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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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CommandLines.h
+1 -1
View File
@@ -4,7 +4,7 @@
#include <pthread.h>
#include <stdint.h>
#define HA_VERSION "0.15.1-r336"
#define HA_VERSION "0.15.3-r339"
#define VERBOSE 0
Overlaps.cpp
+87 -3
View File
@@ -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);
hic.cpp
+17 -16
View File
@@ -6173,7 +6173,8 @@ inline double get_trans_weight_advance(const ha_ug_index* idx, uint64_t x, trans
}
else
{
rate = 0.2;
// rate = 0.2;
rate = 0.4;
}
@@ -13633,11 +13634,11 @@ void resolve_bubble_chain_by_hic(ha_ug_index *idx, kv_u_trans_t *ta, bubble_type
// }
// }
for (i = 0; i < edges.a.n; i++)
{
fprintf(stderr, "s-utg%.6lul<------>d-utg%.6ul\n", (edges.a.a[i].ul>>33) + 1, (edges.a.a[i].v>>1) + 1);
// for (i = 0; i < edges.a.n; i++)
// {
// fprintf(stderr, "s-utg%.6lul<------>d-utg%.6ul\n", (edges.a.a[i].ul>>33) + 1, (edges.a.a[i].v>>1) + 1);
}
// }
/*******************************for debug************************************/
if(edges.a.n > 0)
{
@@ -15250,11 +15251,11 @@ void print_kv_weight(kv_u_trans_t *ta)
fprintf(stderr, "*********ta->n: %u\n", (uint32_t)ta->n);
for (i = 0; i < ta->n; i++)
{
fprintf(stderr, "+qn(%u)->tn(%u): %f\n", ta->a[i].qn, ta->a[i].tn, ta->a[i].nw);
fprintf(stderr, "+s-utg%.6ul->d-utg%.6ul: %f\n", ta->a[i].qn+1, ta->a[i].tn+1, ta->a[i].nw);
get_u_trans_spec(ta, ta->a[i].tn, ta->a[i].qn, &e, NULL);
if(e)
{
fprintf(stderr, "-tn(%u)->qn(%u): %f\n", e->qn, e->tn, e->nw);
fprintf(stderr, "-d-utg%.6ul->s-utg%.6ul: %f\n", e->qn+1, e->tn+1, e->nw);
}
else
{
@@ -15693,12 +15694,12 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
resolve_tangles_hic(idx, &bub, &sl.hits, &k_trans);
measure_distance(idx, idx->ug, &sl.hits, &link, &bub, &(idx->t_ch->k_trans));
if((asm_opt.flag & HA_F_VERBOSE_GFA) && load_ps_t(&s, asm_opt.output_file_name))
{
bub.round_id = bub.n_round;
label_unitigs_sm(s->s, NULL, idx->ug);
goto skip_flipping;
}
// if((asm_opt.flag & HA_F_VERBOSE_GFA) && load_ps_t(&s, asm_opt.output_file_name))
// {
// bub.round_id = bub.n_round;
// label_unitigs_sm(s->s, NULL, idx->ug);
// goto skip_flipping;
// }
s = init_ps_t(11, idx->ug->g->n_seq);
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
@@ -15726,9 +15727,9 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
label_unitigs(&(hap.g_p), idx->ug);
**/
}
write_ps_t(s, asm_opt.output_file_name);
// write_ps_t(s, asm_opt.output_file_name);
skip_flipping:
// skip_flipping:
verbose_het_stat(&bub);
// print_kv_weight(&k_trans);
@@ -15886,7 +15887,7 @@ int hic_short_align_poy(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx,
// }
/*******************************for debug************************************/
}
// write_psg_t(s, asm_opt.output_file_name);
write_psg_t(s, asm_opt.output_file_name);
skip_flipping:
verbose_het_stat(&bub);