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disable integer correction; disable contain dedup

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chhylp123
2023-03-10 09:12:07 -05:00
parent 85c643e85d
commit af4be8ca1a
7 changed files with 1073 additions and 57 deletions
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gfa_ut.cpp
+13 -5
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@@ -1922,6 +1922,8 @@ void flex_asg_t_cleanup(flex_asg_t *fg)
fg->g->is_srt = 0;
}
asg_cleanup(fg->g);
// asg_symm(fg->g);
// asg_arc_del_trans_ul(fg->g, fg->gap_fuzz);
}
void asg_arc_cut_contain(flex_asg_t *fg, asg64_v *in, asg64_v *in0, R_to_U* rI, float ou_rat, uint32_t only_trans_nn)
@@ -2770,7 +2772,7 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
asg_arc_cut_tips(sg, max_tip, &bu, is_ou, is_ou?rI:NULL);
// fprintf(stderr, "[M::%s] count_edges_v_w(sg, 49778, 49847)->%ld\n", __func__, count_edges_v_w(sg, 49778, 49847));
// if(is_ou) dedup_contain_g(uopt, sg);
for (i = 0; i < clean_round; i++, drop += step) {
if(drop > max_ovlp_drop_ratio) drop = max_ovlp_drop_ratio;
if(is_ou) {
@@ -2800,7 +2802,10 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
// prt_specfic_sge(sg, 10531, 10519, "--3--");
// if(is_ou) asg_arc_cut_contain(fg, &bu, &ba, rI, ((i+1)<clean_round)?ou_drop_rate:-1);
if(is_ou) asg_arc_cut_contain(fg, &bu, &ba, rI, ou_drop_rate, 0);
if(is_ou) {
asg_arc_cut_contain(fg, &bu, &ba, rI, ou_drop_rate, 0);
// dedup_contain_g(uopt, sg);
}
asg_arc_identify_simple_bubbles_multi(sg, b_mask_t, 1);
asg_arc_cut_bub_links(sg, &bu, HARD_OL_DROP, HARD_OL_SEC_DROP, HARD_OU_DROP, is_ou, asm_opt.large_pop_bubble_size, rev, rI, max_tip);
@@ -2818,9 +2823,7 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
if(is_ou) {
if(ul_refine_alignment(uopt, sg)) update_sg_uo(sg, src);
// debug_out = 1;
if(clean_contain_g(uopt, sg, 1)) update_sg_uo(sg, src);
// exit(1);
}
}
@@ -2831,6 +2834,7 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
if(is_ou) {
asg_arc_cut_contain(fg, &bu, &ba, rI, ou_drop_rate, 0);
asg_arc_cut_contain(fg, &bu, &ba, rI, -1, 1);
// dedup_contain_g(uopt, sg);
if(clean_contain_g(uopt, sg, 1)) update_sg_uo(sg, src);
}
if(!is_ou) asg_iterative_semi_circ(sg, src, &bu, max_tip, 1);
@@ -2874,7 +2878,11 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
ug_ext_gfa(uopt, sg, ug_ext_len);
// if(is_ou) dedup_contain_g(uopt, sg);
// exit(1)
output_unitig_graph(sg, uopt->coverage_cut, o_file, src, rI, uopt->max_hang, uopt->min_ovlp);
// exit(1);
// flat_bubbles(sg, ruIndex->is_het); free(ruIndex->is_het); ruIndex->is_het = NULL;
flat_soma_v(sg, src, rI);
@@ -17154,7 +17162,7 @@ ul_renew_t *ropt, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, ui
print_raw_uls_aln(uidx, asm_opt.output_file_name);
// }
ul_re_correct(uidx, 3);
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);
// 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);