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phasing improvement

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chhylp123
2021-04-27 21:35:49 -04:00
parent 11430d6a3b
commit 2fc2268268
4 changed files with 403 additions and 37 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-r329"
#define HA_VERSION "0.15.1-r330"
#define VERBOSE 0
Overlaps.cpp
+6 -6
View File
@@ -12764,12 +12764,12 @@ long long gap_fuzz, bub_label_t* b_mask_t)
hic_analysis(ug, sg, cov?cov->t_ch:t_ch);
// char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
// sprintf(gfa_name, "%s.d_utg.noseq.gfa", output_file_name);
// FILE* output_file = fopen(gfa_name, "w");
// ma_ug_print_simple(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "utg", output_file);
// fclose(output_file);
// free(gfa_name);
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.d_utg.noseq.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "utg", output_file);
fclose(output_file);
free(gfa_name);
if(cov) destory_hap_cov_t(&cov);
hic.cpp
+394 -30
View File
@@ -4094,8 +4094,218 @@ void update_ug_by_tigs(asg_t *sg, hc_links *link)
free(flag); kv_destroy(buf.a);
}
/**
#define Get_Ovlp(xs, xe, ys, ye) ((a).occ)
///take care of circle
void idx_hc_links(kvec_pe_hit* hits, ha_ug_index* idx, bubble_type* bub);
void measure_disconnected_dis(ha_ug_index* idx, kvec_pe_hit *hits, hc_links *link, bubble_type *bub)
{
uint32_t k, l, i, m, h_occ;
uint32_t qs[2], qe[2], ts[2], te[2], len;
uint32_t q_beg, q_end, t_beg, t_end, ovlpS[2], ovlpE[2];
uint64_t shif = 64 - idx->uID_bits, qn, tn, u_dis;
pe_hit *h_a = NULL;
hc_linkeage *t = NULL;
u_trans_t *p = NULL;
kv_u_trans_t k_trans;
kv_init(k_trans);
if(hits->idx.n == 0) idx_hc_links(hits, idx, bub);
void measure_distance(const ma_ug_t* ug, kvec_pe_hit* hits, hc_links* link, bubble_type* bub, kv_u_trans_t *ta)
for (qn = 0; qn < hits->idx.n; qn++)
{
if(IF_HOM(qn, *bub)) continue;
h_a = hits->a.a + (hits->idx.a[qn]>>32);
h_occ = (uint32_t)(hits->idx.a[qn]);
len = idx->ug->g->seq[qn].len;
qs[0] = 0;
qe[0] = (len&1? ((len>>1) + 1) : (len>>1));
qs[1] = (len>>1);
qe[1] = len;
for (k = 1, l = 0; k <= h_occ; ++k) ///same qn
{
if (k == h_occ || ((h_a[k].e<<1)>>shif) != ((h_a[l].e<<1)>>shif)) //same qn and tn
{
tn = ((h_a[l].e<<1)>>shif);
if(!IF_HOM(tn, *bub) && tn != qn)
{
t = &(link->a.a[qn]);
for (i = 0, u_dis = (uint64_t)-1; i < t->e.n; i++)
{
if(t->e.a[i].del || t->e.a[i].uID != tn) continue;
u_dis = (t->e.a[i].dis ==(uint64_t)-1? (uint64_t)-1 : t->e.a[i].dis>>3);
break;
}
if(u_dis == (uint64_t)-1)
{
len = idx->ug->g->seq[tn].len;
ts[0] = 0;
te[0] = (len&1? ((len>>1) + 1) : (len>>1));
ts[1] = (len>>1);
te[1] = len;
for (i = l; i < k; i++)
{
ovlpS[0] = ovlpS[1] = 0;
ovlpE[0] = ovlpE[1] = 0;
interpr_hit(idx, h_a[i].s, h_a[i].len>>32, NULL, &s_beg, &s_end);
ovlpS[0] = ((MIN(i_tEcur, q->tEcur) > MAX(i_tScur, q->tScur))?
MIN(i_tEcur, q->tEcur) - MAX(i_tScur, q->tScur):0);
ovlp = ((MIN(i_tEcur, q->tEcur) > MAX(i_tScur, q->tScur))?
MIN(i_tEcur, q->tEcur) - MAX(i_tScur, q->tScur):0);
interpr_hit(idx, h_a[i].e, (uint32_t)h_a[i].len, NULL, &e_beg, &e_end);
}
kv_pushp(u_trans_t, k_trans, &p);
p->qn = qn; p->tn = tn; p->occ = (k-l);
kv_pushp(u_trans_t, k_trans, &p);
p->qn = tn; p->tn = qn; p->occ = (k-l);
}
}
l = k;
}
}
}
radix_sort_u_trans_m(k_trans.a, k_trans.a + k_trans.n);
for (k = 1, l = 0, m = 0; k <= k_trans.n; ++k)
{
if (k == k_trans.n || k_trans.a[l].qn != k_trans.a[k].qn || k_trans.a[l].tn != k_trans.a[k].tn) //same qn and tn
{
for (i = l, h_occ = 0; i < k; i++)
{
h_occ += k_trans.a[i].occ;
}
k_trans.a[m] = k_trans.a[l];
k_trans.a[m].occ = ((uint32_t)-1) - h_occ;
m++;
l = k;
}
}
k_trans.n = m;
radix_sort_u_trans_occ(k_trans.a, k_trans.a + k_trans.n);
for (i = 0; i < k_trans.n; i++)
{
qn = k_trans.a[i].qn;
tn = k_trans.a[i].tn;
fprintf(stderr, "s-utg%.6lul<--->d-utg%.6lul(occ: %u)\n", qn + 1, tn + 1,
((uint32_t)-1) - k_trans.a[i].occ);
}
fprintf(stderr, "########hits########\n");
char dir[2] = {'+', '-'};
for (k = 0; k < hits->a.n; ++k)
{
fprintf(stderr, "%c\tutg%.6dl(len-%u)\t%lu\t%c\tutg%.6dl(len-%u)\t%lu\ti:%lu\n",
dir[hits->a.a[k].s>>63], (int)((hits->a.a[k].s<<1)>>shif)+1,
idx->ug->g->seq[((hits->a.a[k].s<<1)>>shif)].len, hits->a.a[k].s&idx->pos_mode,
dir[hits->a.a[k].e>>63], (int)((hits->a.a[k].e<<1)>>shif)+1,
idx->ug->g->seq[((hits->a.a[k].e<<1)>>shif)].len, hits->a.a[k].e&idx->pos_mode,
hits->a.a[k].id);
}
kv_destroy(k_trans);
}
**/
void idx_hc_links(kvec_pe_hit* hits, ha_ug_index* idx, bubble_type* bub);
void filter_disconnect_edges(ha_ug_index* idx, kvec_pe_hit *hits, hc_links *link, bubble_type *bub, uint32_t thres, double rate)
{
uint32_t k, l, i, m, h_occ, *occ = NULL;
uint64_t shif = 64 - idx->uID_bits, qn, tn, u_dis;
pe_hit *h_a = NULL;
hc_linkeage *t = NULL;
u_trans_t *p = NULL;
hc_edge *e = NULL;
kv_u_trans_t k_trans;
kv_init(k_trans);
if(hits->idx.n == 0) idx_hc_links(hits, idx, bub);
CALLOC(occ, hits->idx.n);
for (qn = 0; qn < hits->idx.n; qn++)
{
if(IF_HOM(qn, *bub)) continue;
h_a = hits->a.a + (hits->idx.a[qn]>>32);
h_occ = (uint32_t)(hits->idx.a[qn]);
for (k = 1, l = 0; k <= h_occ; ++k) ///same qn
{
if (k == h_occ || ((h_a[k].e<<1)>>shif) != ((h_a[l].e<<1)>>shif)) //same qn and tn
{
tn = ((h_a[l].e<<1)>>shif);
if(!IF_HOM(tn, *bub) && tn != qn)
{
t = &(link->a.a[qn]);
for (i = 0, u_dis = (uint64_t)-1; i < t->e.n; i++)
{
if(t->e.a[i].del || t->e.a[i].uID != tn) continue;
u_dis = (t->e.a[i].dis ==(uint64_t)-1? (uint64_t)-1 : t->e.a[i].dis>>3);
break;
}
if(u_dis == (uint64_t)-1)
{
kv_pushp(u_trans_t, k_trans, &p);
p->qn = qn; p->tn = tn; p->occ = (k-l);
kv_pushp(u_trans_t, k_trans, &p);
p->qn = tn; p->tn = qn; p->occ = (k-l);
}
else
{
occ[qn] += (k-l); occ[tn] += (k-l);
}
}
l = k;
}
}
}
radix_sort_u_trans_m(k_trans.a, k_trans.a + k_trans.n);
for (k = 1, l = 0, m = 0; k <= k_trans.n; ++k)
{
if (k == k_trans.n || k_trans.a[l].qn != k_trans.a[k].qn || k_trans.a[l].tn != k_trans.a[k].tn) //same qn and tn
{
if(k - l > 2) fprintf(stderr, "ERROR-3\n");
for (i = l, h_occ = 0; i < k; i++)
{
h_occ += k_trans.a[i].occ;
}
k_trans.a[m] = k_trans.a[l];
// k_trans.a[m].occ = ((uint32_t)-1) - h_occ;
k_trans.a[m].occ = h_occ;
if(h_occ > thres || h_occ >= (occ[k_trans.a[m].qn]*rate) || h_occ >= (occ[k_trans.a[m].tn]*rate))
{
e = get_hc_edge(link, k_trans.a[m].qn, k_trans.a[m].tn, 0);
if(e->dis != (uint64_t)-1) fprintf(stderr, "ERROR-3-0\n");
e->is_cc = 1;
e = get_hc_edge(link, k_trans.a[m].tn, k_trans.a[m].qn, 0);
if(e->dis != (uint64_t)-1) fprintf(stderr, "ERROR-3-0\n");
e->is_cc = 1;
}
m++;
l = k;
}
}
k_trans.n = m;
kv_destroy(k_trans); free(occ);
}
void measure_distance(ha_ug_index* idx, const ma_ug_t* ug, kvec_pe_hit* hits, hc_links* link, bubble_type* bub, kv_u_trans_t *ta)
{
// double index_time = yak_realtime();
MT M;
@@ -4143,9 +4353,20 @@ void measure_distance(const ma_ug_t* ug, kvec_pe_hit* hits, hc_links* link, bubb
update_containment_distance(copy_sg, ta, link);
// update_dis_connected_gfa(copy_sg, link, &M);
asg_destroy(copy_sg);
destory_MT(&M);
for (i = 0; i < link->a.n; i++)
{
for (k = 0; k < link->a.a[i].e.n; k++)
{
link->a.a[i].e.a[k].is_cc = 0;
if(link->a.a[i].e.a[k].del) continue;
if(link->a.a[i].e.a[k].dis == (uint64_t)-1) continue;
link->a.a[i].e.a[k].is_cc = 1;
}
}
// filter_disconnect_edges(idx, hits, link, bub, 1, 0.01);
// fprintf(stderr, "[M::%s::%.3f] ==> Hi-C linkages have been counted\n", __func__, yak_realtime()-index_time);
return;
}
@@ -5828,17 +6049,22 @@ G_partition* clean_bubbles(hc_links* link, bubble_type* bub, min_cut_t* m, const
return x;
}
uint64_t get_hic_distance(pe_hit* hit, hc_links* link, const ha_ug_index* idx)
uint64_t get_hic_distance(pe_hit* hit, hc_links* link, const ha_ug_index* idx, uint32_t *is_cc)
{
uint64_t s_uid, s_dir, e_uid, e_dir, u_dis, k;
long long s_pos, e_pos;
s_uid = ((hit->s<<1)>>(64 - idx->uID_bits)); s_pos = hit->s & idx->pos_mode;
e_uid = ((hit->e<<1)>>(64 - idx->uID_bits)); e_pos = hit->e & idx->pos_mode;
if(s_uid == e_uid) return MAX(s_pos, e_pos) - MIN(s_pos, e_pos);
if(s_uid == e_uid)
{
if(is_cc) (*is_cc) = 1;
return MAX(s_pos, e_pos) - MIN(s_pos, e_pos);
}
hc_linkeage* t = &(link->a.a[s_uid]);
for (k = 0; k < t->e.n; k++)
{
if(t->e.a[k].del || t->e.a[k].uID != e_uid) continue;
if(is_cc) (*is_cc) = t->e.a[k].is_cc;
s_dir = (!!(t->e.a[k].dis&(uint64_t)2));
e_dir = (!!(t->e.a[k].dis&(uint64_t)1));
u_dis = (t->e.a[k].dis ==(uint64_t)-1? (uint64_t)-1 : t->e.a[k].dis>>3);
@@ -5890,27 +6116,35 @@ inline double get_trans_weight_advance(const ha_ug_index* idx, uint64_t x, trans
{
long double rate = 0;
if(x == (uint64_t)-1) x = dis->med;
if(x < dis->max)
///if(x == (uint64_t)-1) x = dis->med;
if(x != (uint64_t)-1)
{
uint64_t i;
for (i = 0; i < dis->n; i++)
if(x < dis->max)
{
if(x < dis->a[i].end && x >= dis->a[i].beg) break;
}
if(i < dis->n)
{
rate = ((double)(dis->a[i].cnt_1))/((double)(dis->a[i].cnt_0 + dis->a[i].cnt_1));
uint64_t i;
for (i = 0; i < dis->n; i++)
{
if(x < dis->a[i].end && x >= dis->a[i].beg) break;
}
if(i < dis->n)
{
rate = ((double)(dis->a[i].cnt_1))/((double)(dis->a[i].cnt_0 + dis->a[i].cnt_1));
}
else
{
rate = get_trans(idx, x);
}
}
else
{
rate = get_trans(idx, x);
}
}
}
else
{
rate = get_trans(idx, x);
rate = 0.2;
}
if(rate < 0) rate = 0;
rate += OFFSET_RATE;
@@ -6010,7 +6244,7 @@ void weight_edges_advance(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, b
if(IF_HOM(beg, *bub)) continue;
if(IF_HOM(end, *bub)) continue;
t_d = get_hic_distance(&(hits->a.a[k]), link, idx);
t_d = get_hic_distance(&(hits->a.a[k]), link, idx, NULL);
if(t_d == (uint64_t)-1) continue;
e1 = get_hc_edge(link, beg, end, 0);
@@ -9083,7 +9317,7 @@ H_partition* hap, int8_t *s, trans_idx* dis)
if(IF_HOM(end, *bub)) continue;
t_d = get_hic_distance(&(hits->a.a[k]), link, idx);
t_d = get_hic_distance(&(hits->a.a[k]), link, idx, NULL);
if(t_d == (uint64_t)-1) continue;
if(beg == end)
{
@@ -9257,7 +9491,7 @@ H_partition* hap, int8_t *s, trans_idx* dis)
if(IF_HOM(end, *bub)) continue;
if(beg == end) continue;
t_d = get_hic_distance(&(hits->a.a[k]), link, idx);
t_d = get_hic_distance(&(hits->a.a[k]), link, idx, NULL);
if(t_d == (uint64_t)-1) continue;
kv_push(uint64_t, buf, t_d);
}
@@ -13748,7 +13982,7 @@ int alignment_worker_pipeline(sldat_t* sl, const enzyme *fn1, const enzyme *fn2)
return 1;
}
void debug_gfa_space(ma_ug_t* ug, trans_chain* t_ch, kv_u_trans_t *ref)
void debug_gfa_space(ha_ug_index* idx, ma_ug_t* ug, trans_chain* t_ch, kv_u_trans_t *ref)
{
bubble_type bub;
memset(&bub, 0, sizeof(bubble_type));
@@ -13759,7 +13993,7 @@ void debug_gfa_space(ma_ug_t* ug, trans_chain* t_ch, kv_u_trans_t *ref)
hc_links link;
init_hc_links(&link, ug->g->n_seq, t_ch);
measure_distance(ug, NULL, &link, &bub, &(t_ch->k_trans));
measure_distance(idx, ug, NULL, &link, &bub, &(t_ch->k_trans));
// uint32_t i, k;
// for (i = 0; i < link.a.n; ++i)
@@ -13858,6 +14092,7 @@ kv_u_trans_t *ta, trans_idx* dis)
u_trans_t *e1 = NULL, *e2 = NULL;
long double weight;
u_trans_t *p = NULL;
uint32_t is_cc;
for (i = 0, ta->idx.n = ta->n = 0; i < link->a.n; i++)
{
@@ -13886,8 +14121,10 @@ kv_u_trans_t *ta, trans_idx* dis)
if(IF_HOM(beg, *bub)) continue;
if(IF_HOM(end, *bub)) continue;
t_d = get_hic_distance(&(hits->a.a[k]), link, idx);
if(t_d == (uint64_t)-1) continue;
t_d = get_hic_distance(&(hits->a.a[k]), link, idx, &is_cc);
// if(t_d == (uint64_t)-1) continue;
// if(t_d == (uint64_t)-1 && is_cc == 0) continue;
// if(t_d == (uint64_t)-1 && !dis) continue;
get_u_trans_spec(ta, beg, end, &e1, NULL);
get_u_trans_spec(ta, end, beg, &e2, NULL);
@@ -13956,7 +14193,7 @@ pe_hit *hits, uint32_t occ, uint32_t qid, uint32_t qs, uint32_t qe, uint32_t tid
if(e_uid != tid) break;
if(!(ts <= e_beg && te >= e_end)) continue;
t_d = get_hic_distance(&hits[k], link, idx);
t_d = get_hic_distance(&hits[k], link, idx, NULL);
if(t_d == (uint64_t)-1) continue;
weight = 1;
@@ -13976,7 +14213,7 @@ pe_hit *hits, uint32_t occ, uint32_t qid, uint32_t qs, uint32_t qe, uint32_t tid
if(e_uid != tid) break;
if(!(ts <= e_beg && te >= e_end)) continue;
t_d = get_hic_distance(&hits[k], link, idx);
t_d = get_hic_distance(&hits[k], link, idx, NULL);
if(t_d == (uint64_t)-1) continue;
weight = 1;
@@ -14151,7 +14388,7 @@ inline uint32_t get_trans_interval_weight(ha_ug_index* idx, hc_links* link, bubb
trans_idx* dis, pe_hit *hit, uint32_t hit_n, uint32_t qn, uint32_t qs, uint32_t qe, uint32_t tn,
uint32_t ts, uint32_t te, double *w_a)
{
uint32_t i, s_uid, s_beg, s_end, e_uid, e_beg, e_end, found;
uint32_t i, s_uid, s_beg, s_end, e_uid, e_beg, e_end, found, is_cc;
uint64_t t_d;
double weight;
(*w_a) = 0; found = 0;
@@ -14165,8 +14402,10 @@ uint32_t ts, uint32_t te, double *w_a)
if(e_uid != tn) continue;
if(!(ts <= e_beg && te >= e_end)) continue;
t_d = get_hic_distance(&hit[i], link, idx);
if(t_d == (uint64_t)-1) continue;
t_d = get_hic_distance(&hit[i], link, idx, &is_cc);
// if(t_d == (uint64_t)-1) continue;
// if(t_d == (uint64_t)-1 && is_cc == 0) continue;
// if(t_d == (uint64_t)-1 && !dis) continue;
weight = 1;
if(dis) weight = get_trans_weight_advance(idx, t_d, dis);
@@ -14265,7 +14504,10 @@ double merge_u_trans_list(u_trans_t* a, uint32_t a_n)
weight += a[i].nw;
}
w += (weight/(double)(a[l].occ));
/*******************************for debug************************************/
// w += (weight/(double)(a[l].occ));
w += weight;
/*******************************for debug************************************/
l = k;
}
}
@@ -14353,6 +14595,29 @@ void print_kv_weight(kv_u_trans_t *ta)
}
}
}
void print_debug_hc_links(ha_ug_index* idx, bubble_type* bub, hc_links* lk, kv_u_trans_t *ta, kvec_pe_hit* hits)
{
uint64_t k, len = 0, shif = 64 - idx->uID_bits, beg, end;
hc_edge *e = NULL;
for (k = 0; k < hits->a.n; ++k)
{
beg = ((hits->a.a[k].s<<1)>>shif);
end = ((hits->a.a[k].e<<1)>>shif);
if(beg == end) continue;
if(IF_HOM(beg, *bub)) continue;
if(IF_HOM(end, *bub)) continue;
len += (hits->a.a[k].len>>32) + ((uint32_t)hits->a.a[k].len);
}
fprintf(stderr, "# total Hi-C aligned bases: %lu\n", len);
for (k = 0; k < ta->n; k++)
{
e = get_hc_edge(lk, ta->a[k].qn, ta->a[k].tn, 0);
fprintf(stderr, "s-utg%.6ul\td-utg%.6ul\tD:%lu\tW:%f\n",
ta->a[k].qn+1, ta->a[k].tn+1, e->dis == (uint64_t)-1? (uint64_t)-1 : e->dis>>3, ta->a[k].nw);
}
}
void renew_kv_u_trans(kv_u_trans_t *ta, hc_links *lk, kvec_pe_hit* hits, kv_u_trans_t *ref,
ha_ug_index* idx, bubble_type* bub, int8_t *s, uint32_t ignore_dis)
{
@@ -14380,6 +14645,10 @@ ha_ug_index* idx, bubble_type* bub, int8_t *s, uint32_t ignore_dis)
if(hits->idx.n == 0) idx_hc_links(hits, idx, bub);
weight_kv_u_trans(idx, hits, lk, bub, ta, is_comples_weight == 1? &dis : NULL);
// if(bub->round_id == bub->n_round-1)
// {
// print_debug_hc_links(idx, bub, lk, ta, hits);
// }
// adjust_weight_kv_u_trans(idx, hits, lk, bub, ta, ref, is_comples_weight == 1? &dis : NULL);
adjust_weight_kv_u_trans_advance(idx, hits, lk, bub, ta, ref, is_comples_weight == 1? &dis : NULL);
kv_destroy(dis);
@@ -14429,6 +14698,94 @@ void verbose_het_stat(bubble_type *bub)
fprintf(stderr, "[M::stat] # heterozygous bases: %lu; # homozygous bases: %lu\n", hetBase, homBase);
}
void debug_output_disconnected_hits(ha_ug_index* idx, kvec_pe_hit *hits, hc_links *link, bubble_type *bub)
{
uint32_t k, l, i, m, h_occ;
uint64_t shif = 64 - idx->uID_bits, qn, tn, u_dis;
pe_hit *h_a = NULL;
hc_linkeage *t = NULL;
u_trans_t *p = NULL;
kv_u_trans_t k_trans;
kv_init(k_trans);
for (qn = 0; qn < hits->idx.n; qn++)
{
if(IF_HOM(qn, *bub)) continue;
h_a = hits->a.a + (hits->idx.a[qn]>>32);
h_occ = (uint32_t)(hits->idx.a[qn]);
for (k = 1, l = 0; k <= h_occ; ++k) ///same qn
{
if (k == h_occ || ((h_a[k].e<<1)>>shif) != ((h_a[l].e<<1)>>shif)) //same qn and tn
{
tn = ((h_a[l].e<<1)>>shif);
if(!IF_HOM(tn, *bub) && tn != qn)
{
t = &(link->a.a[qn]);
for (i = 0, u_dis = (uint64_t)-1; i < t->e.n; i++)
{
if(t->e.a[i].del || t->e.a[i].uID != tn) continue;
u_dis = (t->e.a[i].dis ==(uint64_t)-1? (uint64_t)-1 : t->e.a[i].dis>>3);
break;
}
if(u_dis == (uint64_t)-1)
{
kv_pushp(u_trans_t, k_trans, &p);
p->qn = qn; p->tn = tn; p->occ = (k-l);
kv_pushp(u_trans_t, k_trans, &p);
p->qn = tn; p->tn = qn; p->occ = (k-l);
}
}
l = k;
}
}
}
radix_sort_u_trans_m(k_trans.a, k_trans.a + k_trans.n);
for (k = 1, l = 0, m = 0; k <= k_trans.n; ++k)
{
if (k == k_trans.n || k_trans.a[l].qn != k_trans.a[k].qn || k_trans.a[l].tn != k_trans.a[k].tn) //same qn and tn
{
for (i = l, h_occ = 0; i < k; i++)
{
h_occ += k_trans.a[i].occ;
}
k_trans.a[m] = k_trans.a[l];
k_trans.a[m].occ = ((uint32_t)-1) - h_occ;
m++;
l = k;
}
}
k_trans.n = m;
radix_sort_u_trans_occ(k_trans.a, k_trans.a + k_trans.n);
for (i = 0; i < k_trans.n; i++)
{
qn = k_trans.a[i].qn;
tn = k_trans.a[i].tn;
fprintf(stderr, "s-utg%.6lul<--->d-utg%.6lul(occ: %u)\n", qn + 1, tn + 1,
((uint32_t)-1) - k_trans.a[i].occ);
}
fprintf(stderr, "########hits########\n");
char dir[2] = {'+', '-'};
for (k = 0; k < hits->a.n; ++k)
{
fprintf(stderr, "%c\tutg%.6dl(len-%u)\t%lu\t%c\tutg%.6dl(len-%u)\t%lu\ti:%lu\n",
dir[hits->a.a[k].s>>63], (int)((hits->a.a[k].s<<1)>>shif)+1,
idx->ug->g->seq[((hits->a.a[k].s<<1)>>shif)].len, hits->a.a[k].s&idx->pos_mode,
dir[hits->a.a[k].e>>63], (int)((hits->a.a[k].e<<1)>>shif)+1,
idx->ug->g->seq[((hits->a.a[k].e<<1)>>shif)].len, hits->a.a[k].e&idx->pos_mode,
hits->a.a[k].id);
}
kv_destroy(k_trans);
}
int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
{
double index_time = yak_realtime();
@@ -14470,7 +14827,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
identify_bubbles(idx->ug, &bub, idx->t_ch->is_r_het, &(idx->t_ch->k_trans));
if(bub.round_id == 0)
{
measure_distance(idx->ug, &sl.hits, &link, &bub, &(idx->t_ch->k_trans));
measure_distance(idx, idx->ug, &sl.hits, &link, &bub, &(idx->t_ch->k_trans));
}
renew_kv_u_trans(&k_trans, &link, &sl.hits, &(idx->t_ch->k_trans), idx, &bub, s->s, 0);
@@ -14481,6 +14838,13 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
(bub.round_id == 0? 1 : 0), s->s, 1, /**&bub**/NULL, &(idx->t_ch->k_trans));
/*******************************for debug************************************/
label_unitigs_sm(s->s, idx->ug);
/*******************************for debug************************************/
// if(bub.round_id == bub.n_round - 1)
// {
// debug_output_disconnected_hits(idx, &sl.hits, &link, &bub);
// }
/*******************************for debug************************************/
/**
init_hic_advance((ha_ug_index*)sl.idx, &sl.hits, &link, &bub, &hap, 0);
reset_H_partition(&hap, (bub.round_id == 0? 1 : 0));
rcut.cpp
+2
View File
@@ -2814,6 +2814,8 @@ void mc_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, kv_u_trans_t *ta, ma_u
mc_opt_init(&opt, asm_opt.n_perturb, asm_opt.f_perturb, asm_opt.seed);
mc_g_t *mg = init_mc_g_t(ug, read_g, s, renew_s);
update_mc_edges(mg, ovlp, ta, t_ch, f_rate, is_sys);
fprintf(stderr, "[M::%s:: # edges: %u]\n", __func__, (uint32_t)mg->e->ma.n);
mb_solve_core(&opt, mg, ref, is_sys);
///debug_mc_g_t(mg);