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chhylp123
2021-04-14 18:50:20 -04:00
parent 67c7218264
commit 1e86e3dc02
7 changed files with 845 additions and 178 deletions
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Overlaps.cpp
+135 -24
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@@ -12235,7 +12235,7 @@ trans_chain* init_trans_chain(ma_ug_t *ug, uint64_t r_num)
memset(&(x->b_buf_1), 0, sizeof(buf_t));
kv_init(x->topo_buf);
kv_init(x->topo_res);
MALLOC(x->uLen, x->u_num);
///MALLOC(x->uLen, x->u_num);
kv_init(x->c_buf);
ma_utg_t *u = NULL;
@@ -12263,7 +12263,7 @@ trans_chain* init_trans_chain(ma_ug_t *ug, uint64_t r_num)
offset += (uint32_t)u->a[k];
}
x->uLen[v] = u->len;
///x->uLen[v] = u->len;
}
if(is_dup)
@@ -12315,7 +12315,7 @@ void destory_trans_chain(trans_chain **x)
kv_destroy((*x)->topo_buf);
kv_destroy((*x)->topo_res);
kv_destroy((*x)->c_buf);
free((*x)->uLen);
///free((*x)->uLen);
free((*x));
}
}
@@ -12502,6 +12502,88 @@ void hic_clean(asg_t* read_g)
kv_destroy(ax);
}
void write_trans_chain(trans_chain* t_ch, const char *fn)
{
char *buf = (char*)calloc(strlen(fn) + 25, 1);
sprintf(buf, "%s.hic.trans.bin", fn);
FILE* fp = fopen(buf, "w");
fwrite(&t_ch->u_num, sizeof(t_ch->u_num), 1, fp);
fwrite(&t_ch->r_num, sizeof(t_ch->r_num), 1, fp);
fwrite(t_ch->rUidx, sizeof(uint32_t), t_ch->r_num, fp);
fwrite(t_ch->rUpos, sizeof(uint64_t), t_ch->r_num, fp);
fwrite(t_ch->is_r_het, sizeof(uint8_t), t_ch->r_num, fp);
uint32_t i;
fwrite(&t_ch->bed.n, sizeof(t_ch->bed.n), 1, fp);
for (i = 0; i < t_ch->bed.n; i++)
{
fwrite(&t_ch->bed.a[i].n, sizeof(t_ch->bed.a[i].n), 1, fp);
fwrite(t_ch->bed.a[i].a, sizeof(bed_interval), t_ch->bed.a[i].n, fp);
}
fwrite(&t_ch->k_trans.n, sizeof(t_ch->k_trans.n), 1, fp);
fwrite(t_ch->k_trans.a, sizeof(u_trans_t), t_ch->k_trans.n, fp);
fwrite(&t_ch->k_trans.idx.n, sizeof(t_ch->k_trans.idx.n), 1, fp);
fwrite(t_ch->k_trans.idx.a, sizeof(uint64_t), t_ch->k_trans.idx.n, fp);
fclose(fp);
free(buf);
}
trans_chain* load_hc_hits(const char *fn)
{
uint64_t flag = 0;
char *buf = (char*)calloc(strlen(fn) + 25, 1);
sprintf(buf, "%s.hic.trans.bin", fn);
FILE* fp = NULL;
fp = fopen(buf, "r");
if(!fp) return NULL;
trans_chain *t_ch = NULL;
CALLOC(t_ch, 1);
flag += fread(&t_ch->u_num, sizeof(t_ch->u_num), 1, fp);
flag += fread(&t_ch->r_num, sizeof(t_ch->r_num), 1, fp);
MALLOC(t_ch->rUidx, t_ch->r_num);
flag += fread(t_ch->rUidx, sizeof(uint32_t), t_ch->r_num, fp);
MALLOC(t_ch->rUpos, t_ch->r_num);
flag += fread(t_ch->rUpos, sizeof(uint64_t), t_ch->r_num, fp);
MALLOC(t_ch->is_r_het, t_ch->r_num);
flag += fread(t_ch->is_r_het, sizeof(uint8_t), t_ch->r_num, fp);
uint32_t i;
flag += fread(&t_ch->bed.n, sizeof(t_ch->bed.n), 1, fp);
MALLOC(t_ch->bed.a, t_ch->bed.n); t_ch->bed.m = t_ch->bed.n;
for (i = 0; i < t_ch->bed.n; i++)
{
flag += fread(&t_ch->bed.a[i].n, sizeof(t_ch->bed.a[i].n), 1, fp);
MALLOC(t_ch->bed.a[i].a, t_ch->bed.a[i].n); t_ch->bed.a[i].m = t_ch->bed.a[i].n;
flag += fread(t_ch->bed.a[i].a, sizeof(bed_interval), t_ch->bed.a[i].n, fp);
}
flag += fread(&t_ch->k_trans.n, sizeof(t_ch->k_trans.n), 1, fp);
MALLOC(t_ch->k_trans.a, t_ch->k_trans.n); t_ch->k_trans.m = t_ch->k_trans.n;
flag += fread(t_ch->k_trans.a, sizeof(u_trans_t), t_ch->k_trans.n, fp);
flag += fread(&t_ch->k_trans.idx.n, sizeof(t_ch->k_trans.idx.n), 1, fp);
MALLOC(t_ch->k_trans.idx.a, t_ch->k_trans.idx.n); t_ch->k_trans.idx.m = t_ch->k_trans.idx.n;
flag += fread(t_ch->k_trans.idx.a, sizeof(uint64_t), t_ch->k_trans.idx.n, fp);
fclose(fp);
free(buf);
fprintf(stderr, "[M::%s::] ==> Hi-C cov have been loaded\n", __func__);
return t_ch;
}
void clean_u_trans_t_idx(kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g);
void output_hic_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
@@ -12519,31 +12601,59 @@ bub_label_t* b_mask_t)
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
new_rtg_edges.a.n = 0;
hap_cov_t *cov = NULL;
asg_t *copy_sg = copy_read_graph(sg);
ma_ug_t *copy_ug = copy_untig_graph(ug);
///asm_opt.purge_overlap_len = asm_opt.purge_overlap_len_hic;
///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);
trans_chain* t_ch = load_hc_hits(output_file_name);
if(!t_ch)
{
new_rtg_edges.a.n = 0;
asg_t *copy_sg = copy_read_graph(sg);
ma_ug_t *copy_ug = copy_untig_graph(ug);
///asm_opt.purge_overlap_len = asm_opt.purge_overlap_len_hic;
///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);
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
clean_u_trans_t_idx(&(cov->t_ch->k_trans), ug, sg);
clean_u_trans_t_idx(&(cov->t_ch->k_trans), ug, sg);
new_rtg_edges.a.n = 0;
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges,
max_hang, min_ovlp, asm_opt.hic_inconsist_rate, NULL, NULL, cov);
write_trans_chain(cov->t_ch, output_file_name);
}
new_rtg_edges.a.n = 0;
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges,
max_hang, min_ovlp, asm_opt.hic_inconsist_rate, NULL, NULL, cov);
hic_analysis(ug, sg, cov);
hic_analysis(ug, sg, cov?cov->t_ch:t_ch);
destory_hap_cov_t(&cov);
fprintf(stderr, "sa-0-sa\n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.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);
free(gfa_name);
fprintf(stderr, "sa-1-sa\n");
if(cov) destory_hap_cov_t(&cov);
if(t_ch) destory_trans_chain(&t_ch);
fprintf(stderr, "sa-2-sa\n");
ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a);
@@ -12743,7 +12853,8 @@ void kt_u_trans_t_idx(kv_u_trans_t *ta, uint32_t n)
uint32_t get_u_trans_spec(kv_u_trans_t *ta, uint32_t qn, uint32_t tn, u_trans_t **r_a, uint32_t *occ)
{
(*r_a) = NULL; (*occ) = 0;
if(r_a) (*r_a) = NULL;
if(occ) (*occ) = 0;
u_trans_t *a = NULL;
uint32_t n, st, i;
a = u_trans_a(*ta, qn);
@@ -12754,8 +12865,8 @@ uint32_t get_u_trans_spec(kv_u_trans_t *ta, uint32_t qn, uint32_t tn, u_trans_t
{
if(a[st].tn == tn)
{
(*r_a) = a + st;
(*occ) = i - st;
if(r_a) (*r_a) = a + st;
if(occ) (*occ) = i - st;
return 1;
}
st = i;