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fixed gap filling with UL

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chhylp123
2022-11-25 11:46:37 -05:00
parent 979d83f68d
commit fc76af1285
6 changed files with 760 additions and 182 deletions
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Overlaps.cpp
+19 -12
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@@ -31706,17 +31706,24 @@ int64_t mini_overlap_length, int64_t max_hang_length,
ug_opt_t *uopt, 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)
{
ma_ug_t *iug = ul_realignment_gfa(uopt, *sg, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
asm_opt.max_short_tip, b_mask_t, ha_opt_triobin(&asm_opt), o_file);
asg_t *ng = gen_ng(iug, *sg, uopt, coverage_cut, ruIndex, 256);
ma_ug_destroy(iug); asg_destroy(*sg);
(*sources) = R_INF.paf;
(*reverse_sources) = R_INF.reverse_paf;
(*n_read) = R_INF.total_reads;
(*readLen) = R_INF.read_length;
(*sg) = ng;
ma_hit_contained_advance(*sources, *n_read, *coverage_cut, ruIndex, max_hang_length, mini_overlap_length);
post_rescue(uopt, *sg, (*sources), (*reverse_sources), ruIndex, b_mask_t, 0);
ul_renew_t nopt; memset(&nopt, 0, sizeof(nopt));
nopt.src = sources; nopt.r_src = reverse_sources; nopt.ruIndex = ruIndex;
nopt.n_read = n_read; nopt.readLen = readLen; nopt.sg = sg;
nopt.cov = coverage_cut; nopt.b_mask_t = b_mask_t;
nopt.max_hang = max_hang_length; nopt.mini_ovlp = mini_overlap_length;
ul_realignment_gfa(uopt, *sg, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
asm_opt.max_short_tip, b_mask_t, ha_opt_triobin(&asm_opt), o_file, &nopt);;
// ma_ug_t *iug = ul_realignment_gfa(uopt, *sg, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
// asm_opt.max_short_tip, b_mask_t, ha_opt_triobin(&asm_opt), o_file);
// asg_t *ng = gen_ng(iug, *sg, uopt, coverage_cut, ruIndex, 256);
// ma_ug_destroy(iug); asg_destroy(*sg);
// (*sources) = R_INF.paf;
// (*reverse_sources) = R_INF.reverse_paf;
// (*n_read) = R_INF.total_reads;
// (*readLen) = R_INF.read_length;
// (*sg) = ng;
// ma_hit_contained_advance(*sources, *n_read, *coverage_cut, ruIndex, max_hang_length, mini_overlap_length);
// post_rescue(uopt, *sg, (*sources), (*reverse_sources), ruIndex, b_mask_t, 0);
}
void clean_graph(
@@ -32015,7 +32022,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
*coverage_cut_ptr = coverage_cut;
*sg_ptr = sg;
destory_bub_label_t(&b_mask_t);
free(o_file); if(asm_opt.ar) destory_all_ul_t(&UL_INF);
free(o_file); ///if(asm_opt.ar) destory_all_ul_t(&UL_INF);
fprintf(stderr, "Inconsistency threshold for low-quality regions in BED files: %u%%\n", asm_opt.bed_inconsist_rate);
}