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chhylp123
2021-09-10 17:17:44 -04:00
parent 17b5cb21d3
commit 809ca18dda
18 changed files with 1569 additions and 1031 deletions
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100
Overlaps.cpp
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@@ -1475,14 +1475,6 @@ R_to_U* ruIndex, int max_hang, int min_ovlp)
delete_all_edges(sources, coverage_cut, Get_qn(*h));
set_R_to_U(ruIndex, Get_qn(*h), Get_tn(*h), 0, NULL);
// if(delete_all_edges_carefully(sources, coverage_cut, max_hang, min_ovlp,
// Get_qn(*h))==0)
// {
// set_R_to_U(ruIndex, Get_qn(*h), Get_tn(*h), 0);
// }
// sq->del = 1;
// set_R_to_U(ruIndex, Get_qn(*h), Get_tn(*h), 0);
}
else if (r == MA_HT_TCONT)
{
@@ -1491,15 +1483,6 @@ R_to_U* ruIndex, int max_hang, int min_ovlp)
delete_all_edges(sources, coverage_cut, Get_tn(*h));
set_R_to_U(ruIndex, Get_tn(*h), Get_qn(*h), 0, NULL);
// if(delete_all_edges_carefully(sources, coverage_cut, max_hang,
// min_ovlp, Get_tn(*h)) == 0)
// {
// set_R_to_U(ruIndex, Get_tn(*h), Get_qn(*h), 0);
// no_fully_tn_num++;
// }
// st->del = 1;
// set_R_to_U(ruIndex, Get_tn(*h), Get_qn(*h), 0);
}
}
}
@@ -9673,7 +9656,7 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, uint8_t* r_flag)
r_flag[rId] = 0;
}
return C_bases/R_bases;
return R_bases == 0? 0:C_bases/R_bases;
}
uint32_t get_ug_coverage_aggressive(ma_ug_t *ug, uint32_t uID, asg_t* read_g,
@@ -13158,7 +13141,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
///asm_opt.purge_simi_thres = asm_opt.purge_simi_rate_hic;
adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1, 1/**0**/);
max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1, 0);
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
@@ -13182,7 +13165,6 @@ long long gap_fuzz, bub_label_t* b_mask_t)
}
// char* gfa_name = (char*)malloc(strlen(output_file_name)+50);
// FILE* output_file = NULL;
// 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, sg, coverage_cut, sources, ruIndex, "utg", output_file);
@@ -13744,7 +13726,7 @@ void kt_u_trans_t_symm(kv_u_trans_t *ta, ma_ug_t *ug)
if (i == n || a[i].tn != a[st].tn)
{
get_u_trans_spec(ta, a[st].tn, a[st].qn, &r_a, &r_n);
if(i - st == 1 && r_n == 0)
if(i - st == 1 && r_n == 0)///should be always here
{
st = i;
continue;
@@ -14811,9 +14793,37 @@ void label_r_set(buf_t* b, R_to_U* ruIndex, ma_ug_t *ug, uint32_t flag)
}
}
inline int trio_check(ma_ug_t *ug, uint32_t *a, uint32_t a_n, uint32_t flag)
{
if(flag != FATHER && flag != MOTHER) return 0;
uint32_t flag_occ = 0, non_flag_occ = 0, ambigious = 0, u_n = 0, f, nf, ab, k;
for (k = 0; k < a_n; k++) {
get_unitig_trio_flag(&(ug->u.a[a[k]>>1]), flag, &f, &nf, &ab);
flag_occ += f;
non_flag_occ += nf;
ambigious += ab;
u_n += ug->u.a[a[k]>>1].n;
}
if((flag_occ+non_flag_occ) == 0) return 0;
if(flag_occ <= ((non_flag_occ+flag_occ)*0.75)) return 0;
if(non_flag_occ == 0 && flag_occ >= 20) return 1;
if(u_n >= 100)
{
if(flag_occ < u_n*DOUBLE_CHECK_THRES) return 0;
}
else if(u_n >= 50)
{
if(flag_occ < u_n*DOUBLE_CHECK_THRES*0.5) return 0;
}
else
{
if(flag_occ < u_n*DOUBLE_CHECK_THRES*0.25) return 0;
}
return 1;
}
int asg_arc_cut_trio_long_tip_primary(asg_t *g, ma_ug_t *ug, asg_t *read_sg, ma_hit_t_alloc* reverse_sources,
R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, hap_cov_t *cov, utg_trans_t *o)
R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, uint32_t trio_flag, hap_cov_t *cov, utg_trans_t *o)
{
double startTime = Get_T();
///the reason is that each read has two direction (query->target, target->query)
@@ -14874,6 +14884,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, hap_cov_t *cov, utg
}
if(ll >= (v_maxLen*drop_ratio)) continue;
if(trio_check(ug, b.b.a, b.b.n, trio_flag)) continue;
n_reduced++;
operation = TRIM;
@@ -14934,7 +14945,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, hap_cov_t *cov, utg
}
int asg_arc_cut_trio_long_tip_primary_complex(asg_t *g, ma_ug_t *ug, asg_t *read_sg, ma_hit_t_alloc* reverse_sources,
R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, uint32_t stops_threshold, hap_cov_t *cov, utg_trans_t *o)
R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, uint32_t stops_threshold, hap_cov_t *cov, utg_trans_t *o, uint32_t trio_flag)
{
double startTime = Get_T();
uint32_t v, n_vtx = g->n_seq * 2, n_reduced = 0, convex, in, flag, operation;
@@ -14958,6 +14969,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, uint32_t stops_thre
&max_stop_baseLen, 1, &b);
if(return_flag != MUL_INPUT) continue;
if(trio_check(ug, b.b.a, b.b.n, trio_flag)) continue;
in = convex^1;
get_real_length(g, convex, &convex);
convex = convex^1;
@@ -15177,17 +15189,11 @@ hap_cov_t *cov, utg_trans_t *o)
&max_stop_baseLen, 1, &b);
if(return_flag != END_TIPS) continue;
if(trio_check(ug, b.b.a, b.b.n, trio_flag)) continue;
flag = check_different_haps(g, ug, read_sg, av[base_maxLen_i].v, av[i].v,
reverse_sources, &b_0, &b_1, ruIndex, cov->is_r_het, miniedgeLen, 1);
// if((av[i].v>>1) == 255 && (av[base_maxLen_i].v>>1) == 33)
// if((av[i].v>>1) == 1852 && (av[base_maxLen_i].v>>1) == 2441)
// {
// fprintf(stderr, "max-utg%.6ul (%u), p-utg%.6ul (%u)\n",
// (av[base_maxLen_i].v>>1)+1, av[base_maxLen_i].v, (av[i].v>>1)+1, av[i].v);
// }
// #define UNAVAILABLE (uint32_t)-1
// #define PLOID 0
// #define NON_PLOID 1
@@ -15445,7 +15451,7 @@ R_to_U* ruIndex, uint32_t positive_flag, float drop_rate)
int asg_arc_cut_trio_long_equal_tips_assembly_complex(asg_t *g, ma_ug_t *ug, asg_t *read_sg,
ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex, uint32_t stops_threshold,
hap_cov_t *cov, utg_trans_t *o)
hap_cov_t *cov, utg_trans_t *o, uint32_t trio_flag)
{
double startTime = Get_T();
uint32_t v, n_vtx = g->n_seq * 2, n_reduced = 0, convex, in, flag;
@@ -15471,6 +15477,7 @@ hap_cov_t *cov, utg_trans_t *o)
&max_stop_baseLen, 1, &b);
if(return_flag != MUL_INPUT) continue;
if(trio_check(ug, b.b.a, b.b.n, trio_flag)) continue;
in = convex^1;
get_real_length(g, convex, &convex);
convex = convex^1;
@@ -15955,10 +15962,11 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate, hap_cov_t *cov)
if(just_bubble_pop == 0)
{
///need consider tangles
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, cov, NULL);
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, trio_flag, cov, NULL);
// if(trio_flag == MOTHER) print_debug_gfa(read_g, ug, coverage_cut, "debug_dups", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, trio_flag, cov, NULL);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, cov, NULL);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, cov, NULL);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, cov, NULL, trio_flag);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, cov, NULL, trio_flag);
detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate, ruIndex, NULL, cov->is_r_het);
///need consider tangles
///note we need both the read graph and the untig graph
@@ -15972,10 +15980,11 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate, hap_cov_t *cov)
}
///print_debug_gfa(read_g, ug, coverage_cut, "debug_dups", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
magic_trio_phasing(g, ug, read_g, coverage_cut, sources, reverse_sources, 2, ruIndex, trio_flag, trio_drop_rate);
resolve_tangles(ug, read_g, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, cov->is_r_het, trio_flag, drop_ratio);
drop_semi_circle(ug, g, read_g, reverse_sources, ruIndex, cov->is_r_het);
all_to_all_deduplicate(ug, read_g, coverage_cut, sources, trio_flag, trio_drop_rate, reverse_sources, ruIndex, cov->is_r_het, DOUBLE_CHECK_THRES, asm_opt.trio_flag_occ_thres);
// if(trio_flag == MOTHER) print_untig_by_read(ug, "m54329U_190827_173812/30214441/ccs", (uint32_t)-1, NULL, NULL, "bf-16");
if(is_first)
{
is_first = 0;
@@ -16031,10 +16040,10 @@ int just_bubble_pop, float drop_ratio, hap_cov_t *cov)
if(just_bubble_pop == 0)
{
///need consider tangles
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, cov, NULL);
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, (uint32_t)-1, cov, NULL);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, cov, NULL);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, cov, NULL);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, cov, NULL);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, cov, NULL, (uint32_t)-1);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, cov, NULL, (uint32_t)-1);
detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate, ruIndex, NULL, cov->is_r_het);
if(round != T_ROUND)
{
@@ -16094,10 +16103,10 @@ int min_ovlp, hap_cov_t *cov)
asg_pop_bubble_primary_trio(ug, NULL, (uint32_t)-1, DROP, cov, o, 1);
///need consider tangles
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, cov, o);
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, (uint32_t)-1, cov, o);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, cov, o);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, cov, o);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, cov, o);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, cov, o, (uint32_t)-1);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, cov, o, (uint32_t)-1);
detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate, ruIndex, o, cov->is_r_het);
cur_cons = get_graph_statistic(g);
@@ -23920,6 +23929,8 @@ int write_ruIndex(R_to_U* ruIndex, char* read_file_name)
fwrite(ruIndex->index, sizeof(ruIndex->index[0]), ruIndex->len, fp);
fwrite(R_INF.trio_flag, sizeof(R_INF.trio_flag[0]), ruIndex->len, fp);
// fwrite(ruIndex->is_het, 1, ruIndex->len, fp);
fwrite(&(asm_opt.hom_global_coverage_set), sizeof(asm_opt.hom_global_coverage_set), 1, fp);
fwrite(&(asm_opt.hom_global_coverage), sizeof(asm_opt.hom_global_coverage), 1, fp);
free(index_name);
fflush(fp);
fclose(fp);
@@ -23947,6 +23958,9 @@ int load_ruIndex(R_to_U* ruIndex, char* read_file_name)
// CALLOC(ruIndex->is_het, ruIndex->len);
// f_flag += fread(ruIndex->is_het, 1, ruIndex->len, fp);
f_flag += fread(&(asm_opt.hom_global_coverage_set), sizeof(asm_opt.hom_global_coverage_set), 1, fp);
f_flag += fread(&(asm_opt.hom_global_coverage), sizeof(asm_opt.hom_global_coverage), 1, fp);
free(index_name);
fflush(fp);
fclose(fp);
@@ -24707,7 +24721,7 @@ uint32_t collect_p_trans, uint32_t collect_p_trans_f)
fprintf(stderr, "[M::%s] primary contig coverage range: [%d, infinity]\n",
__func__, asm_opt.recover_atg_cov_min);
}
skip_purge:
recover_utg_by_coverage(ug, read_g, coverage_cut, sources, ruIndex, cov->t_ch);
if(i_cov)
@@ -30869,12 +30883,10 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
output_contig_graph_primary_pre(sg, coverage_cut, o_file, sources, reverse_sources,
asm_opt.small_pop_bubble_size, asm_opt.max_short_tip, ruIndex, max_hang_length, mini_overlap_length);
if (asm_opt.flag & HA_F_VERBOSE_GFA)
{
write_debug_graph(sg, sources, coverage_cut, output_file_name, n_read, reverse_sources, ruIndex);
debug_gfa:;
set_hom_global_coverage(&asm_opt, sg, coverage_cut, sources, reverse_sources, ruIndex, max_hang_length, mini_overlap_length);
}
if (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))