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fixed het/hom node bugs

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chhylp123
2022-12-08 03:07:14 -05:00
parent a3b72457f0
commit a674110b23
6 changed files with 67 additions and 21 deletions
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gfa_ut.cpp
+37 -4
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@@ -14385,9 +14385,12 @@ void u2g_hybrid_detan_iter(ul_resolve_t *uidx, usg_t *ng, uint32_t max_ext, uint
asg64_v b64, ub64; kv_init(b64); kv_init(ub64);
asg64_v tx = {0,0,0}, tb = {0,0,0}, *ob = NULL, *ub = NULL;
ob = (in?(in):(&tx)); ub = (ib?(ib):(&tb)); ob->n = ub->n = 0;
// fprintf(stderr, "\n[M::%s::] asm_opt.is_low_het_ul::%u, max_ext::%u\n",
// __func__, asm_opt.is_low_het_ul, max_ext);
// prt_usg_t(uidx, ng, "ng0");
for (k = 0; k < clean_round; k++) {
ncut += ug_ext_strict(ob, ub, uidx, ng, max_ext, &ff, &ng_occ, &i_idx, &b64, &ub64);
// if(asm_opt.is_low_het_ul) break;
ncut += ug_ext_free(ob, ub, uidx, ng, max_ext, &ff, &ng_occ, &i_idx, &b64, &ub64, 48, 1);
// prt_usg_t(uidx, ng, "ng_python");
ncut += ug_ext_free(ob, ub, uidx, ng, max_ext, &ff, &ng_occ, &i_idx, &b64, &ub64, 16, 1);
@@ -14403,7 +14406,7 @@ void u2g_hybrid_detan_iter(ul_resolve_t *uidx, usg_t *ng, uint32_t max_ext, uint
// prt_usg_t(uidx, ng, "ng.db");
// ncut += ug_ext_free(ob, ub, uidx, ng, max_ext, &ff, &ng_occ, &i_idx, &b64, &ub64, 10);
// ncut += ug_ext_strict(ob, ub, uidx, ng, max_ext, &ff, &ng_occ, &i_idx, &b64, &ub64);
// prt_usg_t(uidx, ng, "ng1");
// prt_usg_t(uidx, ng, "ng.db");
if(ncut) {
usg_cleanup(ng); usg_arc_cut_tips(ng, max_ext, 1, ub);
}
@@ -16479,8 +16482,38 @@ void destroy_ul_resolve_t(ul_resolve_t *uidx)
free(uidx);
}
static void clear_ma_hit_t_alloc(void *data, long i, int tid)
{
ma_hit_t_alloc *src = (ma_hit_t_alloc *)data;
ma_hit_t_alloc *z = &(src[i]); uint32_t k;
for (k = 0; k < z->length; k++) z->buffer[k].del = 0;
}
static void reset_ma_sub_t(void *data, long i, int tid)
{
sset_aux *s = (sset_aux *)data;
if(s->g && s->g->seq[i].del) s->cov[i].del = 1;
else s->cov[i].del = 0;
}
void renew_R_to_U(asg_t *ng, ma_hit_t_alloc* src, ma_hit_t_alloc* r_src, int64_t n_read, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp)
{
sset_aux s; memset(&s, 0, sizeof(s));
kt_for(asm_opt.thread_num, clear_ma_hit_t_alloc, src, n_read);
kt_for(asm_opt.thread_num, clear_ma_hit_t_alloc, r_src, n_read);
s.g = NULL; s.cov = coverage_cut;
kt_for(asm_opt.thread_num, reset_ma_sub_t, &s, n_read);
ma_hit_contained_advance(src, n_read, coverage_cut, ruIndex, max_hang, min_ovlp);
// s.g = ng; s.cov = coverage_cut;
// kt_for(asm_opt.thread_num, reset_ma_sub_t, &s, n_read);
}
void ul_realignment_gfa(ug_opt_t *uopt, asg_t *sg, int64_t clean_round, double min_ovlp_drop_ratio,
double max_ovlp_drop_ratio, int64_t max_tip, bub_label_t *b_mask_t, uint32_t is_trio, char *o_file,
double max_ovlp_drop_ratio, int64_t max_tip, int64_t max_ul_tip, bub_label_t *b_mask_t, uint32_t is_trio, char *o_file,
ul_renew_t *ropt)
{
uint64_t i; uint8_t *r_het = NULL; bubble_type *bub = NULL; ulg_opt_t uu;
@@ -16502,7 +16535,7 @@ ul_renew_t *ropt)
// print_raw_uls_seq(uidx, asm_opt.output_file_name);
// print_raw_uls_aln(uidx, asm_opt.output_file_name);
ul_re_correct(uidx, 3);
init_ulg_opt_t(&uu, uopt, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio, 0.55, max_tip, max_tip<<1, b_mask_t, is_trio);
init_ulg_opt_t(&uu, uopt, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio, 0.55, max_tip, max_ul_tip, b_mask_t, is_trio);
// print_debug_gfa(sg, init_ug, uopt->coverage_cut, "UL.debug0", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 1);
/**ul2ul_idx_t *u2o = **/gen_ul2ul(uidx, uopt, &uu, 0);
// print_ul_alignment(init_ug, &UL_INF, 47072, "after-3");
@@ -16529,7 +16562,7 @@ ul_renew_t *ropt)
asg_destroy((*(ropt->sg))); (*(ropt->sg)) = ng;
(*(ropt->src)) = R_INF.paf; (*(ropt->r_src)) = R_INF.reverse_paf;
(*(ropt->n_read)) = R_INF.total_reads; (*(ropt->readLen)) = R_INF.read_length;
ma_hit_contained_advance((*(ropt->src)), (*(ropt->n_read)), (*(ropt->cov)), ropt->ruIndex, ropt->max_hang, ropt->mini_ovlp);
renew_R_to_U(ng, (*(ropt->src)), (*(ropt->r_src)), (*(ropt->n_read)), (*(ropt->cov)), ropt->ruIndex, ropt->max_hang, ropt->mini_ovlp);
post_rescue(uopt, (*(ropt->sg)), (*(ropt->src)), (*(ropt->r_src)), ropt->ruIndex, ropt->b_mask_t, 0);
// print_raw_uls_aln(uidx, asm_opt.output_file_name);
// exit(0);