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chhylp123
2021-05-30 09:02:25 -04:00
parent a39f01f4d8
commit e774a83be2
18 changed files with 2497 additions and 207 deletions
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hic.cpp
+250 -34
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@@ -44,6 +44,11 @@ KRADIX_SORT_INIT(u_trans_occ, u_trans_t, u_trans_occ_key, member_size(u_trans_t,
#define is_hom_hit(a) ((a).id == (uint64_t)-1)
typedef struct {
kv_gg_status sg;
uint64_t xs;
} psg_t;
typedef struct{
kvec_t(char) name;
kvec_t(uint64_t) name_Len;
@@ -780,7 +785,9 @@ ha_ug_index* build_unitig_index(ma_ug_t *ug, int k, uint64_t up_occ, uint64_t lo
ha_ug_index* idx = NULL; CALLOC(idx, 1);
pldat_t pl; pl.h = idx; pl.is_cnt = 1;
double index_time = yak_realtime(), beg_time;
fprintf(stderr, "sa-0\n");
init_ha_ug_index_opt(idx, ug, k, &pl, up_occ, low_occ, thread_num);
fprintf(stderr, "sa-1\n");
beg_time = yak_realtime();
pl.is_cnt = 1;
@@ -2960,7 +2967,7 @@ uint32_t get_specific_shortest_path(pdq_spec *p)
{
pop_pdq(p->pq, &(p->v), &w);
p->pq->vis.a[p->v] = 1;
if(p->dest[p->v] == p->flag) p->occ++;
if(p->dest && p->dest[p->v] == p->flag) p->occ++;
if(p->occ > p->df_occ) return 0;
av = asg_arc_a(p->sg, p->v);
@@ -2979,7 +2986,8 @@ uint32_t get_specific_shortest_path(pdq_spec *p)
if(p->pre) p->pre[u] = p->v;
}
}
if(p->dest[p->v] == p->flag) return 1;
if(p->dest && p->dest[p->v] == p->flag) return 1;
if(!p->dest) return 1;
}
return 0;
@@ -3073,6 +3081,22 @@ double rate, long long *dis)
}
void set_utg_by_dis(uint32_t v, pdq* pq, asg_t *g, kvec_t_u32_warp *res, uint32_t dis)
{
uint64_t r;
pdq_spec a;
a.v = (uint64_t)-1; a.src = v; a.pq = pq; a.sg = g; a.df_occ = (uint64_t)-1;
a.occ = 0; a.flag = (uint8_t)-1; a.dest = NULL; a.pre = NULL;
reset_pdq(a.pq);
while (1)
{
r = get_specific_shortest_path(&a);
if(!r) return;
if(a.pq->dis.a[a.v] <= dis) kv_push(uint32_t, res->a, a.v);
else return;
}
}
uint64_t LCA_distance(long long d_x, long long d_y, long long xLen, long long yLen, uint8_t* rev)
{
(*rev) = 0;
@@ -9307,14 +9331,37 @@ void get_forward_distance(uint32_t src, uint32_t dest, asg_t *sg, hc_links* link
// ((e->dis>>2)&1)?"back":"forw", e->dis>>3);
}
uint32_t is_same_phase(uint64_t bid, uint64_t eid, H_partition* hap, int8_t *s, mc_gg_status *sa)
{
if(bid == eid) return 1;
if(hap || s)
{
int beg_status, end_status;
beg_status = (hap? get_phase_status(hap, bid):s[bid]);
if(beg_status != 1 && beg_status != -1) return (uint32_t)-1;
end_status = (hap? get_phase_status(hap, eid):s[eid]);
if(end_status != 1 && end_status != -1) return (uint32_t)-1;
if(beg_status == end_status) return 1;
return 0;
}
if(sa)
{
if(sa[bid].s == 0 || sa[eid].s == 0) return (uint32_t)-1;
return !!(sa[bid].s&sa[eid].s);
}
return (uint32_t)-1;
}
int get_trans_rate_function_advance(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type* bub,
H_partition* hap, int8_t *s, trans_idx* dis)
H_partition* hap, int8_t *s, mc_gg_status *sa, trans_idx* dis)
{
kvec_t(uint64_t) buf;
kv_init(buf);
uint64_t beg, end, cnt[2];
uint64_t k, i, t_d, r_idx, f_idx, med = (uint64_t)-1;
int beg_status, end_status;
uint32_t is_s;
// int beg_status, end_status;
buf.n = 0;
for (k = 0; k < hits->a.n; ++k)
@@ -9329,25 +9376,28 @@ H_partition* hap, int8_t *s, trans_idx* dis)
t_d = get_hic_distance(&(hits->a.a[k]), link, idx, NULL);
if(t_d == (uint64_t)-1) continue;
if(beg == end)
{
t_d = (t_d << 1);
}
else
{
beg_status = (hap? get_phase_status(hap, beg):s[beg]);
if(beg_status != 1 && beg_status != -1) continue;
end_status = (hap? get_phase_status(hap, end):s[end]);
if(end_status != 1 && end_status != -1) continue;
if(beg_status != end_status)
{
t_d = (t_d << 1) + 1;
}
else
{
t_d = (t_d << 1);
}
}
// if(beg == end)
// {
// t_d = (t_d << 1);
// }
// else
// {
// beg_status = (hap? get_phase_status(hap, beg):s[beg]);
// if(beg_status != 1 && beg_status != -1) continue;
// end_status = (hap? get_phase_status(hap, end):s[end]);
// if(end_status != 1 && end_status != -1) continue;
// if(beg_status != end_status)
// {
// t_d = (t_d << 1) + 1;
// }
// else
// {
// t_d = (t_d << 1);
// }
// }
is_s = is_same_phase(beg, end, hap, s, sa);
if(is_s == (uint32_t)-1) continue;
t_d = (t_d << 1) + 1 - is_s;
kv_push(uint64_t, buf, t_d);
}
@@ -9532,7 +9582,7 @@ void init_hic_advance(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubbl
if(bub->round_id > 0 && ignore_dis == 0)
{
is_comples_weight = get_trans_rate_function_advance(idx, hits, link, bub, hap, NULL, &dis);
is_comples_weight = get_trans_rate_function_advance(idx, hits, link, bub, hap, NULL, NULL, &dis);
}
@@ -14265,7 +14315,7 @@ void label_unitigs(G_partition* g_p, ma_ug_t* ug)
///fprintf(stderr, "# Mother reads: %lu\n", occ);
}
void label_unitigs_sm(int8_t *s, ma_ug_t* ug)
void label_unitigs_sm(int8_t *s, mc_gg_status *sa, ma_ug_t* ug)
{
memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads * sizeof(uint8_t));
uint32_t i, k, flag = AMBIGU;
@@ -14273,8 +14323,20 @@ void label_unitigs_sm(int8_t *s, ma_ug_t* ug)
for (i = 0; i < ug->g->n_seq; i++)
{
if(ug->g->seq[i].del || s[i] == 0) continue;
flag = (s[i] > 0? FATHER:MOTHER);
if(ug->g->seq[i].del) continue;
flag = 0;
if(s)
{
if(s[i] == 0) continue;
flag = (s[i] > 0? FATHER:MOTHER);
}
if(sa)
{
if(sa[i].s != 1 && sa[i].s != 2) continue;
flag = sa[i].s;
}
u = &ug->u.a[i];
if(u->m == 0) continue;
for (k = 0; k < u->n; k++)
@@ -15186,6 +15248,7 @@ void print_kv_weight(kv_u_trans_t *ta)
{
uint32_t i;
u_trans_t *e = NULL;
fprintf(stderr, "\n[M::%s]\n", __func__);
fprintf(stderr, "*********ta->n: %u\n", (uint32_t)ta->n);
for (i = 0; i < ta->n; i++)
{
@@ -15227,14 +15290,14 @@ void print_debug_hc_links(ha_ug_index* idx, bubble_type* bub, hc_links* lk, kv_u
}
}
void renew_kv_u_trans(kv_u_trans_t *ta, hc_links *lk, kvec_pe_hit* hits, kv_u_trans_t *ref,
ha_ug_index* idx, bubble_type* bub, int8_t *s, uint32_t ignore_dis)
ha_ug_index* idx, bubble_type* bub, int8_t *s, mc_gg_status *sa, uint32_t ignore_dis)
{
uint64_t k, i, m, is_comples_weight = 0;
trans_idx dis;
kv_init(dis);
if(bub->round_id > 0 && ignore_dis == 0)
{
is_comples_weight = get_trans_rate_function_advance(idx, hits, lk, bub, NULL, s, &dis);
is_comples_weight = get_trans_rate_function_advance(idx, hits, lk, bub, NULL, s, sa, &dis);
}
for (i = 0; i < lk->a.n; i++)
@@ -15635,21 +15698,21 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
if((asm_opt.flag & HA_F_VERBOSE_GFA) && load_ps_t(&s, asm_opt.output_file_name))
{
bub.round_id = bub.n_round;
label_unitigs_sm(s->s, idx->ug);
label_unitigs_sm(s->s, NULL, idx->ug);
goto skip_flipping;
}
s = init_ps_t(11, idx->ug->g->n_seq);
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
// identify_bubbles(idx->ug, &bub, idx->t_ch->is_r_het, &(idx->t_ch->k_trans));
renew_kv_u_trans(&k_trans, &link, &sl.hits, &(idx->t_ch->k_trans), idx, &bub, s->s, 0);
renew_kv_u_trans(&k_trans, &link, &sl.hits, &(idx->t_ch->k_trans), idx, &bub, s->s, NULL, 0);
// if(bub.round_id == 0) init_phase(idx, &k_trans, &bub, s);
// update_trans_g(idx, &k_trans, &bub);
/*******************************for debug************************************/
mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag,
(bub.round_id == 0? 1 : 0), s->s, 1, /**&bub**/NULL, &(idx->t_ch->k_trans));
/*******************************for debug************************************/
label_unitigs_sm(s->s, idx->ug);
label_unitigs_sm(s->s, NULL, idx->ug);
/*******************************for debug************************************/
// if(bub.round_id == bub.n_round - 1)
@@ -15670,6 +15733,8 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
skip_flipping:
verbose_het_stat(&bub);
print_kv_weight(&k_trans);
// horder_t *ho = init_horder_t(&sl.hits, idx->uID_bits, idx->pos_mode, idx->read_g, idx->ug, &bub, &(idx->t_ch->k_trans), opt, 3);
///print_hc_links(&link, 0, &hap);
@@ -15711,8 +15776,156 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
return 1;
}
int load_psg_t(psg_t **sg, const char *fn)
{
uint64_t flag = 0;
char *buf = (char*)calloc(strlen(fn) + 25, 1);
sprintf(buf, "%s.hic.pst.bin", fn);
FILE* fp = NULL;
fp = fopen(buf, "r");
if(!fp) return 0;
CALLOC(*sg, 1);
flag += fread(&((*sg)->xs), sizeof((*sg)->xs), 1, fp);
flag += fread(&((*sg)->sg.n), sizeof((*sg)->sg.n), 1, fp);
(*sg)->sg.m = (*sg)->sg.n;
MALLOC((*sg)->sg.a, (*sg)->sg.n);
flag += fread((*sg)->sg.a, sizeof(mc_gg_status), (*sg)->sg.n, fp);
void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch, ug_opt_t *opt)
fclose(fp);
free(buf);
return 1;
}
void write_psg_t(psg_t *sg, const char *fn)
{
char *buf = (char*)calloc(strlen(fn) + 25, 1);
sprintf(buf, "%s.hic.pst.bin", fn);
FILE* fp = fopen(buf, "w");
fwrite(&(sg->xs), sizeof(sg->xs), 1, fp);
fwrite(&(sg->sg.n), sizeof(sg->sg.n), 1, fp);
fwrite(sg->sg.a, sizeof(mc_gg_status), sg->sg.n, fp);
fclose(fp);
free(buf);
}
psg_t* init_psg_t(uint64_t seed, ma_ug_t* ug, asg_t* rg, ug_opt_t *opt)
{
psg_t *s = NULL; CALLOC(s, 1);
s->xs = seed;
kv_gg_status *sa = init_mc_gg_status(ug, rg, opt->coverage_cut, opt->sources, opt->ruIndex,
asm_opt.hom_global_coverage_set?asm_opt.hom_global_coverage:((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE),
asm_opt.polyploidy);
s->sg = *sa;
free(sa);
return s;
}
void destory_psg_t(psg_t **s)
{
free((*s)->sg.a);
free((*s));
}
int hic_short_align_poy(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_opt_t *opt)
{
double index_time = yak_realtime();
sldat_t sl;
kvec_hc_edge back_hc_edge;
kv_init(back_hc_edge.a);
sl.idx = idx;
sl.t_ch = idx->t_ch;
sl.chunk_size = 20000000;
sl.n_thread = asm_opt.thread_num;
sl.total_base = sl.total_pair = 0;
idx->hap_cnt = asm_opt.hap_occ;
kv_init(sl.hits.a); kv_init(sl.hits.idx); kv_init(sl.hits.occ);
if(!load_hc_hits(&sl.hits, asm_opt.output_file_name))
{
alignment_worker_pipeline(&sl, fn1, fn2);
write_hc_hits(&sl.hits, asm_opt.output_file_name);
}
hc_links link;
init_hc_links(&link, idx->ug->g->n_seq, idx->t_ch);
///H_partition hap;
bubble_type bub;
kv_u_trans_t k_trans;
kv_init(k_trans); kv_init(k_trans.idx);
psg_t *s = NULL;
mb_nodes_t u;
kv_init(u.bid); kv_init(u.idx); kv_init(u.u);
memset(&bub, 0, sizeof(bubble_type));
bub.round_id = 0; bub.n_round = asm_opt.n_weight;
resolve_tangles_hic(idx, &bub, &sl.hits, &k_trans);
measure_distance(idx, idx->ug, &sl.hits, &link, &bub, &(idx->t_ch->k_trans));
// if((asm_opt.flag & HA_F_VERBOSE_GFA) && load_psg_t(&s, asm_opt.output_file_name))
// {
// bub.round_id = bub.n_round;
// goto skip_flipping;
// }
s = init_psg_t(11, idx->ug, idx->read_g, opt);
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
// identify_bubbles(idx->ug, &bub, idx->t_ch->is_r_het, &(idx->t_ch->k_trans));
renew_kv_u_trans(&k_trans, &link, &sl.hits, &(idx->t_ch->k_trans), idx, &bub, NULL, s->sg.a, 0);
// if(bub.round_id == 0) init_phase(idx, &k_trans, &bub, s);
// update_trans_g(idx, &k_trans, &bub);
/*******************************for debug************************************/
mc_solve_general(&k_trans, idx->ug->u.n, &(s->sg), asm_opt.polyploidy, 0, 1);
/*******************************for debug************************************/
/*******************************for debug************************************/
// if(bub.round_id == bub.n_round - 1)
// {
// debug_output_disconnected_hits(idx, &k_trans, &sl.hits, &link, &bub, s->s);
// }
/*******************************for debug************************************/
}
// write_psg_t(s, asm_opt.output_file_name);
skip_flipping:
verbose_het_stat(&bub);
if(asm_opt.polyploidy == 2) label_unitigs_sm(NULL, s->sg.a, idx->ug);
// print_kv_weight(&k_trans);
// horder_t *ho = init_horder_t(&sl.hits, idx->uID_bits, idx->pos_mode, idx->read_g, idx->ug, &bub, &(idx->t_ch->k_trans), opt, 3);
///print_hc_links(&link, 0, &hap);
// print_kv_u_trans(&k_trans, &link, s->s);
///print_bubbles(idx->ug, &bub, sl.hits.a.n?&sl.hits:NULL, idx->link, idx);
///print_hits(idx, &sl.hits, fn1);
///print_debug_bubble_graph(&bub, idx->ug, asm_opt.output_file_name);
// print_bubble_chain(&bub);
// destory_contig_partition(&hap);
// destory_horder_t(&ho);
kv_destroy(back_hc_edge.a);
kv_destroy(sl.hits.a);
kv_destroy(sl.hits.idx);
kv_destroy(sl.hits.occ);
destory_hc_links(&link);
kv_destroy(k_trans);
kv_destroy(k_trans.idx);
destory_psg_t(&s);
kv_destroy(u.bid); kv_destroy(u.idx); kv_destroy(u.u);
fprintf(stderr, "[M::%s::%.3f] processed %lu pairs; %lu bases\n", __func__, yak_realtime()-index_time, sl.total_pair, sl.total_base);
return 1;
}
void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch, ug_opt_t *opt, uint32_t is_poy)
{
ug_index = NULL;
int exist = (asm_opt.load_index_from_disk?
@@ -15723,11 +15936,14 @@ void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch, ug_opt_t *opt)
ug_index->read_g = read_g;
ug_index->t_ch = t_ch;
///test_unitig_index(ug_index, ug);
hic_short_align(asm_opt.hic_reads[0], asm_opt.hic_reads[1], ug_index, opt);
if(!is_poy) hic_short_align(asm_opt.hic_reads[0], asm_opt.hic_reads[1], ug_index, opt);
else hic_short_align_poy(asm_opt.hic_reads[0], asm_opt.hic_reads[1], ug_index, opt);
destory_hc_pt_index(ug_index);
}
void init_ug_idx(ma_ug_t *ug, uint64_t k, uint64_t up_bound, uint64_t low_bound, uint64_t build_idx)
{
ug_index = NULL;