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keep l1 trans

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chhylp123
2021-04-04 14:00:28 -04:00
parent ebfc04d253
commit 8e75eb5a05
6 changed files with 356 additions and 72 deletions
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Overlaps.cpp
+58 -14
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@@ -11304,9 +11304,13 @@ void collect_trans_cov(const char* cmd, buf_t* pri, buf_t* aux, ma_ug_t *ug, asg
chain_trans_ovlp(cov, ug, read_sg, pri, len_aux, &thre_pri);
if(thre_pri > 0)
{
// fprintf(stderr, "\n%s, thre_pri: %u\n", cmd, thre_pri);
/*******************************for debug************************************/
// fprintf(stderr, "\n%s, thre_pri: %u, len_aux: %lu\n", cmd, thre_pri, len_aux);
// print_buf_t(ug, pri, "pri");
// print_buf_t(ug, aux, "aux");
/*******************************for debug************************************/
for (i = uCov = 0, p_uId = (uint32_t)-1; i < aux->b.n; i++)
{
@@ -12111,25 +12115,32 @@ bub_label_t* b_mask_t)
ma_ug_t *copy_ug = copy_untig_graph(ug);
///asm_opt.purge_overlap_len = asm_opt.purge_overlap_len_hic;
///asm_opt.purge_simi_thres = asm_opt.purge_simi_rate_hic;
fprintf(stderr, "sb0sb\n");
adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1);
fprintf(stderr, "sb1sb\n");
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
fprintf(stderr, "sb2sb\n");
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges,
max_hang, min_ovlp, asm_opt.hic_inconsist_rate, NULL, NULL, cov);
fprintf(stderr, "sb3sb\n");
fprintf(stderr, "sb4sb\n");
new_rtg_edges.a.n = 0;
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp);
///classify_untigs(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, &new_rtg_edges, max_hang, min_ovlp);
fprintf(stderr, "sb5sb\n");
hic_analysis(ug, sg, cov);
fprintf(stderr, "sb6sb\n");
destory_hap_cov_t(&cov);
ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a);
@@ -14107,7 +14118,7 @@ int just_bubble_pop, float drop_ratio, hap_cov_t *cov)
#define T_ROUND 2
asg_t *g = ug->g;
int round = T_ROUND;
redo:
///print_graph_statistic(g, "beg");
///print_debug_gfa(read_g, ug, coverage_cut, "debug_trans_ovlp_hg002", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
@@ -16899,8 +16910,9 @@ uint64_t get_s_bub_pop_max_dist_advance(asg_t *g, buf_s_t *b)
int asg_pop_bubble_primary_trio(ma_ug_t *ug, uint64_t* i_max_dist, uint32_t positive_flag, uint32_t negative_flag, hap_cov_t *cov, uint32_t is_update_chain)
{
asg_t *g = ug->g;
uint32_t v, n_vtx = g->n_seq * 2;
uint32_t v, n_vtx = g->n_seq * 2, n_arc, nv, i;
uint64_t n_pop = 0, max_dist;
asg_arc_t *av = NULL;
buf_t b;
if (!g->is_symm) asg_symm(g);
memset(&b, 0, sizeof(buf_t));
@@ -16908,27 +16920,57 @@ int asg_pop_bubble_primary_trio(ma_ug_t *ug, uint64_t* i_max_dist, uint32_t posi
b.a = (binfo_t*)calloc(n_vtx, sizeof(binfo_t));
if(i_max_dist) max_dist = (*i_max_dist);
else max_dist = get_bub_pop_max_dist_advance(g, &b);
uint8_t* bs_flag = NULL; CALLOC(bs_flag, n_vtx);
if(max_dist > 0)
{
//traverse all node with two directions
for (v = 0; v < n_vtx; ++v) {
uint32_t i, n_arc = 0, nv = asg_arc_n(g, v);
asg_arc_t *av = asg_arc_a(g, v);
for (v = 0; v < n_vtx; ++v)
{
if(bs_flag[v] != 0) continue;
nv = asg_arc_n(g, v);
av = asg_arc_a(g, v);
///some node could be deleted
if (nv < 2 || g->seq[v>>1].del || g->seq[v>>1].c == ALTER_LABLE) continue;
///some edges could be deleted
for (i = 0; i < nv; ++i) // asg_bub_pop1() may delete some edges/arcs
for (i = n_arc = 0; i < nv; ++i) // asg_bub_pop1() may delete some edges/arcs
if (!av[i].del) ++n_arc;
if (n_arc < 2) continue;
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, max_dist, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0))
{
//beg is v, end is b.S.a[0]
//note b.b include end, does not include beg
for (i = 0; i < b.b.n; i++)
{
if(b.b.a[i]==v || b.b.a[i]==b.S.a[0]) continue;
bs_flag[b.b.a[i]] = bs_flag[b.b.a[i]^1] = 1;
}
bs_flag[v] = 2; bs_flag[b.S.a[0]^1] = 3;
}
}
//traverse all node with two directions
for (v = 0; v < n_vtx; ++v) {
if(bs_flag[v] !=2) continue;
nv = asg_arc_n(g, v);
av = asg_arc_a(g, v);
///some node could be deleted
if (nv < 2 || g->seq[v>>1].del || g->seq[v>>1].c == ALTER_LABLE) continue;
///some edges could be deleted
for (i = n_arc = 0; i < nv; ++i) // asg_bub_pop1() may delete some edges/arcs
if (!av[i].del) ++n_arc;
if (n_arc > 1)
n_pop += asg_bub_pop1_primary_trio(ug->g, ug, v, max_dist, &b, positive_flag, negative_flag, 1, NULL, NULL, cov, is_update_chain);
}
free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a);
if (n_pop) asg_cleanup(g);
if(VERBOSE >= 1)
{
fprintf(stderr, "[M::%s] popped %lu bubbles\n", __func__, (unsigned long)n_pop);
}
}
free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a);
if (n_pop) asg_cleanup(g);
free(bs_flag);
return n_pop;
}
@@ -22675,6 +22717,7 @@ uint32_t collect_p_trans)
EvaluateLen((*ug)->u, v) = (*ug)->u.a[v].n;
}
clean_primary_untig_graph(*ug, read_g, sources, reverse_sources, coverage_cut, tipsLen, tip_drop_ratio,
stops_threshold, ruIndex, NULL, NULL, 0, 0, 0, chimeric_rate, 0, 0, drop_ratio, cov);
delete_useless_nodes(ug);
@@ -22684,6 +22727,7 @@ uint32_t collect_p_trans)
if(asm_opt.purge_level_primary > 0)
{
///print_debug_gfa(read_g, *ug, coverage_cut, "debug_purge", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
just_contain = 0;
if(asm_opt.purge_level_primary == 1) just_contain = 1;
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
@@ -22701,7 +22745,7 @@ uint32_t collect_p_trans)
rescue_contained_reads_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
min_ovlp, 10, 0, 1, NULL, NULL, b_mask_t);
renew_utg(ug, read_g, new_rtg_edges);
// if(asm_opt.purge_level_primary > 0)
// {
// just_contain = 0;