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low hamming for sampels with low het rate

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chhylp123
2021-06-09 20:10:50 -04:00
parent ca67e7a9b3
commit 9dc530cbfb
3 changed files with 105 additions and 20 deletions
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Overlaps.cpp
+87 -3
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@@ -13295,9 +13295,9 @@ long long gap_fuzz, bub_label_t* b_mask_t)
if(t_ch) destory_trans_chain(&t_ch);
// gfa_name = (char*)malloc(strlen(output_file_name)+25);
// char* gfa_name = (char*)malloc(strlen(output_file_name)+50);
// sprintf(gfa_name, "%s.after.clean_d_utg.noseq.gfa", output_file_name);
// output_file = fopen(gfa_name, "w");
// FILE* output_file = fopen(gfa_name, "w");
// ma_ug_print_simple(ug, sg, coverage_cut, sources, ruIndex, "utg", output_file);
// fclose(output_file);
// free(gfa_name);
@@ -16308,7 +16308,7 @@ uint8_t is_final_check, float double_check_rate, uint8_t flag, float drop_rate)
if(is_final_check)
{
if(non_flag_occ < u->n*double_check_rate) continue;
/**if(non_flag_occ < u->n*double_check_rate) continues**/;
}
else
{
@@ -16361,6 +16361,88 @@ uint8_t is_final_check, float double_check_rate, uint8_t flag, float drop_rate)
}
void force_trio_clean(ma_ug_t* ug, asg_t* read_g, ma_sub_t* coverage_cut,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex,
uint8_t flag, float self_drop_rate, float contig_drop_rate, uint32_t min_occ)
{
asg_t* nsg = ug->g;
uint32_t beg, end, n_vtx = nsg->n_seq<<1, k, i, rId, tf_occ, tnf_occ, flag_occ, non_flag_occ, n_reduce = 1;
long long nodeLen, baseLen, max_stop_nodeLen, max_stop_baseLen;
buf_t b; memset(&b, 0, sizeof(buf_t));
ma_utg_t *u = NULL;
uint8_t* primary_flag = (uint8_t*)calloc(read_g->n_seq, sizeof(uint8_t));
while (n_reduce)
{
n_reduce = 0;
n_vtx = nsg->n_seq;
for (beg = 0; beg < n_vtx; ++beg)
{
if(nsg->seq[beg>>1].del || asg_arc_n(nsg, beg) <= 0 || get_real_length(nsg, beg, NULL)<=0)
{
continue;
}
if(get_real_length(nsg, beg^1, NULL) == 1)///check if beg is the tig end
{
get_real_length(nsg, beg^1, &end);
if(get_real_length(nsg, end^1, NULL) == 1) continue;
}
b.b.n = 0; tf_occ = tnf_occ = 0;
get_unitig(nsg, ug, beg, &end, &nodeLen, &baseLen, &max_stop_nodeLen, &max_stop_baseLen, 1, &b);
for (i = 0; i < b.b.n; i++)
{
u = &((ug)->u.a[b.b.a[i]>>1]);
for (k = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
if(R_INF.trio_flag[rId] == AMBIGU) continue;
if(R_INF.trio_flag[rId] == DROP) continue;
if(R_INF.trio_flag[rId] == flag) tf_occ++;
if(R_INF.trio_flag[rId] != flag) tnf_occ++;
}
}
if(tnf_occ <= ((tnf_occ+tf_occ)*contig_drop_rate)) continue;
for (i = 0; i < b.b.n; i++)
{
flag_occ = non_flag_occ = 0;
u = &((ug)->u.a[b.b.a[i]>>1]);
for (k = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
if(R_INF.trio_flag[rId] == AMBIGU) continue;
if(R_INF.trio_flag[rId] == DROP) continue;
if(R_INF.trio_flag[rId] == flag) flag_occ++;
if(R_INF.trio_flag[rId] != flag) non_flag_occ++;
}
if(non_flag_occ <= min_occ) continue;
if(non_flag_occ <= ((non_flag_occ+flag_occ)*self_drop_rate)) continue;
if(non_flag_occ <= ((tf_occ+tnf_occ)*contig_drop_rate)) continue;
if(if_primary_unitig(u, read_g, coverage_cut, sources, ruIndex, primary_flag))
{
continue;
}
if(u->m != 0)
{
u->circ = u->end = u->len = u->m = u->n = u->start = 0;
free(u->a);
u->a = NULL;
}
asg_seq_del(nsg, b.b.a[i]>>1);
n_reduce++;
}
}
}
free(b.b.a);
asg_cleanup(nsg);
free(primary_flag);
}
void get_candidate_uids(asg_t* nsg, ma_utg_t* nsu, kvec_t_u64_warp* u_vecs,
ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex)
{
@@ -16943,6 +17025,8 @@ kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t)
update_unitig_graph((*ug), read_g, coverage_cut, sources, reverse_sources, ruIndex, 0,
DOUBLE_CHECK_THRES, flag, drop_rate);
force_trio_clean((*ug), read_g, coverage_cut, sources, reverse_sources, ruIndex, flag, 0.55, 0.01, 5);
///if(flag == MOTHER) print_debug_gfa(read_g, *ug, coverage_cut, "debug_trio_1", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
renew_utg(ug, read_g, new_rtg_edges);