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path-max and path-min to avoid misassemblies

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chhylp123
2023-03-13 11:13:57 -04:00
parent 3407c7029e
commit f67faa9c34
4 changed files with 34 additions and 9 deletions
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gfa_ut.cpp
+8 -8
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@@ -15934,11 +15934,11 @@ void u2g_clean(ul_resolve_t *uidx, ulg_opt_t *ulopt, uint32_t keep_raw_utg, uint
// char sb[1000];
// output_integer_graph(uidx, iug, "ig_h0", 0);
// fprintf(stderr, "\n[M::%s::] max_path_drop_ratio::%f, min_path_drop_ratio::%f\n", __func__, ulopt->max_path_drop_ratio, ulopt->min_path_drop_ratio);
for (ss = 0; ss < 2; ss++) {
for (i = 0, drop = ulopt->min_path_drop_ratio; i < ulopt->clean_round; i++, drop += step) {
if(drop > ulopt->max_path_drop_ratio) drop = ulopt->max_path_drop_ratio;
// fprintf(stderr, "\n[M::%s::] Starting round-%ld, drop::%f\n", __func__, i, drop);
// fprintf(stderr, "[M::%s::] Starting round-%ld, drop::%f\n", __func__, i, drop);
cnt = 1; topo_level = 2; mm_tip = ulopt->max_tip;
while (cnt) {
cnt = 0;
@@ -17246,11 +17246,11 @@ 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);
@@ -17274,7 +17274,7 @@ ul_renew_t *ropt, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, ui
// }
ul_re_correct(uidx, asm_opt.integer_correct_round/**3**/);
init_ulg_opt_t(&uu, uopt, clean_round, 0.2, 0.6, min_ovlp_drop_ratio, max_ovlp_drop_ratio, 0.55, max_tip, max_ul_tip, b_mask_t, is_trio);
init_ulg_opt_t(&uu, uopt, clean_round, asm_opt.min_path_drop_rate, asm_opt.max_path_drop_rate, 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, is_bridg);
// print_ul_alignment(init_ug, &UL_INF, 47072, "after-3");