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resolve centromere

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chhylp123
2021-05-06 07:59:51 -04:00
parent 24e5453781
commit 9ea4f6917f
5 changed files with 163 additions and 67 deletions
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Overlaps.cpp
+27 -33
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@@ -8994,8 +8994,8 @@ UC_Read* r_read, UC_Read* q_read, int max_hang, int min_ovlp, kvec_asg_arc_t_war
// generate unitig sequences
int ma_ug_seq(ma_ug_t *g, asg_t *read_g, All_reads *RNF, ma_sub_t *coverage_cut,
ma_hit_t_alloc* sources, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp, kvec_asg_arc_t_warp *E)
int ma_ug_seq(ma_ug_t *g, asg_t *read_g, ma_sub_t *coverage_cut, ma_hit_t_alloc* sources,
kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp, kvec_asg_arc_t_warp *E, uint32_t is_polish)
{
UC_Read g_read;
init_UC_Read(&g_read);
@@ -9013,8 +9013,12 @@ ma_hit_t_alloc* sources, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp,
for (i = 0; i < g->u.n; ++i) {
ma_utg_t *u = &g->u.a[i];
if(u->m == 0) continue;
polish_unitig(u, read_g, sources, coverage_cut, edge, max_hang, min_ovlp, E);
polish_unitig_advance(u, read_g, RNF, sources, coverage_cut, edge, &g_read, &tmp, max_hang, min_ovlp, E);
if(is_polish)
{
polish_unitig(u, read_g, sources, coverage_cut, edge, max_hang, min_ovlp, E);
polish_unitig_advance(u, read_g, &R_INF, sources, coverage_cut, edge, &g_read, &tmp, max_hang, min_ovlp, E);
}
g->g->seq[i].len = u->len;
uint32_t l = 0;
@@ -9031,12 +9035,12 @@ ma_hit_t_alloc* sources, kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp,
if(eLen == 0) continue;
if(rId < read_g->r_seq)
{
recover_UC_Read(&g_read, RNF, rId);
recover_UC_Read(&g_read, &R_INF, rId);
}
else
{
recover_fake_read(&g_read, &tmp, &(read_g->F_seq[rId-read_g->r_seq]),
RNF, coverage_cut);
&R_INF, coverage_cut);
}
readS = g_read.seq + coverage_cut[rId].s;
@@ -12153,7 +12157,7 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
ma_ug_t *ug = NULL;
ug = ma_ug_gen(sg);
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0);
ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
fprintf(stderr, "Writing raw unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
@@ -12493,7 +12497,7 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp, kvec_asg_a
NULL, &asm_opt.b_high_cov, asm_opt.m_rate);
}
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, new_rtg_edges, max_hang, min_ovlp, 0);
ma_ug_seq(ug, sg, coverage_cut, sources, new_rtg_edges, max_hang, min_ovlp, 0, 1);
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
@@ -12723,7 +12727,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
new_rtg_edges.a.n = 0;
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, &d_edges);///polish
ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, &d_edges, 1);///polish
hap_cov_t *cov = NULL;
@@ -12763,7 +12767,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
}
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.clean_d_utg.noseq.gfa", output_file_name);
sprintf(gfa_name, "%s.pre.clean_d_utg.noseq.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "utg", output_file);
fclose(output_file);
@@ -12774,6 +12778,14 @@ long long gap_fuzz, bub_label_t* b_mask_t)
if(cov) destory_hap_cov_t(&cov);
if(t_ch) destory_trans_chain(&t_ch);
gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.after.clean_d_utg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "utg", output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a);
@@ -13752,7 +13764,7 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
}
}
ma_ug_seq(ug, read_g, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0);
ma_ug_seq(ug, read_g, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
fprintf(stderr, "Writing raw unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
@@ -16160,7 +16172,7 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench,
///debug_utg_graph(ug, sg, 0, 0);
///debug_untig_length(ug, tipsLen, gfa_name);
///print_untig_by_read(ug, "m64011_190901_095311/125831121/ccs", 2310925, "end");
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0);
ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
if(is_bench)
{
free(gfa_name);
@@ -18831,24 +18843,6 @@ long long asg_arc_del_simple_circle_untig(ma_hit_t_alloc* sources, ma_sub_t* cov
}
uint32_t* build_unitig_index(asg_t *sg, ma_ug_t *ug)
{
if(sg == NULL && ug == NULL) return NULL;
uint32_t* index = (uint32_t*)calloc(sg->n_seq, sizeof(uint32_t));
uint32_t i, j;
for (i = 0; i < ug->u.n; ++i)
{
ma_utg_t *u = &(ug->u.a[i]);
for (j = 0; j < u->n; j++)
{
index[(u->a[j]>>33)] = i;
}
}
return index;
}
int double_check_tangle(uint32_t vBeg, uint32_t vEnd, uint32_t* u_vecs, uint32_t n, asg_t *nsg)
{
uint32_t v, nv, k, i, j;
@@ -24049,7 +24043,7 @@ R_to_U* ruIndex, int max_hang, int min_ovlp)
}
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0);
ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
fprintf(stderr, "Writing processed unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
@@ -24100,7 +24094,7 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, &new_rtg_edges, max_hang, min_ovlp,
NULL, &asm_opt.b_high_cov, asm_opt.m_rate);
}
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0);
ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
fprintf(stderr, "Writing primary contig GFA to disk... \n");
@@ -24144,7 +24138,7 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
// break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, &new_rtg_edges, max_hang, min_ovlp, asm_opt.b_low_cov);
// }
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0);
ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
fprintf(stderr, "Writing alternate contig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);