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chhylp123
2021-11-29 15:11:02 -05:00
parent 763634e1a9
commit 1e2a9518e5
3 changed files with 86 additions and 20 deletions
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Overlaps.cpp
+84 -18
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@@ -13174,7 +13174,7 @@ bub_label_t* b_mask_t, uint32_t hapN)
update_poly_trio(1<<i, hapS, sg->n_seq);
sprintf(fp, "hap%u", i+1);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, tipsLen, tip_drop_ratio,
stops_threshold, ruIndex, chimeric_rate, drop_ratio, max_hang, min_ovlp, is_bench, b_mask_t, fp);
stops_threshold, ruIndex, chimeric_rate, drop_ratio, max_hang, min_ovlp, is_bench, b_mask_t, fp, NULL, NULL);
}
free(fp); free(hapS);
}
@@ -13353,9 +13353,9 @@ long long gap_fuzz, bub_label_t* b_mask_t)
reduce_hamming_error(sg, sources, coverage_cut, max_hang, min_ovlp, gap_fuzz);
ug_fa = output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t, NULL);
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t, NULL, NULL, NULL);
ug_mo = output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t, NULL);
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t, NULL, NULL, NULL);
if(rhits)
{
ha_aware_order(rhits, sg, ug_fa, ug_mo, cov?&(cov->t_ch->k_trans):&(t_ch->k_trans), &opt, 3);
@@ -13612,9 +13612,9 @@ long long gap_fuzz, bub_label_t* b_mask_t)
reduce_hamming_error(sg, sources, coverage_cut, max_hang, min_ovlp, gap_fuzz);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL, NULL, NULL);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL, NULL, NULL);
}
void set_trio_flag_by_cov(ma_ug_t *ug, asg_t *read_g, hap_cov_t *cov)
@@ -14409,9 +14409,9 @@ bub_label_t* b_mask_t)
kv_destroy(new_rtg_edges.a);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL, NULL, NULL);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL, NULL, NULL);
}
ma_ug_t* merge_utg(ma_ug_t **dest, ma_ug_t **src)
@@ -14478,11 +14478,11 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, bub_label_t*
{
ma_ug_t *ug_1 = output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources,
reverse_sources, tipsLen, tip_drop_ratio, stops_threshold, ruIndex,
chimeric_rate, drop_ratio, max_hang, min_ovlp, 1, b_mask_t, NULL);
chimeric_rate, drop_ratio, max_hang, min_ovlp, 1, b_mask_t, NULL, NULL, NULL);
ma_ug_t *ug_2 = output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources,
reverse_sources, tipsLen, tip_drop_ratio, stops_threshold, ruIndex,
chimeric_rate, drop_ratio, max_hang, min_ovlp, 1, b_mask_t, NULL);
chimeric_rate, drop_ratio, max_hang, min_ovlp, 1, b_mask_t, NULL, NULL, NULL);
fprintf(stderr, "ug_1->u.n: %u, ug_2->u.n: %u\n", (uint32_t)ug_1->u.n, (uint32_t)ug_2->u.n);
ma_ug_t *ug = merge_utg(&ug_1, &ug_2);
fprintf(stderr, "ug->u.n: %u\n", (uint32_t)ug->u.n);
@@ -17325,7 +17325,7 @@ ma_ug_t* output_trio_unitig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* outpu
uint8_t flag, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long tipsLen, float tip_drop_ratio, long long stops_threshold, R_to_U* ruIndex,
float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench, bub_label_t* b_mask_t,
char *f_prefix)
char *f_prefix, uint8_t *kpt_buf, kvec_asg_arc_t_warp *r_edges)
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+100);
sprintf(gfa_name, "%s.%s.p_ctg.gfa", output_file_name, f_prefix?f_prefix:(flag==FATHER?"hap1":"hap2"));
@@ -17354,12 +17354,23 @@ char *f_prefix)
NULL, &asm_opt.b_high_cov, asm_opt.m_rate);
}
if(kpt_buf)
{
update_dump_trio(R_INF.trio_flag, sg->n_seq, kpt_buf, ug);
}
if(is_bench)
{
free(gfa_name);
if(r_edges && new_rtg_edges.a.n > 0) {
kv_resize(asg_arc_t, r_edges->a, r_edges->a.n + new_rtg_edges.a.n);
memcpy(r_edges->a.a + r_edges->a.n, new_rtg_edges.a.a, new_rtg_edges.a.n*sizeof(asg_arc_t));
r_edges->a.n += new_rtg_edges.a.n;
}
kv_destroy(new_rtg_edges.a);
return ug;
}
fprintf(stderr, "Writing %s to disk... \n", gfa_name);
///debug_utg_graph(ug, sg, 0, 0);
///debug_untig_length(ug, tipsLen, gfa_name);
@@ -17388,19 +17399,78 @@ char *f_prefix)
return NULL;
}
void filter_set_kug(uint8_t* trio_flag, asg_t *rg, uint8_t *rf, kvec_asg_arc_t_warp *r_edges, float f_rate, ma_ug_t **ug)
{
asg_t* nsg = (*ug)->g; ma_utg_t *u = NULL;
uint32_t k, v, n_vtx = nsg->n_seq, rn = rg->n_seq;
int64_t flag_occ;
for (k = 0; k < rn; k++) {
trio_flag[k] = rf[k]>>1;
if(trio_flag[k] != FATHER && trio_flag[k] != MOTHER) trio_flag[k] = AMBIGU;
}
for (k = 0; k < nsg->n_arc; k++) nsg->arc[k].del = 1;
for (v = 0; v < n_vtx; ++v) {
if (nsg->seq[v].del) continue;
u = &((*ug)->u.a[v]);
if(u->m == 0) continue;
for (k = flag_occ = 0; k < u->n; k++) flag_occ += (rf[u->a[k]>>33]&1);
if (flag_occ == (int64_t)u->n || flag_occ >= (int64_t)(u->n*f_rate)) {
if(u->m != 0){
u->circ = u->end = u->len = u->m = u->n = u->start = 0;
free(u->a);
u->a = NULL;
}
nsg->seq[v].del = 1;
}
}
asg_cleanup(nsg);
renew_utg(ug, rg, r_edges);
char name[32];
for (v = 0, n_vtx = (*ug)->g->n_seq; v < n_vtx; ++v) {
u = &((*ug)->u.a[v]);
if(u->m == 0) continue;
for (k = flag_occ = 0; k < u->n; k++) flag_occ += (rf[u->a[k]>>33]&1);
sprintf(name, "ptg%.6d%c", v + 1, "lc"[u->circ]);
fprintf(stderr, "S\t%s\t*\tTN:i:%u\tUN:i:%ld\n", name, u->n, flag_occ);
}
}
void output_trio_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long tipsLen, float tip_drop_ratio, long long stops_threshold, R_to_U* ruIndex,
float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench, bub_label_t* b_mask_t)
{
uint8_t *rf = NULL;
if(asm_opt.kpt_rate > 0) CALLOC(rf, sg->n_seq);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources,
reverse_sources, tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate,
drop_ratio, max_hang, min_ovlp, is_bench, b_mask_t, NULL);
drop_ratio, max_hang, min_ovlp, is_bench, b_mask_t, NULL, rf, NULL);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources,
reverse_sources, tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate,
drop_ratio, max_hang, min_ovlp, is_bench, b_mask_t, NULL);
drop_ratio, max_hang, min_ovlp, is_bench, b_mask_t, NULL, rf, NULL);
if(rf) {
kvec_asg_arc_t_warp r_edges; kv_init(r_edges.a);
ma_ug_t *kug = NULL;
char* kug_n = (char*)malloc(strlen(output_file_name)+100);
sprintf(kug_n, "%s.kdp", output_file_name);
update_dump_trio(R_INF.trio_flag, sg->n_seq, rf, NULL);
kug = output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources,
reverse_sources, tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate,
drop_ratio, max_hang, min_ovlp, 1, b_mask_t, NULL, NULL, &r_edges);
filter_set_kug(R_INF.trio_flag, sg, rf, &r_edges, asm_opt.kpt_rate, &kug);
print_utg(kug, sg, coverage_cut, kug_n, sources, ruIndex, max_hang, min_ovlp, &r_edges);
free(kug_n), kv_destroy(r_edges.a); ma_ug_destroy(kug);
free(rf);
}
}
void output_read_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name, long long n_read)
@@ -31256,12 +31326,8 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
else if (ha_opt_triobin(&asm_opt))
{
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;
output_trio_unitig_graph(sg, coverage_cut, o_file, FATHER, sources,
reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t, NULL);
output_trio_unitig_graph(sg, coverage_cut, o_file, MOTHER, sources,
reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t, NULL);
output_trio_graph(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2),
0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t);
}
else if(ha_opt_hic(&asm_opt))
{