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chhylp123
2023-02-20 14:50:55 -05:00
parent b55e4396d2
commit 3abd3793fb
6 changed files with 836 additions and 164 deletions
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gfa_ut.cpp
+17 -17
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@@ -7678,7 +7678,7 @@ void print_raw_uls_seq(ul_resolve_t *uidx, const char *nn)
// for (k = 0; k < a_n && ug_occ_w(a[k].ts, a[k].te, &(ug->u.a[a[k].hid])) == 0; k++);
for (; k < a_n; k++) {
// if(ug_occ_w(a[k].ts, a[k].te, &(ug->u.a[a[k].hid])) == 0) break;
fprintf(fp, "utg%.6d%c(%c)\t", a[k].hid + 1, "lc"[ug->u.a[a[k].hid].circ], "+-"[a[k].rev]);
fprintf(fp, "utg%.6d%c(%c)(n::%lu)\t", a[k].hid + 1, "lc"[ug->u.a[a[k].hid].circ], "+-"[a[k].rev], ug_occ_w(a[k].ts, a[k].te, &(ug->u.a[a[k].hid])));
}
fprintf(fp,"\n");
}
@@ -16892,7 +16892,7 @@ ul_renew_t *ropt, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, ui
// 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);
// 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);
@@ -16912,7 +16912,7 @@ ul_renew_t *ropt, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, ui
// print_ul_alignment(init_ug, &UL_INF, 47072, "after-2");
// exit(1);
// if(free_uld) {
// print_raw_uls_seq(uidx, asm_opt.output_file_name);
print_raw_uls_seq(uidx, asm_opt.output_file_name);
// print_raw_uls_aln(uidx, asm_opt.output_file_name);
// }
@@ -17443,20 +17443,20 @@ double min_ovlp_drop_ratio, double max_ovlp_drop_ratio, double ou_rat, int64_t m
cal_bub_best_by_len(sl, &b, max_ext, is_trio, sl->is_ou, sl->len_rat, sl->ou_rat, min_ou);
}
if(is_ou) {
uint64_t k; sl->is_ou = 0;
for (k = 0; k < sl->ug->g->n_arc; k++) sl->ug->g->arc[k].ou = 0;
max_ovlp_drop_ratio = 0.6;
if(max_ovlp_drop_ratio > min_ovlp_drop_ratio) {
step = (clean_round==1?max_ovlp_drop_ratio:((max_ovlp_drop_ratio-min_ovlp_drop_ratio)/(clean_round-1)));
for (i = 0, sl->len_rat = min_ovlp_drop_ratio; i < clean_round; i++, sl->len_rat += step) {
if(sl->len_rat > max_ovlp_drop_ratio) sl->len_rat = max_ovlp_drop_ratio;
update_ug_clean_t(sl);
kt_for(asm_opt.thread_num, cal_bub_best, sl, sl->ug->g->n_seq);
cal_bub_best_by_len(sl, &b, max_ext, is_trio, sl->is_ou, sl->len_rat, sl->ou_rat, min_ou);
}
}
}
// if(is_ou) {
// uint64_t k; sl->is_ou = 0;
// for (k = 0; k < sl->ug->g->n_arc; k++) sl->ug->g->arc[k].ou = 0;
// max_ovlp_drop_ratio = 0.6;
// if(max_ovlp_drop_ratio > min_ovlp_drop_ratio) {
// step = (clean_round==1?max_ovlp_drop_ratio:((max_ovlp_drop_ratio-min_ovlp_drop_ratio)/(clean_round-1)));
// for (i = 0, sl->len_rat = min_ovlp_drop_ratio; i < clean_round; i++, sl->len_rat += step) {
// if(sl->len_rat > max_ovlp_drop_ratio) sl->len_rat = max_ovlp_drop_ratio;
// update_ug_clean_t(sl);
// kt_for(asm_opt.thread_num, cal_bub_best, sl, sl->ug->g->n_seq);
// cal_bub_best_by_len(sl, &b, max_ext, is_trio, sl->is_ou, sl->len_rat, sl->ou_rat, min_ou);
// }
// }
// }
// update_ug_clean_t(sl);
// cal_bub_best_by_topo(sl, &b, max_ext, is_trio, sl->is_ou, sl->len_rat, sl->ou_rat, min_ou, long_tip);