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cleaner assembly graph

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chhylp123
2022-12-06 09:52:00 -05:00
parent 786f8bdff0
commit a3b72457f0
8 changed files with 426 additions and 38 deletions
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Overlaps.cpp
+24 -1
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@@ -13823,6 +13823,8 @@ long long gap_fuzz, bub_label_t* b_mask_t)
if((asm_opt.flag & HA_F_VERBOSE_GFA)) write_trans_chain(cov->t_ch, output_file_name);
}
///for debug
// char* gfa_name = (char*)malloc(strlen(output_file_name)+50);
// sprintf(gfa_name, "%s.pre.clean_d_utg.noseq.gfa", output_file_name);
@@ -13830,7 +13832,11 @@ long long gap_fuzz, bub_label_t* b_mask_t)
// ma_ug_print_simple(ug, sg, coverage_cut, sources, ruIndex, "utg", output_file);
// fclose(output_file);
// free(gfa_name);
// exit(1);
///for debug
hic_analysis(ug, sg, cov?cov->t_ch:t_ch, &opt, 0, asm_opt.scffold?&rhits:NULL);
@@ -14876,12 +14882,29 @@ void filter_u_trans_t(kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g, uint32_t thr
kt_u_trans_t_idx(ta, ug->g->n_seq);
}
void dbg_prt_utg_trans(kv_u_trans_t *ta, ma_ug_t *ug, const char *o_n)
{
char* gfa_name = (char*)malloc(strlen(o_n)+100);
FILE *fn = NULL; sprintf(gfa_name, "%s.tran.dbg.ovlp.log", o_n);
u_trans_t *p = NULL; uint32_t i; fn = fopen(gfa_name, "w");
for (i = 0; i < ta->n; i++) {
p = &(ta->a[i]);
fprintf(fn, "utg%.6u%c\t%u\t%u\t%u\t%c\tutg%.6u%c\t%u\t%u\t%u\tw(%f)\tf(%u)\n",
p->qn+1, "lc"[ug->u.a[p->qn].circ], ug->u.a[p->qn].len, p->qs, p->qe, "+-"[p->rev],
p->tn+1, "lc"[ug->u.a[p->tn].circ], ug->u.a[p->tn].len, p->ts, p->te, p->nw, p->f);
}
fclose(fn); free(gfa_name); fprintf(stderr, "[M::%s::] done\n", __func__);
}
void clean_u_trans_t_idx(kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g)
{
// dbg_prt_utg_trans(ta, ug, "pre");
kt_u_trans_t_idx(ta, ug->g->n_seq);
kt_u_trans_t_symm(ta, ug);
filter_u_trans_t(ta, ug, read_g, 3);
///debug_u_trans_t(ta);
// dbg_prt_utg_trans(ta, ug, "after");
}
@@ -32112,7 +32135,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
// flat_bubbles(sg, ruIndex->is_het); free(ruIndex->is_het); ruIndex->is_het = NULL;
flat_soma_v(sg, sources, ruIndex);
**/
if(!(ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))) {
if(!ha_opt_triobin(&asm_opt)) {
// output_unitig_graph(sg, coverage_cut, "pre_clean", sources, ruIndex, max_hang_length, mini_overlap_length);
hic_clean_adv(sg, &uopt);
}