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chhylp123
2021-09-26 13:51:13 -04:00
parent ed814abf35
commit 7dd4a848b9
13 changed files with 2747 additions and 61 deletions
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Overlaps.cpp
+106 -21
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@@ -13090,6 +13090,61 @@ void hic_clean(asg_t* read_g)
kv_destroy(ax);
}
void update_poly_trio(uint32_t mm, uint32_t *hapS, uint32_t rn)
{
uint32_t i;
for (i = 0; i < rn; i++) {
if(R_INF.trio_flag[i] == DROP) continue;
R_INF.trio_flag[i] = AMBIGU;
if(!hapS[i]) continue;
R_INF.trio_flag[i] = (hapS[i]&mm?FATHER:MOTHER);
}
}
void debug_hapS(uint32_t *hapS, uint32_t rn)
{
uint32_t i, p, tot, nt, max_tot = 0, *occ = NULL, *freq = NULL;
for (i = 0; i < rn; i++) {
for (p = hapS[i], tot = 0; p; p>>=1, tot++);
max_tot = MAX(max_tot, tot);
}
fprintf(stderr, "[M::%s:] ==> %u haplotypes in total\n", __func__, max_tot);
if(max_tot){
CALLOC(occ, max_tot+1);
CALLOC(freq, max_tot+1);
for (i = 0; i < rn; i++) {
for (p = hapS[i], tot = nt = 0; p; p>>=1, tot++){
if(p&1) occ[tot+1]++, nt++;
}
freq[nt]++;
}
for (i = 1; i <= max_tot; i++) {
fprintf(stderr, "[M::%s:] ==> # reads in hap%u: %u\n", __func__, i, occ[i]);
}
for (i = 0; i <= max_tot; i++) {
fprintf(stderr, "[M::%s:] ==> # reads within %u haplotypes: %u\n", __func__, i, freq[i]);
}
free(occ); free(freq);
}
}
void output_poly_trio(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, uint32_t hapN)
{
uint32_t i;
uint32_t *hapS = ha_polybin_list(&asm_opt);
// debug_hapS(hapS, sg->n_seq);
char *fp = NULL; MALLOC(fp, 100);
for (i = 0; i < hapN; i++){
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);
}
free(fp); free(hapS);
}
void output_contig_graph_alternative(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp);
void clean_u_trans_t_idx(kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g);
@@ -13212,9 +13267,9 @@ 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);
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t, 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);
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t, NULL);
if(rhits)
{
ha_aware_order(rhits, sg, ug_fa, ug_mo, cov?&(cov->t_ch->k_trans):&(t_ch->k_trans), &opt, 3);
@@ -13320,9 +13375,9 @@ 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);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, 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);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL);
}
void set_trio_flag_by_cov(ma_ug_t *ug, asg_t *read_g, hap_cov_t *cov)
@@ -14117,9 +14172,9 @@ 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);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, 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);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL);
}
ma_ug_t* merge_utg(ma_ug_t **dest, ma_ug_t **src)
@@ -14186,11 +14241,11 @@ 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);
chimeric_rate, drop_ratio, max_hang, min_ovlp, 1, b_mask_t, 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);
chimeric_rate, drop_ratio, max_hang, min_ovlp, 1, b_mask_t, 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);
@@ -15258,10 +15313,7 @@ hap_cov_t *cov, utg_trans_t *o)
uint8_t if_primary_unitig(ma_utg_t* u, asg_t* read_g, ma_sub_t* coverage_cut,
ma_hit_t_alloc* sources, R_to_U* ruIndex, uint8_t* r_flag)
{
if(asm_opt.recover_atg_cov_min < 0 || asm_opt.recover_atg_cov_max < 0)
{
return 0;
}
if(asm_opt.recover_atg_cov_min < 0 || asm_opt.recover_atg_cov_max < 0) return 0;
long long R_bases = 0, C_bases = 0, C_bases_primary = 0, C_bases_alter = 0;
long long total_C_bases = 0, total_C_bases_primary = 0;
uint32_t available_reads = 0, k, j, rId, tn, is_Unitig;
@@ -15979,7 +16031,7 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate, hap_cov_t *cov)
cut_trio_tip_primary(g, ug, tipsLen, trio_flag, 0, read_g, reverse_sources, ruIndex, cov->is_r_het, 2);
}
///print_debug_gfa(read_g, ug, coverage_cut, "debug_dups", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
// 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);
@@ -16870,6 +16922,31 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex)
return u_flag;
}
void purge_dump(ma_ug_t* ug)
{
asg_t* nsg = ug->g;
uint32_t v, n_vtx = nsg->n_seq, k, rId;
ma_utg_t *u = NULL;
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 = 0; k < u->n; k++){
rId = u->a[k]>>33;
if(R_INF.trio_flag[rId] != AMBIGU && R_INF.trio_flag[rId] != DROP) break;
}
if(k >= u->n){
if(u->m != 0){
u->circ = u->end = u->len = u->m = u->n = u->start = 0;
free(u->a);
u->a = NULL;
}
asg_seq_del(nsg, v);
}
}
asg_cleanup(nsg);
}
void adjust_utg_by_trio(ma_ug_t **ug, asg_t* read_g, uint8_t flag, float drop_rate,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, ma_sub_t* coverage_cut,
@@ -16974,6 +17051,7 @@ kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t)
set_drop_trio_flag(*ug);
destory_hap_cov_t(&cov);
// purge_dump(*ug);
renew_utg(ug, read_g, new_rtg_edges);
}
@@ -16999,10 +17077,11 @@ int debug_untig_length(ma_ug_t *g, uint32_t tipsLen, const char* name)
ma_ug_t* output_trio_unitig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
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)
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* gfa_name = (char*)malloc(strlen(output_file_name)+100);
sprintf(gfa_name, "%s.%s.p_ctg.gfa", output_file_name, (flag==FATHER?"hap1":"hap2"));
sprintf(gfa_name, "%s.%s.p_ctg.gfa", output_file_name, f_prefix?f_prefix:(flag==FATHER?"hap1":"hap2"));
FILE* output_file = NULL;
if(is_bench == 0) output_file = fopen(gfa_name, "w");
@@ -17043,13 +17122,13 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench,
ma_ug_print(ug, sg, coverage_cut, sources, ruIndex, (flag==FATHER?"h1tg":"h2tg"), output_file);
fclose(output_file);
sprintf(gfa_name, "%s.%s.p_ctg.noseq.gfa", output_file_name, (flag==FATHER?"hap1":"hap2"));
sprintf(gfa_name, "%s.%s.p_ctg.noseq.gfa", output_file_name, f_prefix?f_prefix:(flag==FATHER?"hap1":"hap2"));
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, sg, coverage_cut, sources, ruIndex, (flag==FATHER?"h1tg":"h2tg"), output_file);
fclose(output_file);
if(asm_opt.bed_inconsist_rate != 0)
{
sprintf(gfa_name, "%s.%s.p_ctg.lowQ.bed", output_file_name, (flag==FATHER?"hap1":"hap2"));
sprintf(gfa_name, "%s.%s.p_ctg.lowQ.bed", output_file_name, f_prefix?f_prefix:(flag==FATHER?"hap1":"hap2"));
output_file = fopen(gfa_name, "w");
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges,
max_hang, min_ovlp, asm_opt.bed_inconsist_rate, (flag==FATHER?"h1tg":"h2tg"), output_file, NULL);
@@ -30888,8 +30967,14 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
write_debug_graph(sg, sources, coverage_cut, output_file_name, n_read, reverse_sources, ruIndex);
debug_gfa:;
}
if (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))
if(asm_opt.fn_bin_poy)
{
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;
output_poly_trio(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, asm_opt.polyploidy);
}
else if (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))
{
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;
benchmark_hic_graph(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3,
@@ -30900,10 +30985,10 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
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);
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);
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t, NULL);
}
else if(ha_opt_hic(&asm_opt))
{