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update for low coverge data

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chhylp123
2024-12-16 06:25:31 -05:00
parent 4889f1c6d8
commit 3067771783
8 changed files with 1073 additions and 154 deletions
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gfa_ut.cpp
+115 -6
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@@ -1574,6 +1574,107 @@ uint32_t is_topo, uint32_t min_diff, uint32_t min_ou, uint32_t test_bub, ma_hit_
}
void asg_arc_cut_chimeric_cmk(asg_t *g, asg64_v *in, int32_t max_ext, float len_rat, float ou_rat, uint32_t is_ou, uint32_t is_topo, uint32_t min_ou, uint32_t test_bub, uint8_t *cmk, uint32_t cmk_cut)
{
asg64_v tx = {0,0,0}, *b = NULL; asg_arc_t *av, *aw, *ve, *we;
uint32_t i, k, v, w, n_vtx = g->n_seq<<1, nv, nw, kv, kw, ol_max, ou_max, to_del, cnt = 0, mm_ol, mm_ou;
if(in) b = in;
else b = &tx;
b->n = 0;
for (v = 0; v < n_vtx; ++v) {
// if((v>>1)==17078) fprintf(stderr, "[M::%s::] v:%u, del:%u, seq_vis:%u\n", __func__, v, g->seq[v>>1].del, g->seq_vis[v]);
if (g->seq[v>>1].del) continue;
if (cmk[v>>1] > cmk_cut) continue;
if((test_bub == 0) || (g->seq_vis[v] == 0)) {
av = asg_arc_a(g, v); nv = asg_arc_n(g, v);
if (nv < 2) continue;
for (i = kv = 0; i < nv; ++i) {
if(av[i].del) continue;
kv++;
}
if(kv < 2) continue;
for (i = 0; i < nv; ++i) {
if(av[i].del) continue;
kv_push(uint64_t, *b, (((uint64_t)av[i].ol)<<32) | ((uint64_t)(av-g->arc+i)));
}
}
}
radix_sort_srt64(b->a, b->a + b->n);
for (k = 0; k < b->n; k++) {
if(g->arc[(uint32_t)b->a[k]].del) continue;
v = g->arc[(uint32_t)b->a[k]].ul>>32; w = g->arc[(uint32_t)b->a[k]].v^1;
if(g->seq[v>>1].del || g->seq[w>>1].del) continue;
nv = asg_arc_n(g, v); nw = asg_arc_n(g, w);
av = asg_arc_a(g, v); aw = asg_arc_a(g, w);
if(nv<=1 && nw <= 1) continue;
ve = &(g->arc[(uint32_t)b->a[k]]);
for (i = 0; i < nw; ++i) {
if (aw[i].v == (v^1)) {
we = &(aw[i]);
break;
}
}
///mm_ol and mm_ou are used to make edge with long indel more easy to be cutted
mm_ol = MIN(ve->ol, we->ol); mm_ou = MIN(ve->ou, we->ou);
for (i = kv = ol_max = ou_max = 0; i < nv; ++i) {
if(av[i].del) continue;
kv++;
if(ol_max < av[i].ol) ol_max = av[i].ol;
if(ou_max < av[i].ou) ou_max = av[i].ou;
}
if (kv < 1) continue;
if (kv >= 2) {
if (mm_ol > ol_max*len_rat) continue;
if (is_ou && mm_ou > ou_max*ou_rat && mm_ou > min_ou) continue;
}
for (i = kw = ol_max = ou_max = 0; i < nw; ++i) {
if(aw[i].del) continue;
kw++;
if(ol_max < aw[i].ol) ol_max = aw[i].ol;
if(ou_max < aw[i].ou) ou_max = aw[i].ou;
}
if (kw < 1) continue;
if (kw >= 2) {
if (mm_ol > ol_max*len_rat) continue;
if (is_ou && mm_ou > ou_max*ou_rat && mm_ou > min_ou) continue;
}
if (kv <= 1 && kw <= 1) continue;
to_del = 0;
if(is_topo) {
if (kv > 1 && kw > 1) {
to_del = 1;
} else if (kw == 1) {
if (asg_topocut_aux(g, w^1, max_ext) < max_ext) to_del = 1;
} else if (kv == 1) {
if (asg_topocut_aux(g, v^1, max_ext + 1) < max_ext + 1) to_del = 1;
}
}
if (to_del) {
asg_seq_del(g, v>>1); ++cnt;
}
}
// stats_sysm(g);
if(!in) free(tx.a);
if (cnt > 0) asg_cleanup(g);
// fprintf(stderr, "[M::%s::] cnt:%u\n", __func__, cnt);
}
void asg_arc_cut_length_adv(asg_t *g, asg64_v *in, int32_t max_ext, float len_rat, float ou_rat, uint32_t is_ou, uint32_t is_trio,
uint32_t is_topo, uint32_t min_diff, ma_hit_t_alloc *rev, R_to_U* rI, uint32_t *max_drop_len)
@@ -2909,22 +3010,22 @@ void print_raw_u2rgfa_seq(all_ul_t *aln, R_to_U* rI, uint32_t is_detail)
}
void post_rescue(ug_opt_t *uopt, asg_t *sg, ma_hit_t_alloc *src, ma_hit_t_alloc *rev, R_to_U* rI, bub_label_t *b_mask_t, long long no_trio_recover)
void post_rescue(ug_opt_t *uopt, asg_t *sg, ma_hit_t_alloc *src, ma_hit_t_alloc *rev, R_to_U* rI, bub_label_t *b_mask_t, long long no_trio_recover, uint8_t *cmk)
{
rescue_contained_reads_aggressive(NULL, sg, src, uopt->coverage_cut, rI, uopt->max_hang, uopt->min_ovlp, 10, 1, 0, NULL, NULL, b_mask_t);
rescue_missing_overlaps_aggressive(NULL, sg, src, uopt->coverage_cut, rI, uopt->max_hang, uopt->min_ovlp, 1, 0, NULL, b_mask_t);
rescue_missing_overlaps_backward(NULL, sg, src, uopt->coverage_cut, rI, uopt->max_hang, uopt->min_ovlp, 10, 1, 0, b_mask_t);
if(cmk) rescue_chimeric_reads_aggressive(NULL, sg, src, uopt->coverage_cut, rI, uopt->max_hang, uopt->min_ovlp, 10, 1, 0, NULL, NULL, b_mask_t, cmk);
// rescue_wrong_overlaps_to_unitigs(NULL, sg, sources, reverse_sources, coverage_cut, ruIndex,
// max_hang_length, mini_overlap_length, bubble_dist, NULL);
// rescue_no_coverage_aggressive(sg, sources, reverse_sources, &coverage_cut, ruIndex, max_hang_length,
// mini_overlap_length, bubble_dist, 10);
set_hom_global_coverage(&asm_opt, sg, uopt->coverage_cut, src, rev, rI, uopt->max_hang, uopt->min_ovlp);
rescue_bubble_by_chain(sg, uopt->coverage_cut, src, rev, (asm_opt.max_short_tip*2), 0.15, 3, rI, 0.05, 0.9, uopt->max_hang,
uopt->min_ovlp, 10, uopt->gap_fuzz, b_mask_t, no_trio_recover);
rescue_bubble_by_chain(sg, uopt->coverage_cut, src, rev, (asm_opt.max_short_tip*2), 0.15, 3, rI, 0.05, 0.9, uopt->max_hang, uopt->min_ovlp, 10, uopt->gap_fuzz, b_mask_t, no_trio_recover, cmk);
}
void ul_clean_gfa(ug_opt_t *uopt, asg_t *sg, ma_hit_t_alloc *src, ma_hit_t_alloc *rev, R_to_U* rI, int64_t clean_round, double min_ovlp_drop_ratio, double max_ovlp_drop_ratio,
double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, int32_t is_ou, int32_t is_trio, uint32_t ou_thres, char *o_file)
double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, int32_t is_ou, int32_t is_trio, uint32_t ou_thres, uint8_t *cmk, char *o_file)
{
#define HARD_OU_DROP 0.75
#define HARD_OL_DROP 0.6
@@ -3010,6 +3111,14 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
// print_debug_gfa(sg, NULL, uopt->coverage_cut, "UL.dirty3.debug", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 1, 0, 0);
// // exit(1);
// }
/**
if(cmk && asm_opt.chemical_cov > FORCE_CUT) {
asg_arc_identify_simple_bubbles_multi(sg, b_mask_t, 0);
asg_arc_cut_chimeric_cmk(sg, &bu, max_tip, 1.1, 1.1, is_ou, 1, 1, 1, cmk, asm_opt.chemical_cov);
asg_arc_cut_tips(sg, max_tip, &bu, is_ou, is_ou?rI:NULL, uopt->te);
}
**/
if(is_ou) {
if(ul_refine_alignment(uopt, sg)) update_sg_uo(sg, src);
@@ -3074,7 +3183,7 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
set_hom_global_coverage(&asm_opt, sg, uopt->coverage_cut, src, rev, rI, uopt->max_hang, uopt->min_ovlp);
rescue_bubble_by_chain(sg, uopt->coverage_cut, src, rev, (asm_opt.max_short_tip*2), 0.15, 3, rI, 0.05, 0.9, uopt->max_hang, uopt->min_ovlp, 10, uopt->gap_fuzz, b_mask_t);
**/
post_rescue(uopt, sg, src, rev, rI, b_mask_t, is_ou);
post_rescue(uopt, sg, src, rev, rI, b_mask_t, is_ou, cmk);
ug_ext_gfa(uopt, sg, ug_ext_len);
@@ -17580,7 +17689,7 @@ ul_renew_t *ropt, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, ui
(*(ropt->src)) = R_INF.paf; (*(ropt->r_src)) = R_INF.reverse_paf;
(*(ropt->n_read)) = R_INF.total_reads; (*(ropt->readLen)) = R_INF.read_length;
renew_R_to_U(ng, (*(ropt->src)), (*(ropt->r_src)), (*(ropt->n_read)), (*(ropt->cov)), ropt->ruIndex, ropt->max_hang, ropt->mini_ovlp);
post_rescue(uopt, (*(ropt->sg)), (*(ropt->src)), (*(ropt->r_src)), ropt->ruIndex, ropt->b_mask_t, 0);
post_rescue(uopt, (*(ropt->sg)), (*(ropt->src)), (*(ropt->r_src)), ropt->ruIndex, ropt->b_mask_t, 0, NULL);
// print_raw_uls_aln(uidx, asm_opt.output_file_name);
// exit(0);
}