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coverage adjustment for polyploidy

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chhylp123
2023-03-12 17:02:29 -04:00
parent 2218bac8aa
commit 3407c7029e
7 changed files with 344 additions and 30 deletions
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gfa_ut.cpp
+21 -9
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@@ -2995,7 +2995,7 @@ void ug_ext_gfa(ug_opt_t *uopt, asg_t *sg, uint32_t max_len)
}
bubble_type *gen_bubble_chain(asg_t *sg, ma_ug_t *ug, ug_opt_t *uopt, uint8_t **ir_het)
bubble_type *gen_bubble_chain(asg_t *sg, ma_ug_t *ug, ug_opt_t *uopt, uint8_t **ir_het, uint8_t avoid_het)
{
kvec_asg_arc_t_warp new_rtg_edges;
kv_init(new_rtg_edges.a);
@@ -3013,7 +3013,14 @@ bubble_type *gen_bubble_chain(asg_t *sg, ma_ug_t *ug, ug_opt_t *uopt, uint8_t **
// fprintf(stderr, "1[M::%s]\n", __func__);
CALLOC(bub, 1); (*ir_het) = cov->t_ch->ir_het;
cov->t_ch->ir_het = NULL; cov->is_r_het = NULL;
identify_bubbles(ug, bub, (*ir_het), NULL);
if(!avoid_het) {
identify_bubbles(ug, bub, (*ir_het), NULL);
} else {
uint8_t *pr_het; CALLOC(pr_het, sg->n_seq);
identify_bubbles_recal_poy(sg, ug, bub, pr_het, uopt->sources, uopt->ruIndex, NULL);
free(pr_het);
}
// fprintf(stderr, "2[M::%s]\n", __func__);
kv_destroy(new_rtg_edges.a); destory_hap_cov_t(&cov);
if(asm_opt.purge_level_primary == 0) {///all nodes are het
@@ -13621,7 +13628,12 @@ void renew_usg_t_bub(ul_resolve_t *uidx, usg_t *ng, uint32_t *id_map, uint8_t *f
// fprintf(stderr, "[M::%s] homozygous read coverage threshold: %d\n", __func__, asm_opt.hom_global_coverage_set?
// asm_opt.hom_global_coverage:(int)(((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE)));
// identify_bubbles(ug, uidx->bub, uidx->r_het, NULL);
identify_bubbles_recal(uidx->sg, ug, uidx->bub, uidx->r_het, uidx->uopt->sources, uidx->uopt->ruIndex, NULL);
if(asm_opt.polyploidy <= 2) {
identify_bubbles_recal(uidx->sg, ug, uidx->bub, uidx->r_het, uidx->uopt->sources, uidx->uopt->ruIndex, NULL);
} else {
identify_bubbles_recal_poy(uidx->sg, ug, uidx->bub, uidx->r_het, uidx->uopt->sources, uidx->uopt->ruIndex, NULL);
}
// fprintf(stderr, "0[M::%s::] f[51]::%u\n", __func__, ff[51]);
for (i = 0; i < ng->n; i++) {
if(id_map[i] != (uint32_t)-1) {
@@ -17234,18 +17246,18 @@ ul_renew_t *ropt, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, ui
// fprintf(stderr, "2[M::%s]\n", __func__);
// exit(1);
// char* gfa_name = NULL; MALLOC(gfa_name, strlen(o_file)+strlen(bin_file)+50);
// sprintf(gfa_name, "%s.%s", o_file, bin_file);
// print_debug_gfa(sg, init_ug, uopt->coverage_cut, gfa_name, uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 0);
// print_debug_gfa(sg, init_ug, uopt->coverage_cut, gfa_name, uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 1);
// free(gfa_name);
char* gfa_name = NULL; MALLOC(gfa_name, strlen(o_file)+strlen(bin_file)+50);
sprintf(gfa_name, "%s.%s", o_file, bin_file);
print_debug_gfa(sg, init_ug, uopt->coverage_cut, gfa_name, uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 0);
print_debug_gfa(sg, init_ug, uopt->coverage_cut, gfa_name, uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 1);
free(gfa_name);
filter_sg_by_ug(sg, init_ug, uopt);
// fprintf(stderr, "-0-[M::%s]\tUL_INF.a[25].rlen::%u\n", __func__, UL_INF.a[25].rlen);
// print_debug_gfa(sg, init_ug, uopt->coverage_cut, "UL.debug", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 0);
// print_ul_alignment(init_ug, &UL_INF, 47072, "after-0");
bub = gen_bubble_chain(sg, init_ug, uopt, &r_het);
bub = gen_bubble_chain(sg, init_ug, uopt, &r_het, ((asm_opt.polyploidy>2)?1:0));
// fprintf(stderr, "4[M::%s]\n", __func__);
// print_ul_alignment(init_ug, &UL_INF, 47072, "after-1");
ul_resolve_t *uidx = init_ul_resolve_t(sg, init_ug, bub, &UL_INF, uopt, r_het);