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chhylp123
2022-11-10 19:37:52 -05:00
parent 46acc8a2f6
commit 2c7b164f11
11 changed files with 1919 additions and 111 deletions
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16
Overlaps.cpp
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@@ -17798,6 +17798,7 @@ char *f_prefix, uint8_t *kpt_buf, kvec_asg_arc_t_warp *r_edges)
return NULL;
}
void filter_set_kug(uint8_t* trio_flag, asg_t *rg, uint8_t *rf, kvec_asg_arc_t_warp *r_edges, float f_rate, ma_ug_t **ug)
{
asg_t* nsg = (*ug)->g; ma_utg_t *u = NULL;
@@ -24843,14 +24844,16 @@ int load_ruIndex(R_to_U* ruIndex, char* read_file_name)
(ruIndex)->index = (uint32_t*)malloc(sizeof(uint32_t)*(ruIndex)->len);
f_flag += fread((ruIndex)->index, sizeof((ruIndex)->index[0]), (ruIndex)->len, fp);
R_INF.trio_flag = (uint8_t*)malloc(sizeof(uint8_t)*(ruIndex)->len);
f_flag += fread(R_INF.trio_flag, sizeof(R_INF.trio_flag[0]), (ruIndex)->len, fp);
if(!(asm_opt.ar)) {
R_INF.trio_flag = (uint8_t*)malloc(sizeof(uint8_t)*(ruIndex)->len);
f_flag += fread(R_INF.trio_flag, sizeof(R_INF.trio_flag[0]), (ruIndex)->len, fp);
}
// 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);
// 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);
@@ -25187,7 +25190,7 @@ uint32_t is_collect_trans)
MALLOC(x->pos_idx, x->n); memset(x->pos_idx, -1, x->n*sizeof(uint64_t));
CALLOC(set, read_g->n_seq<<1);
CALLOC(x->cov, x->n);
for (i = 0; i < n_ux; i++)
for (i = 0; i < n_ux; i++)//get the coverage for each read
{
if(ug->g->seq[i].del) continue;
u = &(ug->u.a[i]);
@@ -31767,10 +31770,11 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
debug_gfa:;
gen_ug_opt_t(&uopt, sources, reverse_sources, max_hang_length, mini_overlap_length, gap_fuzz, min_dp, readLen, coverage_cut, ruIndex,
(asm_opt.max_short_tip*2), 0.15, 3, 0.05, 0.9, &b_mask_t);
set_hom_global_coverage(&asm_opt, sg, coverage_cut, sources, reverse_sources, ruIndex, max_hang_length, mini_overlap_length);
}
if(asm_opt.ar) {
ul_realignment_gfa(&uopt, sg, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
asm_opt.max_short_tip, &b_mask_t, ha_opt_triobin(&asm_opt));
asm_opt.max_short_tip, &b_mask_t, ha_opt_triobin(&asm_opt), o_file);
}
// print_debug_gfa(sg, NULL, coverage_cut, "UL.debug", sources, ruIndex, max_hang_length, mini_overlap_length, 0, 0, 0);
/**