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kpt_dup

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chhylp123
2021-11-28 19:35:32 -05:00
parent 26aacdcc2c
commit 763634e1a9
7 changed files with 704 additions and 145 deletions
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Overlaps.cpp
+117 -2
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@@ -13091,6 +13091,40 @@ void hic_clean(asg_t* read_g)
kv_destroy(ax);
}
void update_dump_trio(uint8_t* trio_flag, uint32_t rn, uint8_t *rf, ma_ug_t *ug)
{
uint32_t k, i, x;
ma_utg_t *p = NULL;
if(ug) {
for (i = 0; i < ug->u.n; ++i) { // the Segment lines in GFA
p = &ug->u.a[i];
if(p->m == 0) continue;
for (k = 0; k < p->n; k++) {
x = p->a[k]>>33;
if(trio_flag[x] == FATHER || trio_flag[x] == MOTHER) {
rf[x] = trio_flag[x];
} else if(rf[x] != FATHER && rf[x] != MOTHER) {
rf[x] = DROP;
}
}
}
} else {
for (i = 0; i < rn; i++) {
if(rf[i]) {
rf[i] <<= 1; rf[i] += 1;
} else {
rf[i] = trio_flag[i]; rf[i] <<= 1;
}
if(trio_flag[i] == FATHER || trio_flag[i] == MOTHER) {
trio_flag[i] = ((rf[i]&1)?MOTHER:FATHER);
} else {
trio_flag[i] = ((rf[i]&1)?DROP:AMBIGU);
}
}
}
}
void update_poly_trio(uint32_t mm, uint32_t *hapS, uint32_t rn)
{
uint32_t i;
@@ -13145,6 +13179,58 @@ bub_label_t* b_mask_t, uint32_t hapN)
free(fp); free(hapS);
}
uint32_t test_dbug(ma_ug_t* ug, FILE* fp)
{
uint32_t f_flag = 0, t, i, r_flag = 0;
size_t tt;
ma_utg_t ua, *ub = NULL; memset(&ua, 0, sizeof(ua));
f_flag = fread(&tt, sizeof(tt), 1, fp);
if(f_flag == 0 || tt != ug->u.n) goto DES;
for (i = 0; i < tt; i++)
{
ub = &(ug->u.a[i]);
f_flag = fread(&t, sizeof(t), 1, fp);
if(f_flag == 0 || t != ub->len) goto DES;
f_flag = fread(&t, sizeof(t), 1, fp);
if(f_flag == 0 || t != ub->circ) goto DES;
f_flag = fread(&(ua.start), sizeof(ua.start), 1, fp);
if(f_flag == 0 || ua.start != ub->start) goto DES;
f_flag = fread(&(ua.end), sizeof(ua.end), 1, fp);
if(f_flag == 0 || ua.end != ub->end) goto DES;
f_flag = fread(&(ua.n), sizeof(ua.n), 1, fp);
if(f_flag == 0 || ua.n != ub->n) goto DES;
t = ua.n;
ua.n = 0;
kv_resize(uint64_t, ua, t);
ua.n = t;
f_flag = fread(ua.a, sizeof(uint64_t), ua.n, fp);
if(f_flag == 0 || memcmp(ua.a, ub->a, ua.n)) goto DES;
}
r_flag = 1;
DES:
free(ua.a);
return r_flag;
}
void write_dbug(ma_ug_t* ug, FILE* fp)
{
ma_utg_t *u = NULL;
uint32_t t, i;
fwrite(&(ug->u.n), sizeof(ug->u.n), 1, fp);
for (i = 0; i < ug->u.n; i++)
{
u = &(ug->u.a[i]);
t = u->len;
fwrite(&t, sizeof(t), 1, fp);
t = u->circ;
fwrite(&t, sizeof(t), 1, fp);
fwrite(&(u->start), sizeof(u->start), 1, fp);
fwrite(&(u->end), sizeof(u->end), 1, fp);
fwrite(&(u->n), sizeof(u->n), 1, fp);
fwrite(u->a, sizeof(uint64_t), u->n, fp);
}
}
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);
@@ -13198,7 +13284,6 @@ long long gap_fuzz, bub_label_t* b_mask_t)
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, 0);
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
@@ -13207,7 +13292,6 @@ long long gap_fuzz, bub_label_t* b_mask_t)
output_contig_graph_alternative(copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp);
}
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
@@ -13229,6 +13313,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
hic_analysis(ug, sg, cov?cov->t_ch:t_ch, &opt, 0, asm_opt.scffold?&rhits:NULL);
if(!rhits && cov) destory_hap_cov_t(&cov);
if(!rhits && t_ch) destory_trans_chain(&t_ch);
@@ -14696,6 +14781,16 @@ void print_untig(ma_ug_t *g, uint32_t uId, const char* info, uint32_t is_print_r
}
void reset_untig_hap_label(ma_ug_t *g, uint32_t uId, uint8_t trio_flag, uint8_t* bin_res)
{
uint32_t k;
ma_utg_t *u = &g->u.a[uId];
for (k = 0; k < u->n; k++) {
if(bin_res[u->a[k]>>33] == AMBIGU) bin_res[u->a[k]>>33] = trio_flag;
}
}
void print_read_all(ma_ug_t *ug, const char* name, ma_hit_t_alloc* sources,
ma_hit_t_alloc* reverse_sources, const char* info)
{
@@ -17294,6 +17389,20 @@ char *f_prefix)
}
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)
{
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);
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);
}
void output_read_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name, long long n_read)
{
fprintf(stderr, "Writing read GFA to disk... \n");
@@ -25027,6 +25136,12 @@ R_to_U* ruIndex, int max_hang, int min_ovlp)
renew_utg(&ug, sg, &new_rtg_edges);
}
// reset_untig_hap_label(ug, 7, FATHER, R_INF.trio_flag);
// reset_untig_hap_label(ug, 35, FATHER, R_INF.trio_flag);
// reset_untig_hap_label(ug, 713, FATHER, R_INF.trio_flag);
// reset_untig_hap_label(ug, 273, FATHER, R_INF.trio_flag);
// reset_untig_hap_label(ug, 822, FATHER, R_INF.trio_flag);
ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);