerVis.a[src] = 1;
while (1)
{
p = kdq_shift(uint64_t, x->q);
if(!p) break;
v = (uint32_t)(*p); d = ((uint64_t)(*p))>>32;
v = v<<1;
av = asg_arc_a(sg, v);
nv = asg_arc_n(sg, v);
for (i = 0; i < nv; i++)
{
if(av[i].del) continue;
u = av[i].v>>1;
if(x->rGraphVis.a[u]) continue;
x->rGraphVis.a[u] = 1;
if(bub->index[u] > bub->num.n)
{
if(d < k) kdq_push(uint64_t, x->q, set_dv(u, d+1));
}
else
{
x->bmerVis.a[u] = 1;
kdq_push(uint64_t, x->q, set_dv(u , d));
b_mer_d = d;
}
}
v = v + 1;
av = asg_arc_a(sg, v);
nv = asg_arc_n(sg, v);
for (i = 0; i < nv; i++)
{
if(av[i].del) continue;
u = av[i].v>>1;
if(x->rGraphVis.a[u]) continue;
x->rGraphVis.a[u] = 1;
if(bub->index[u] > bub->num.n)
{
if(d < k) kdq_push(uint64_t, x->q, set_dv(u, d+1));
}
else
{
kdq_push(uint64_t, x->q, set_dv(u , d));
b_mer_d = d;
if(bub->index[u] < bub->num.n && x->bmerVis.a[u] == 0)
{
get_bubbles((bubble_type*)bub, bub->index[u], &beg, &sink, &a, &n);
for (j = 0; j < n; j++) x->bmerVis.a[(a[j]>>1)] = 1;
}
//must be here
x->bmerVis.a[u] = 1;
}
}
}
return b_mer_d;
}
void get_bmer_unitgs(min_cut_t* x, const bubble_type* bub, uint64_t k, uint64_t src)
{
memset(x->bmerVis.a, 0, x->bmerVis.n);
select_bmer(src, k, bub, x);
/*******************************for debug************************************/
uint64_t i;
for (i = 0; i < x->bmerVis.n; ++i)
{
if(x->bmerVis.a[i] == 0) continue;
fprintf(stderr, "(k)utg%.6dl\n", (int)(i+1));
}
// for (i = 0; i < x->bmerVis.n; ++i)
// {
// fprintf(stderr, "(label)utg%.6dl: %u, (num)%u\n", (int)(i+1), bub->index[i], bub->num.n);
// }
/*******************************for debug************************************/
}
void clean_hap(hc_links* link, bubble_type* bub, const ma_ug_t *ug)
{
min_cut_t x;
@@ -2286,6 +2399,10 @@ void clean_hap(hc_links* link, bubble_type* bub, const ma_ug_t *ug)
/*******************************for debug************************************/
if(!select_large_node(ug, &x, x.src, x.dest, 10, 10)) continue;
get_bmer_unitgs(&x, bub, x.b_mer, x.src);
x.bmerVis.a[x.src] = x.bmerVis.a[x.dest] = 1;
/*******************************for debug************************************/
graph_cut(x.src, x.dest, &x);