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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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horder.cpp
+141 -18
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@@ -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)
{