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update 0.15.5

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chhylp123
2021-07-22 00:59:52 -04:00
parent a531a4cbda
commit 62b7418257
16 changed files with 1146 additions and 68 deletions
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horder.cpp
+98 -24
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@@ -454,6 +454,26 @@ void resolve_hit(uint64_t x, uint32_t rLen, uint64_t uID_bits, uint64_t pos_mode
if(end) (*end) = p_end + 1;
}
void idx_hits(kvec_pe_hit* hits, uint64_t n)
{
uint64_t k, l;
kv_resize(uint64_t, hits->idx, n);
hits->idx.n = n;
memset(hits->idx.a, 0, hits->idx.n*sizeof(uint64_t));
radix_sort_pe_hit_idx_hn1(hits->a.a, hits->a.a + hits->a.n);
for (k = 1, l = 0; k <= hits->a.n; ++k)
{
if (k == hits->a.n || (get_hit_suid(*hits, k) != get_hit_suid(*hits, l)))
{
if (k - l > 1) radix_sort_pe_hit_idx_hn2(hits->a.a + l, hits->a.a + k);
hits->idx.a[get_hit_suid(*hits, l)] = (uint64_t)l << 32 | (k - l);
l = k;
}
}
}
kvec_pe_hit *get_r_hits_for_trio(kvec_pe_hit *u_hits, asg_t* r_g, ma_ug_t* ug, bubble_type* bub, uint64_t uID_bits, uint64_t pos_mode)
{
kvec_pe_hit *r_hits = NULL;
@@ -674,6 +694,7 @@ void get_r_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, asg_t* r_g, ma_ug_t* u
r_hits->uID_bits = ubits;
r_hits->pos_mode = p_mode;
idx_hits(r_hits, r_g->n_seq);
}
uint64_t get_corresp_usite(uint64_t rid, uint64_t rpos, uint64_t rev, uint64_t rlen, u_hits_t *x, uint64_t ubits, uint64_t p_mode, kvec_t_u64_warp *buf)
@@ -694,26 +715,6 @@ uint64_t get_corresp_usite(uint64_t rid, uint64_t rpos, uint64_t rev, uint64_t r
return a_n;
}
void idx_hits(kvec_pe_hit* hits, uint64_t n)
{
uint64_t k, l;
kv_resize(uint64_t, hits->idx, n);
hits->idx.n = n;
memset(hits->idx.a, 0, hits->idx.n*sizeof(uint64_t));
radix_sort_pe_hit_idx_hn1(hits->a.a, hits->a.a + hits->a.n);
for (k = 1, l = 0; k <= hits->a.n; ++k)
{
if (k == hits->a.n || (get_hit_suid(*hits, k) != get_hit_suid(*hits, l)))
{
if (k - l > 1) radix_sort_pe_hit_idx_hn2(hits->a.a + l, hits->a.a + k);
hits->idx.a[get_hit_suid(*hits, l)] = (uint64_t)l << 32 | (k - l);
l = k;
}
}
}
void update_u_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, ma_ug_t* ug, asg_t* r_g)
{
u_hits_t x; memset(&x, 0, sizeof(x));
@@ -744,7 +745,7 @@ void update_u_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, ma_ug_t* ug, asg_t*
}
radix_sort_hit_aux_ruid(x.a, x.a + x.n);
x.idx.n = x.idx.m = (x.n?(x.a[x.n-1].ruid>>33)+1:0);
x.idx.n = x.idx.m = (x.n?(x.a[x.n-1].ruid>>33)+1:0);///how many unitigs
CALLOC(x.idx.a, x.idx.n);
for (k = 1, l = 0; k <= x.n; ++k)
{
@@ -2329,6 +2330,9 @@ void generate_haplotypes(horder_t *h, ug_opt_t *opt)
ug_1 = get_trio_unitig_graph(h->r_g, FATHER, opt);
ug_2 = get_trio_unitig_graph(h->r_g, MOTHER, opt);
// kv_push(uint64_t, h->occ, ug_1->u.n);
// kv_push(uint64_t, h->occ, ug_2->u.n);
h->ug = ug_1;
///update unitigs
@@ -2345,6 +2349,9 @@ void generate_haplotypes(horder_t *h, ug_opt_t *opt)
ma_ug_destroy(ug_2);
asg_destroy(h->ug->g);
h->ug->g = NULL;
// MALLOC(h->hf.a, h->ug->u.n); h->hf.n = h->hf.m = h->ug->u.n;
// for (i = 0; i < h->ug->u.n; i++) h->hf.a[i] = (i < h->occ.a[0]? 0 : 1);
}
osg_t *osg_init(void)
@@ -2726,7 +2733,7 @@ void update_scg(horder_t *h, trans_col_t *t_idx)
for (i = 0, e.n = 0; i < hits->a.n; i++)
{
if(!hits->a.a[i].id) continue;
if(!hits->a.a[i].id) continue;//hom hits
suid = get_hit_suid(*hits, i);
euid = get_hit_euid(*hits, i);
if(suid == euid) continue;
@@ -3773,6 +3780,8 @@ void scaffold_hap(horder_t *h, ug_opt_t *opt, trans_col_t *t_idx, uint32_t round
h->ug = get_trio_unitig_graph(h->r_g, flag, opt);
asg_destroy(h->ug->g);
h->ug->g = NULL;
// kv_push(uint64_t, h->occ, h->ug->u.n);
// CALLOC(h->hf.a, h->ug->u.n); h->hf.n = h->hf.m = h->ug->u.n;
print_N50(h->ug);
@@ -3795,6 +3804,51 @@ void scaffold_hap(horder_t *h, ug_opt_t *opt, trans_col_t *t_idx, uint32_t round
free(gfa_name);
}
void scaffold_ug(horder_t *h, ma_ug_t *ug, ug_opt_t *opt, uint32_t round, char *output_file_name, uint8_t flag)
{
uint32_t i;
kv_destroy(h->u_hits.a);
kv_destroy(h->u_hits.idx);
kv_destroy(h->u_hits.occ);
memset(&(h->u_hits), 0, sizeof(h->u_hits));
kv_destroy(h->avoid);
h->avoid.m = h->avoid.n = 0;
h->avoid.a = NULL;
osg_destroy(h->sg.g);
h->sg.g = NULL;
h->ug = ug;
asg_destroy(h->ug->g);
h->ug->g = NULL;
// kv_push(uint64_t, h->occ, h->ug->u.n);
// CALLOC(h->hf.a, h->ug->u.n); h->hf.n = h->hf.m = h->ug->u.n;
print_N50(h->ug);
fprintf(stderr, "[M::%s::]***0***\n", __func__);
for (i = 0; i < round; i++)
{
fprintf(stderr, "[M::%s::]*i->%u*\n", __func__, i);
update_u_hits(&(h->u_hits), &(h->r_hits), h->ug, h->r_g);
fprintf(stderr, "[M::%s::]**i->%u**\n", __func__, i);
update_scg(h, NULL);
fprintf(stderr, "[M::%s::]***i->%u***\n", __func__, i);
layout_scg(h, 1.001, 19);
fprintf(stderr, "[M::%s::]****i->%u****\n", __func__, i);
renew_scaffold(h);
fprintf(stderr, "[M::%s::]*****i->%u*****\n", __func__, i);
}
char* gfa_name = (char*)malloc(strlen(output_file_name)+100);
sprintf(gfa_name, "%s.%s", output_file_name, (flag==FATHER?"hap1":"hap2"));
print_scaffold(h->ug, h->r_g, opt->coverage_cut, gfa_name,
opt->sources, opt->reverse_sources, opt->tipsLen, opt->tip_drop_ratio,
opt->stops_threshold, opt->ruIndex, opt->chimeric_rate, opt->drop_ratio,
opt->max_hang, opt->min_ovlp);
free(gfa_name);
}
void output_hic_rtg(ma_ug_t *ug, asg_t *rg, ug_opt_t *opt, char* output_file_name)
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+50);
@@ -3817,13 +3871,13 @@ asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, kv_u_trans_t *ref, ug_opt_t *opt,
t_idx = init_trans_col(i_ug, h->r_g->n_seq, ref);
// output_hic_rtg(i_ug, h->r_g, opt, asm_opt.output_file_name);
// reduce_hamming_error(h->r_g, opt->sources, opt->coverage_cut, opt->max_hang, opt->min_ovlp, opt->gap_fuzz);
reduce_hamming_error(h->r_g, opt->sources, opt->coverage_cut, opt->max_hang, opt->min_ovlp, opt->gap_fuzz);
/**
scaffold_hap(h, t_idx, opt, round, asm_opt.output_file_name, FATHER);
scaffold_hap(h, t_idx, opt, round, asm_opt.output_file_name, MOTHER);
**/
generate_haplotypes(h, opt);
print_N50(h->ug);
@@ -3848,6 +3902,18 @@ asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, kv_u_trans_t *ref, ug_opt_t *opt,
return h;
}
void ha_aware_order(kvec_pe_hit *r_hits, asg_t *rg, ma_ug_t *ug_fa, ma_ug_t *ug_mo, kv_u_trans_t *ref,
ug_opt_t *opt, uint32_t round)
{
horder_t *h = NULL; CALLOC(h, 1);
h->r_hits = *r_hits;
h->r_g = rg;
scaffold_ug(h, ug_fa, opt, round, asm_opt.output_file_name, FATHER);
scaffold_ug(h, ug_mo, opt, round, asm_opt.output_file_name, MOTHER);
}
void destory_horder_t(horder_t **h)
{
kv_destroy((*h)->r_hits.a);
@@ -3865,4 +3931,12 @@ void destory_horder_t(horder_t **h)
ma_ug_destroy((*h)->ug);
asg_destroy((*h)->r_g);
free((*h));
}
kvec_pe_hit *get_r_hits_order(kvec_pe_hit *uhits, uint64_t hits_uid_bits, uint64_t hits_pos_mode,
asg_t *rg, ma_ug_t* ug, bubble_type* bub)
{
kvec_pe_hit *r_hits = NULL; CALLOC(r_hits, 1);
get_r_hits(uhits, r_hits, rg, ug, bub, hits_uid_bits, hits_pos_mode);
return r_hits;
}