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chhylp123
2021-06-16 16:44:08 -04:00
parent 5b0a0c85ef
commit e3b721c29a
3 changed files with 459 additions and 42 deletions
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hic.cpp
+299 -24
View File
@@ -274,6 +274,10 @@ KRADIX_SORT_INIT(hc_s_hit_off_cnt, s_hit, hc_s_hit_off_cnt_key, 8)
KRADIX_SORT_INIT(hc_edge_u, hc_edge, hc_edge_key_u, 4)
#define hc_edge_key_d(a) ((a).dis)
KRADIX_SORT_INIT(hc_edge_d, hc_edge, hc_edge_key_d, member_size(hc_edge, dis))
#define k_trans_qs_key(a) ((a).qs)
KRADIX_SORT_INIT(k_trans_qs, u_trans_t, k_trans_qs_key, member_size(u_trans_t, qs))
#define get_hit_suid(x, k) (((x).a.a[(k)].s<<1)>>(64 - (x).uID_bits))
#define get_hit_spos(x, k) ((x).a.a[(k)].s & (x).pos_mode)
#define get_hit_euid(x, k) (((x).a.a[(k)].e<<1)>>(64 - (x).uID_bits))
@@ -15116,7 +15120,7 @@ kv_u_trans_t *res, uint32_t qn, uint32_t tn)
kv_pushp(u_trans_t, *res, &p);
memset(p, 0, sizeof(u_trans_t));
p->qn = qn; p->tn = r_a[i].tn;
p->nw = w;
p->nw = w/**r_a[i].occ**/;
p->occ = MIN(occ_q, occ_t);
kv_pushp(u_trans_t, *res, &q);
@@ -15147,7 +15151,7 @@ kv_u_trans_t *res, uint32_t qn, uint32_t tn)
kv_pushp(u_trans_t, *res, &p);
memset(p, 0, sizeof(u_trans_t));
p->qn = tn; p->tn = r_a[i].tn;
p->nw = w;
p->nw = w/**r_a[i].occ**/;
p->occ = MIN(occ_q, occ_t);
kv_pushp(u_trans_t, *res, &q);
@@ -15208,7 +15212,7 @@ kv_u_trans_t *ta, kv_u_trans_t *ref, trans_idx* dis)
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
if (k == h_occ || ((h_a[k].e<<1)>>shif) != ((h_a[l].e<<1)>>shif)) //same tn
{
tn = ((h_a[l].e<<1)>>shif);
if(!IF_HOM(tn, *bub))
@@ -15678,7 +15682,7 @@ typedef struct{
void insert_dip_chain(kv_f_chain *x, u_trans_t *p, double LenRate)
{
uint32_t i;
uint64_t ovlp = 0, tLen = MIN(x->tov, p->qe-p->qs), qs, qe;
uint64_t ovlp = 0, tLen = MIN(x->tov, p->qe-p->qs);
int64_t dp, old_dp, start = 0;
f_chain_t *t = NULL;
double r;
@@ -15740,7 +15744,37 @@ void insert_dip_chain(kv_f_chain *x, u_trans_t *p, double LenRate)
}
}
void filter_kv_u_trans_t(kv_u_trans_t *ta, ma_ug_t* ug)
uint32_t get_MAPQ(u_trans_t *a, uint32_t a_n, uint32_t idx, double secondRate)
{
uint32_t i;
u_trans_t *p = &(a[idx]);
uint64_t ovlp = 0;
double aw = 0;
for (i = 0; i < a_n; i++)
{
if(i == idx) continue;
ovlp = ((MIN(a[i].qe, p->qe) > MAX(a[i].qs, p->qs))?
(MIN(a[i].qe, p->qe) - MAX(a[i].qs, p->qs)):0);
// if(p->qn == 447 && p->tn == 5495)
// {
// fprintf(stderr, "ovlp: %lu, secondRate: %f, len: %u\n", ovlp, secondRate, MIN(a[i].qe - a[i].qs, p->qe - p->qs));
// }
if(ovlp == 0) continue;
if(ovlp <= (secondRate*MIN(a[i].qe - a[i].qs, p->qe - p->qs))) continue;
aw += a[i].nw;
}
// if(p->qn == 447 && p->tn == 5495) fprintf(stderr, "aw: %f\n", aw);
aw = aw/p->nw;
// if(p->qn == 447 && p->tn == 5495) fprintf(stderr, "aw: %f\n", aw);
if(aw >= 1) return 16;
if(aw >= 0.75) return 8;
if(aw >= 0.5) return 4;
if(aw >= 0.25) return 2;
return 1;
}
void filter_kv_u_trans_t(kv_u_trans_t *ta, ma_ug_t* ug, double secondRate)
{
kv_f_chain x;
memset(&x, 0, sizeof(kv_f_chain)); x.tw = 0;
@@ -15756,28 +15790,267 @@ void filter_kv_u_trans_t(kv_u_trans_t *ta, ma_ug_t* ug)
for (i = 0; i < n; i++)
{
if(a[i].del) continue;
insert_dip_chain(&x, &(a[i]), 0.5);
//if(a[i].del) is_clean = 1;
insert_dip_chain(&x, &(a[i]), secondRate);
}
// if(is_clean)
// {
// fprintf(stderr, "\n***utg%.6ul, w: %f, cov: %lu, len: %u\n", a[0].qn+1, x.tw, x.tov, ug->g->seq[a[0].qn].len);
// for (i = 0; i < x.n; i++)
// {
// fprintf(stderr, "s: %lu, e: %lu\n", x.a[i].s, x.a[i].e);
// }
// u_trans_t *p = NULL;
// for (i = 0; i < n; i++)
// {
// p = &(a[i]);
// fprintf(stderr, "qs(%u)\tqe(%u)\tt-utg%.6ul(len:%u)\tts(%u)\tte(%u)\trev(%u)\tw(%f)\tdel(%u)\n",
// p->qs, p->qe, p->tn+1, ug->g->seq[p->tn].len, p->ts, p->te, p->rev, p->nw, p->del);
// }
// }
}
free(x.a); free(x.b.a);
kt_u_trans_t_idx(ta, ug->g->n_seq);
kt_u_trans_t_simple_symm(ta, ug->g->n_seq, 0);
/**
for (k = 0; k < ta->idx.n; k++)
{
a = u_trans_a(*ta, k);
n = u_trans_n(*ta, k);
if(n == 0) continue;
// radix_sort_k_trans_qs(a, a+n);
for (i = 0; i < n; i++)
{
a[i].occ = get_MAPQ(a, n, i, secondRate);
// if(a[i].occ != 1)
// {
// uint32_t debug_i;
// fprintf(stderr, "\nq-utg%.6ul\tt-utg%.6ul\tocc-%u\n", a[i].qn+1, a[i].tn+1, a[i].occ);
// for (debug_i = 0; debug_i < n; debug_i++)
// {
// fprintf(stderr, "q-utg%.6ul\tqs(%u)\tqe(%u)\tt-utg%.6ul\tts(%u)\tte(%u)\trev(%u)\tw(%f)\tf(%u)\n",
// a[debug_i].qn+1, a[debug_i].qs, a[debug_i].qe, a[debug_i].tn+1, a[debug_i].ts,
// a[debug_i].te, a[debug_i].rev, a[debug_i].nw, a[debug_i].f);
// }
// }
}
}
for (k = 0; k < ta->n; k++)
{
if(ta->a[k].del || ta->a[k].qn > ta->a[k].tn) continue;
get_u_trans_spec(ta, ta->a[k].tn, ta->a[k].qn, &r_a, NULL);
a = &(ta->a[k]);
a->occ = r_a->occ = MAX(a->occ, r_a->occ);
}
**/
}
uint64_t check_ovlp(f_chain_t *o, uint64_t on, uint64_t qs, uint64_t qe)
{
uint64_t i, ovlp;
for (i = 0; i < on; i++)
{
ovlp = ((MIN(o[i].e, qe) > MAX(o[i].s, qs))?
(MIN(o[i].e, qe) - MAX(o[i].s, qs)):0);
if(ovlp) return 1;
}
return 0;
}
void flter_by_cov(ha_ug_index* idx, kvec_pe_hit *hits, int64_t min_dp)
{
uint64_t i, m, k, l, pos_bits = 64 - idx->uID_bits - 1, uid, pM = ((uint64_t)-1)>>idx->uID_bits, *a = NULL, a_n;
uint32_t s_uid, s_beg, s_end, e_uid, e_beg, e_end;
int64_t dp, old_dp, start = 0;
f_chain_t *t = NULL;
kvec_t(uint64_t) b; kv_init(b);
kvec_t(f_chain_t) x; kv_init(x);
uint64_t *index = NULL; CALLOC(index, idx->ug->u.n);
for (i = 0; i < hits->a.n; i++)
{
interpr_hit(idx, hits->a.a[i].s, hits->a.a[i].len>>32, &s_uid, &s_beg, &s_end);
m = s_uid; m <<= pos_bits; m += s_beg; m <<= 1; kv_push(uint64_t, b, m);
m = s_uid; m <<= pos_bits; m += s_end; m <<= 1; m += 1; kv_push(uint64_t, b, m);
interpr_hit(idx, hits->a.a[i].e, (uint32_t)hits->a.a[i].len, &e_uid, &e_beg, &e_end);
m = e_uid; m <<= pos_bits; m += e_beg; m <<= 1; kv_push(uint64_t, b, m);
m = e_uid; m <<= pos_bits; m += e_end; m <<= 1; m += 1; kv_push(uint64_t, b, m);
}
radix_sort_hc64(b.a, b.a + b.n);
for (k = 1, l = 0; k <= b.n; ++k)
{
if (k == b.n || (b.a[k]>>(64 - idx->uID_bits)) != (b.a[l]>>(64 - idx->uID_bits)))
{
uid = (b.a[l]>>(64 - idx->uID_bits));
a = b.a + l; a_n = k - l; index[uid] = x.n;
for (i = 0, dp = 0, start = 0; i < a_n; ++i)
{
old_dp = dp;
///if a[j] is qe
if (a[i]&1) --dp;
else ++dp;
if (old_dp < min_dp && dp >= min_dp) ///old_dp < dp, b.a[j] is qs
{
///case 2, a[j] is qs
start = (a[i]&pM)>>1;
}
else if (old_dp >= min_dp && dp < min_dp) ///old_dp > min_dp, b.a[j] is qe
{
kv_pushp(f_chain_t, x, &t);
t->s = start; t->e = (a[i]&pM)>>1;
}
}
index[uid] |= ((uint64_t)(x.n - index[uid]))<<32;
l = k;
}
}
for (i = m = 0; i < hits->a.n; i++)
{
interpr_hit(idx, hits->a.a[i].s, hits->a.a[i].len>>32, &s_uid, &s_beg, &s_end);
if(!check_ovlp(x.a+((uint32_t)index[s_uid]), index[s_uid]>>32, s_beg, s_end)) continue;
interpr_hit(idx, hits->a.a[i].e, (uint32_t)hits->a.a[i].len, &e_uid, &e_beg, &e_end);
if(!check_ovlp(x.a+((uint32_t)index[e_uid]), index[e_uid]>>32, e_beg, e_end)) continue;
hits->a.a[m] = hits->a.a[i];
m++;
}
fprintf(stderr, "[M::%s::] # old Hi-C pairs: %lu, # new Hi-C pairs: %lu\n",
__func__, hits->a.n, m);
hits->a.n = m;
kv_destroy(b); kv_destroy(x); free(index);
}
void set_tag_pre_read(uint64_t *r_tag, uint64_t id, uint64_t off, uint64_t pos, ma_hit_t_alloc* sources)
{
uint64_t i, tn;
ma_hit_t *h = NULL;
if(r_tag[id] == (uint64_t)-1) r_tag[id] = 0;
r_tag[id] += off;
// if(id == 2531247) fprintf(stderr, "***id: %lu, off: %lu, pos: %lu\n", id, off, pos);
for (i = 0; i < (uint64_t)(sources[id].length); i++)
{
h = &(sources[id].buffer[i]);
if(!h->el) continue;
tn = Get_tn((*h));
if(pos >= Get_qs((*h)) && pos < Get_qe((*h)))
{
// if(tn == 2531247) fprintf(stderr, "###id: %lu, off: %lu, tn: %lu, pos: %lu\n", id, off, tn, pos);
if(r_tag[tn] == (uint64_t)-1) r_tag[tn] = 0;
r_tag[tn] += off;
}
}
}
void tag_reads(ha_ug_index* idx, kvec_pe_hit *u_hits, bubble_type* bub, int8_t *s, ma_hit_t_alloc* sources)
{
kvec_pe_hit *r_hits = get_r_hits_for_trio(u_hits, idx->read_g, idx->ug, bub, idx->uID_bits, idx->pos_mode);
uint64_t *r_tag = NULL, i, k, srid, erid, /**rid, occ, a_occ, **/flag = AMBIGU, cons = 0, incons = 0/**, max, min**/;
ma_utg_t *u = NULL;
ma_ug_t* ug = idx->ug;
int8_t ss, es, sr;
CALLOC(r_tag, idx->read_g->n_seq);
cons = 0, incons = 0;
memset(r_tag, -1, sizeof(uint64_t)*idx->read_g->n_seq);
for (i = 0; i < r_hits->a.n; i++)
{
srid = get_hit_suid(*r_hits, i);
erid = get_hit_euid(*r_hits, i);
ss = s[r_hits->a.a[i].id>>32];
es = s[(uint32_t)r_hits->a.a[i].id];
if(ss == 0 || es == 0) continue;
if((r_hits->a.a[i].id>>32) == ((uint32_t)r_hits->a.a[i].id)) continue;
set_tag_pre_read(r_tag, srid, es < 0? 1 : ((uint64_t)1<<32), get_hit_spos(*r_hits, i), sources);
set_tag_pre_read(r_tag, erid, ss < 0? 1 : ((uint64_t)1<<32), get_hit_epos(*r_hits, i), sources);
if(ss == es) cons++;
else incons++;
}
/**
for (k = 0; k < ug->u.n; k++)
{
if(ug->g->seq[k].del) continue;
u = &(ug->u.a[k]); occ = a_occ = 0;
for (i = 0; i < u->n; i++)
{
rid = u->a[i]>>33;
if(r_tag[rid] == (uint64_t)-1) continue;
max = MAX((r_tag[rid]>>32), ((uint32_t)r_tag[rid]));
min = MIN((r_tag[rid]>>32), ((uint32_t)r_tag[rid]));
///if(max <= (total*0.7) && max != total)
if(max - min <= max *0.1)
{
fprintf(stderr, "max-%lu, min-%lu\n", max, min);
a_occ++;
}
occ++;
}
if(occ == 0) continue;
if(a_occ > occ*0.85) s[k] = 0, filter++, fprintf(stderr, "k: %lu, a_occ: %lu, occ: %lu\n", k, a_occ, occ);
}
fprintf(stderr, "[M::%s::] # consistent Hi-C pairs: %lu, # inconsistent Hi-C pairs: %lu, # filter: %lu\n",
__func__, cons, incons, filter);
memset(r_tag, -1, sizeof(uint64_t)*idx->read_g->n_seq);
for (i = 0; i < r_hits->a.n; i++)
{
srid = get_hit_suid(*r_hits, i);
erid = get_hit_euid(*r_hits, i);
ss = s[r_hits->a.a[i].id>>32];
es = s[(uint32_t)r_hits->a.a[i].id];
if(ss == 0 || es == 0) continue;
if((r_hits->a.a[i].id>>32) == ((uint32_t)r_hits->a.a[i].id)) continue;
set_tag_pre_read(r_tag, srid, es > 0? 1 : ((uint64_t)1<<32), get_hit_spos(*r_hits, i), sources);
set_tag_pre_read(r_tag, erid, ss > 0? 1 : ((uint64_t)1<<32), get_hit_epos(*r_hits, i), sources);
}
**/
fprintf(stderr, "[M::%s::] # consistent Hi-C pairs: %lu, # inconsistent Hi-C pairs: %lu\n",
__func__, cons, incons);
cons = 0, incons = 0;
memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads * sizeof(uint8_t));
for (i = 0; i < ug->g->n_seq; i++)
{
if(ug->g->seq[i].del) continue;
flag = 0;
if(s[i] == 0) continue;
flag = (s[i] > 0? FATHER:MOTHER);
u = &ug->u.a[i];
if(u->m == 0) continue;
for (k = 0; k < u->n; k++)
{
if(r_tag[u->a[k]>>33] == (uint64_t)-1) continue;
if((r_tag[u->a[k]>>33]>>32) == ((uint32_t)r_tag[u->a[k]>>33])) continue;
sr = (r_tag[u->a[k]>>33]>>32) > ((uint32_t)r_tag[u->a[k]>>33])?1:-1;
if(sr == s[i])
{
R_INF.trio_flag[u->a[k]>>33] = flag;
fprintf(stderr, "*rid: %lu, s[i]: %d, 1-occ: %u, (-1)-occ: %u\n", u->a[k]>>33, s[i], (uint32_t)(r_tag[u->a[k]>>33]>>32), ((uint32_t)r_tag[u->a[k]>>33]));
// cons_occ += (r_tag[u->a[k]>>33]>>32) + ((uint32_t)r_tag[u->a[k]>>33]);
cons++;
}
else
{
// R_INF.trio_flag[u->a[k]>>33] = -flag;
fprintf(stderr, "#rid: %lu, s[i]: %d, 1-occ: %u, (-1)-occ: %u\n", u->a[k]>>33, s[i], (uint32_t)(r_tag[u->a[k]>>33]>>32), ((uint32_t)r_tag[u->a[k]>>33]));
// incons_occ += (r_tag[u->a[k]>>33]>>32) + ((uint32_t)r_tag[u->a[k]>>33]);
incons++;
}
}
}
free(r_tag);
kv_destroy(r_hits->a);
kv_destroy(r_hits->idx);
kv_destroy(r_hits->occ);
free(r_hits);
fprintf(stderr, "[M::%s::] # consistent reads: %lu, # inconsistent reads: %lu\n", __func__, cons, incons);
}
int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_opt_t *opt)
@@ -15800,7 +16073,8 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
alignment_worker_pipeline(&sl, fn1, fn2);
write_hc_hits(&sl.hits, asm_opt.output_file_name);
}
filter_kv_u_trans_t(&(idx->t_ch->k_trans), idx->ug);
filter_kv_u_trans_t(&(idx->t_ch->k_trans), idx->ug, 0.5);
// flter_by_cov(idx, &sl.hits, 2);
// update_hits(idx, &sl.hits, idx->t_ch->is_r_het);
///debug_hc_hits_v14(&sl.hits, asm_opt.output_file_name, sl.idx);
////dedup_hits(&(sl.hits), sl.idx);
@@ -15855,10 +16129,11 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
**/
}
// write_ps_t(s, asm_opt.output_file_name);
// skip_flipping:
verbose_het_stat(&bub);
// tag_reads(idx, &sl.hits, &bub, s->s, opt->sources);
// print_kv_weight(&k_trans, s->s);
// horder_t *ho = init_horder_t(&sl.hits, idx->uID_bits, idx->pos_mode, idx->read_g, idx->ug, &bub, &(idx->t_ch->k_trans), opt, 3);
horder.cpp
+141 -18
View File
@@ -26,24 +26,6 @@ KRADIX_SORT_INIT(ho64, uint64_t, generic_key, 8)
#define osg_arc_key(a) ((a).u)
KRADIX_SORT_INIT(osg, osg_arc_t, osg_arc_key, member_size(osg_arc_t, u))
#define get_hit_srev(x, k) ((x).a.a[(k)].s>>63)
#define get_hit_slen(x, k) ((x).a.a[(k)].len>>32)
#define get_hit_suid(x, k) (((x).a.a[(k)].s<<1)>>(64 - (x).uID_bits))
#define get_hit_spos(x, k) ((x).a.a[(k)].s & (x).pos_mode)
#define get_hit_spos_e(x, k) (get_hit_srev((x),(k))?\
((get_hit_spos((x),(k))+1>=get_hit_slen((x),(k)))?\
(get_hit_spos((x),(k))+1-get_hit_slen((x),(k))):0)\
:(get_hit_spos((x),(k))+get_hit_slen((x),(k))-1))
#define get_hit_erev(x, k) ((x).a.a[(k)].e>>63)
#define get_hit_elen(x, k) ((uint32_t)((x).a.a[(k)].len))
#define get_hit_euid(x, k) (((x).a.a[(k)].e<<1)>>(64 - (x).uID_bits))
#define get_hit_epos(x, k) ((x).a.a[(k)].e & (x).pos_mode)
#define get_hit_epos_e(x, k) (get_hit_erev((x),(k))?\
((get_hit_epos((x),(k))+1>=get_hit_elen((x),(k)))?\
(get_hit_epos((x),(k))+1-get_hit_elen((x),(k))):0)\
:(get_hit_epos((x),(k))+get_hit_elen((x),(k))-1))
#define OVL(s_0, e_0, s_1, e_1) ((MIN((e_0), (e_1)) > MAX((s_0), (s_1)))? MIN((e_0), (e_1)) - MAX((s_0), (s_1)):0)
#define BREAK_THRES 5000000
#define BREAK_CUTOFF 0.1
@@ -221,6 +203,145 @@ void destory_trans_col(trans_col_t **p)
free(*p);
}
void resolve_hit(uint64_t x, uint32_t rLen, uint64_t uID_bits, uint64_t pos_mode, uint64_t *uid, uint64_t *beg, uint64_t *end)
{
if(uid) (*uid) = ((x<<1)>>(64 - uID_bits));
uint32_t rev = (x>>63);
long long ref_p = x & pos_mode;
long long p_beg, p_end;
if(rev)
{
p_end = ref_p;
p_beg = p_end + 1 - rLen;
}
else
{
p_beg = ref_p;
p_end = p_beg + rLen - 1;
}
if(p_beg < 0) p_beg = 0;
if(p_end < 0) p_end = 0;
if(beg) (*beg) = p_beg;
if(end) (*end) = p_end + 1;
}
kvec_pe_hit *get_r_hits_for_trio(kvec_pe_hit *u_hits, asg_t* r_g, ma_ug_t* ug, bubble_type* bub, uint64_t uID_bits, uint64_t pos_mode)
{
kvec_pe_hit *r_hits = NULL;
CALLOC(r_hits, 1);
uint64_t k, l, i, r_i, offset, rid, rev, rBeg, rEnd, ubits, p_mode, upos, rpos, update, ubeg, uend, suid, euid;
ma_utg_t *u = NULL;
memset(r_hits, 0, sizeof(*r_hits));
r_hits->uID_bits = uID_bits;
r_hits->pos_mode = pos_mode;
//reset for reads
for (ubits=1; (uint64_t)(1<<ubits)<(uint64_t)r_g->n_seq; ubits++);
p_mode = ((uint64_t)-1) >> (ubits + 1);
u_hits->uID_bits = uID_bits; u_hits->pos_mode = pos_mode;
for (i = r_i = 0; i < u_hits->a.n; i++)
{
suid = get_hit_suid(*u_hits, i);
euid = get_hit_euid(*u_hits, i);
if(IF_HOM(suid, *bub)) continue;
if(IF_HOM(euid, *bub)) continue;
if(suid == euid) continue;
kv_push(pe_hit, r_hits->a, u_hits->a.a[i]);
resolve_hit(r_hits->a.a[r_i].s, r_hits->a.a[r_i].len>>32, r_hits->uID_bits,
r_hits->pos_mode, NULL, &ubeg, &uend);
upos = (ubeg+uend-1)>>1;
r_hits->a.a[r_i].s -= get_hit_spos(*r_hits, r_i);
r_hits->a.a[r_i].s += upos;
resolve_hit(r_hits->a.a[r_i].e, (uint32_t)r_hits->a.a[r_i].len, r_hits->uID_bits,
r_hits->pos_mode, NULL, &ubeg, &uend);
upos = (ubeg+uend-1)>>1;
r_hits->a.a[r_i].e -= get_hit_epos(*r_hits, r_i);///pos at unitig
r_hits->a.a[r_i].e += upos;
r_hits->a.a[r_i].id = (suid<<32)|euid;
r_i++;
}
radix_sort_pe_hit_idx_hn1(r_hits->a.a, r_hits->a.a + r_hits->a.n);
for (k = 1, l = 0; k <= r_hits->a.n; ++k)
{
if (k == r_hits->a.n || get_hit_suid(*r_hits, k) != get_hit_suid(*r_hits, l))//same suid
{
///already sort by spos
u = &(ug->u.a[get_hit_suid(*r_hits, l)]);
update = 0;
for (i = offset = 0, r_i = l; i < u->n; i++)
{
rid = u->a[i]>>33;
rBeg = offset;
rEnd = rBeg + r_g->seq[rid].len - 1;
for (; r_i < k; r_i++)
{
upos = get_hit_spos(*r_hits, r_i);///pos at unitig
if(upos > rEnd) break;
if(upos >= rBeg && upos <= rEnd)
{
rpos = (((u->a[i]>>32)&1)? rEnd - upos : upos - rBeg);///pos at read
rev = ((u->a[i]>>32)&1) ^ (r_hits->a.a[r_i].s>>63);
r_hits->a.a[r_i].s = (rev<<63) | ((rid << (64-ubits))>>1) | (rpos & p_mode);
update++;
}
}
offset += (uint32_t)u->a[i];
}
if(r_i != k || update != k - l) fprintf(stderr, "ERROR-r_i\n");
l = k;
}
}
radix_sort_pe_hit_idx_hn2(r_hits->a.a, r_hits->a.a + r_hits->a.n);
for (k = 1, l = 0; k <= r_hits->a.n; ++k)
{
if (k == r_hits->a.n || get_hit_euid(*r_hits, k) != get_hit_euid(*r_hits, l))//same euid
{
///already sort by epos
u = &(ug->u.a[get_hit_euid(*r_hits, l)]);
update = 0;
for (i = offset = 0, r_i = l; i < u->n; i++)
{
rid = u->a[i]>>33;
rBeg = offset;
rEnd = rBeg + r_g->seq[rid].len - 1;
for (; r_i < k; r_i++)
{
upos = get_hit_epos(*r_hits, r_i);///pos at unitig
if(upos > rEnd) break;
if(upos >= rBeg && upos <= rEnd)
{
rpos = (((u->a[i]>>32)&1)? rEnd - upos : upos - rBeg);///pos at read
rev = ((u->a[i]>>32)&1) ^ (r_hits->a.a[r_i].e>>63);
r_hits->a.a[r_i].e = (rev<<63) | ((rid << (64-ubits))>>1) | (rpos & p_mode);
update++;
}
}
offset += (uint32_t)u->a[i];
}
if(r_i != k || update != k - l) fprintf(stderr, "ERROR-r_i\n");
l = k;
}
}
r_hits->uID_bits = ubits;
r_hits->pos_mode = p_mode;
return r_hits;
}
void get_r_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, asg_t* r_g, ma_ug_t* ug, bubble_type* bub, uint64_t uID_bits, uint64_t pos_mode)
{
uint64_t k, l, i, r_i, offset, rid, rev, rBeg, rEnd, ubits, p_mode, upos, rpos, update;
@@ -250,6 +371,7 @@ void get_r_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, asg_t* r_g, ma_ug_t* u
for (; r_i < k; r_i++)
{
upos = get_hit_spos(*r_hits, r_i);///pos at unitig
if(upos > rEnd) break;
if(upos >= rBeg && upos <= rEnd)
{
@@ -293,6 +415,7 @@ void get_r_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, asg_t* r_g, ma_ug_t* u
for (; r_i < k; r_i++)
{
upos = get_hit_epos(*r_hits, r_i);///pos at unitig
if(upos > rEnd) break;
if(upos >= rBeg && upos <= rEnd)
{
horder.h
+19
View File
@@ -3,6 +3,24 @@
#include <stdint.h>
#include "hic.h"
#define get_hit_srev(x, k) ((x).a.a[(k)].s>>63)
#define get_hit_slen(x, k) ((x).a.a[(k)].len>>32)
#define get_hit_suid(x, k) (((x).a.a[(k)].s<<1)>>(64 - (x).uID_bits))
#define get_hit_spos(x, k) ((x).a.a[(k)].s & (x).pos_mode)
#define get_hit_spos_e(x, k) (get_hit_srev((x),(k))?\
((get_hit_spos((x),(k))+1>=get_hit_slen((x),(k)))?\
(get_hit_spos((x),(k))+1-get_hit_slen((x),(k))):0)\
:(get_hit_spos((x),(k))+get_hit_slen((x),(k))-1))
#define get_hit_erev(x, k) ((x).a.a[(k)].e>>63)
#define get_hit_elen(x, k) ((uint32_t)((x).a.a[(k)].len))
#define get_hit_euid(x, k) (((x).a.a[(k)].e<<1)>>(64 - (x).uID_bits))
#define get_hit_epos(x, k) ((x).a.a[(k)].e & (x).pos_mode)
#define get_hit_epos_e(x, k) (get_hit_erev((x),(k))?\
((get_hit_epos((x),(k))+1>=get_hit_elen((x),(k)))?\
(get_hit_epos((x),(k))+1-get_hit_elen((x),(k))):0)\
:(get_hit_epos((x),(k))+get_hit_elen((x),(k))-1))
typedef struct {
uint32_t v;
uint32_t u;
@@ -40,4 +58,5 @@ horder_t *init_horder_t(kvec_pe_hit *i_hits, uint64_t i_hits_uid_bits, uint64_t
asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, kv_u_trans_t *ref, ug_opt_t *opt, uint32_t round);
void destory_horder_t(horder_t **h);
void horder_clean_sg_by_utg(asg_t *sg, ma_ug_t *ug);
kvec_pe_hit *get_r_hits_for_trio(kvec_pe_hit *u_hits, asg_t* r_g, ma_ug_t* ug, bubble_type* bub, uint64_t uID_bits, uint64_t pos_mode);
#endif