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integer correction update

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chhylp123
2022-06-20 01:51:19 -04:00
parent a21bc8a336
commit 3934167770
1 changed files with 284 additions and 20 deletions
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gfa_ut.cpp
+284 -20
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@@ -178,8 +178,12 @@ typedef struct {
typedef struct{ typedef struct{
uint64_t pge, ule; uint64_t pge, ule;
uint32_t ulid;
} emap_t; } emap_t;
#define emap_t_srt_key(x) ((x).pge)
KRADIX_SORT_INIT(emap_t_srt, emap_t, emap_t_srt_key, member_size(emap_t, pge))
typedef struct { typedef struct {
kvec_t(poa_nid_t) seq; kvec_t(poa_nid_t) seq;
kvec_t(poa_arc_t) arc; kvec_t(poa_arc_t) arc;
@@ -208,6 +212,7 @@ typedef struct {
kvec_t(ul_chain_t) sc; kvec_t(ul_chain_t) sc;
kvec_t(ul_snp_t) snp; kvec_t(ul_snp_t) snp;
poa_g_t pg; poa_g_t pg;
kvec_t(uint64_t) res_dump;
}integer_t; }integer_t;
typedef struct { typedef struct {
@@ -3609,7 +3614,7 @@ void clean_poa_g_t(poa_g_t *g)
void append_unmatch_integer_seq(poa_g_t *g, ma_ug_t *ug, uc_block_t *raw, ul_str_t *str, int64_t s, int64_t e, int64_t is_rev, int64_t str_id) void append_unmatch_integer_seq(poa_g_t *g, ma_ug_t *ug, uc_block_t *raw, ul_str_t *str, int64_t s, int64_t e, int64_t is_rev, int64_t str_id)
{ {
int64_t k; poa_nid_t *nn; poa_arc_t *ae; uint32_t v; uc_block_t *z; int64_t k; poa_nid_t *nn; poa_arc_t *ae; uint32_t v; uc_block_t *z; emap_t *em;
for (k = s; k < e; k++) { for (k = s; k < e; k++) {
if(is_rev) { if(is_rev) {
v = (((uint32_t)str->a[str->cn-k-1])^1); v = (((uint32_t)str->a[str->cn-k-1])^1);
@@ -3630,11 +3635,18 @@ void append_unmatch_integer_seq(poa_g_t *g, ma_ug_t *ug, uc_block_t *raw, ul_str
kv_pushp(poa_arc_t, g->arc, &ae); kv_pushp(poa_arc_t, g->arc, &ae);
ae->ul = g->seq.n-2; ae->ul <<= 33; ae->ul += 1; ae->ul = g->seq.n-2; ae->ul <<= 33; ae->ul += 1;
ae->v = g->seq.n-1; ae->v <<= 1; ae->v = g->seq.n-1; ae->v <<= 1;
kv_pushp(emap_t, g->e_idx, &em);
em->pge = g->seq.n-2; em->pge <<= 32; em->pge += g->seq.n-1;
em->ule = (is_rev?(str->cn-k):(k-1)); em->ule <<= 32; em->ule += (is_rev?(str->cn-k-1):(k));
em->ulid = str_id;
// assert((g->seq.a[em->pge>>32].nid^(is_rev?1:0)) == ((uint32_t)str->a[em->ule>>32]));
// assert((g->seq.a[(uint32_t)em->pge].nid^(is_rev?1:0)) == ((uint32_t)str->a[(uint32_t)em->ule]));
} }
} }
} }
void update_poa_nid_occ(ma_ug_t *ug, uc_block_t *raw, poa_g_t *g, int64_t gidx, uint64_t *str, int64_t str_idx, int64_t is_rev, int64_t str_id, int64_t str_off) void update_poa_nid_occ(ma_ug_t *ug, uc_block_t *raw, poa_g_t *g, int64_t gidx, uint64_t *str, int64_t str_idx, int64_t is_rev)
{ {
uint32_t g_v, str_v, new_occ; uc_block_t *z; uint32_t g_v, str_v, new_occ; uc_block_t *z;
///update ///update
@@ -3649,7 +3661,7 @@ void update_poa_nid_occ(ma_ug_t *ug, uc_block_t *raw, poa_g_t *g, int64_t gidx,
void insert_poa_nodes_0(ma_ug_t *ug, uc_block_t *raw, poa_g_t *g, uint64_t *str, int64_t str_occ, uint64_t is_rev, int64_t str_id, int64_t str_off) void insert_poa_nodes_0(ma_ug_t *ug, uc_block_t *raw, poa_g_t *g, uint64_t *str, int64_t str_occ, uint64_t is_rev, int64_t str_id, int64_t str_off)
{ {
int64_t k; poa_nid_t *nn; poa_arc_t *ae; uint32_t v; uc_block_t *z; int64_t k; poa_nid_t *nn; poa_arc_t *ae; uint32_t v; uc_block_t *z; emap_t *em;
for (k = 0; k < str_occ; k++) { for (k = 0; k < str_occ; k++) {
if(is_rev == 0) { if(is_rev == 0) {
v = ((uint32_t)str[k]); z = &(raw[str[k]>>32]); v = ((uint32_t)str[k]); z = &(raw[str[k]>>32]);
@@ -3668,13 +3680,33 @@ void insert_poa_nodes_0(ma_ug_t *ug, uc_block_t *raw, poa_g_t *g, uint64_t *str,
kv_pushp(poa_arc_t, g->arc, &ae); kv_pushp(poa_arc_t, g->arc, &ae);
ae->ul = g->seq.n-2; ae->ul <<= 33; ae->ul += 1; ae->ul = g->seq.n-2; ae->ul <<= 33; ae->ul += 1;
ae->v = g->seq.n-1; ae->v <<= 1; ae->v = g->seq.n-1; ae->v <<= 1;
kv_pushp(emap_t, g->e_idx, &em);
em->pge = g->seq.n-2; em->pge <<= 32; em->pge += g->seq.n-1;
em->ule = str_off + (is_rev?(str_occ-k):(k-1)); em->ule <<= 32;
em->ule += str_off + (is_rev?(str_occ-k-1):(k));
em->ulid = str_id;
// if(!((g->seq.a[em->pge>>32].nid^(is_rev?1:0)) == ((uint32_t)debug_str->a[em->ule>>32]))) {
// fprintf(stderr, "[M::%s::k->%ld::str_occ->%ld] is_rev->%lu, pg_v->%u, str_v->%u, str_off->%ld, str_k->%lu, str_cn->%u, address_diff->%u\n",
// __func__, k, str_occ, is_rev, (g->seq.a[em->pge>>32].nid^(is_rev?1:0)),
// ((uint32_t)debug_str->a[em->ule>>32]), str_off, em->ule>>32, debug_str->cn, (uint32_t)(str - debug_str->a));
// uint64_t debug_k;
// for (debug_k = 0; debug_k < debug_str->cn; debug_k++) {
// fprintf(stderr, "[M::%s::debug_k->%lu] str_v->%u\n",
// __func__, debug_k, ((uint32_t)debug_str->a[debug_k]));
// }
// }
// assert((g->seq.a[em->pge>>32].nid^(is_rev?1:0)) == ((uint32_t)debug_str->a[em->ule>>32]));
// assert((g->seq.a[(uint32_t)em->pge].nid^(is_rev?1:0)) == ((uint32_t)debug_str->a[(uint32_t)em->ule]));
} }
} }
} }
void push_poa_arch_0(poa_g_t *g, uint32_t src, uint32_t des) void push_poa_arch_0(poa_g_t *g, uint32_t src, uint32_t des, int64_t str_id, int64_t str_src, int64_t str_des)
{ {
poa_arc_t *ae; poa_arc_t *ae; emap_t *em;
kv_pushp(poa_arc_t, g->arc, &ae); kv_pushp(poa_arc_t, g->arc, &ae);
ae->ul = des; ae->ul <<= 33; ae->ul += ((uint64_t)(0x100000000)); ae->ul += 1; ae->ul = des; ae->ul <<= 33; ae->ul += ((uint64_t)(0x100000000)); ae->ul += 1;
ae->v = src; ae->v <<= 1; ae->v += 1; ae->v = src; ae->v <<= 1; ae->v += 1;
@@ -3682,18 +3714,26 @@ void push_poa_arch_0(poa_g_t *g, uint32_t src, uint32_t des)
kv_pushp(poa_arc_t, g->arc, &ae); kv_pushp(poa_arc_t, g->arc, &ae);
ae->ul = src; ae->ul <<= 33; ae->ul += 1; ae->ul = src; ae->ul <<= 33; ae->ul += 1;
ae->v = des; ae->v <<= 1; ae->v = des; ae->v <<= 1;
kv_pushp(emap_t, g->e_idx, &em);
em->pge = src; em->pge <<= 32; em->pge += des;
em->ule = str_src; em->ule <<= 32; em->ule += str_des;
em->ulid = str_id;
// assert((g->seq.a[em->pge>>32].nid^(debug_is_rev?1:0)) == ((uint32_t)debug_str->a[em->ule>>32]));
// assert((g->seq.a[(uint32_t)em->pge].nid^(debug_is_rev?1:0)) == ((uint32_t)debug_str->a[(uint32_t)em->ule]));
} }
void update_poa_arch_0(poa_g_t *g, uint32_t src, uint32_t des) void update_poa_arch_0(poa_g_t *g, uint32_t src, uint32_t des, int64_t str_id, int64_t str_src, int64_t str_des)
{ {
uint32_t k, v, w, a_n; poa_arc_t *a; uint32_t k, v, w, a_n; poa_arc_t *a; emap_t *em;
v = src<<1; w = des<<1; v = src<<1; w = des<<1;
a_n = poa_arc_n(g, v); a = poa_arc_a(g, v); a_n = poa_arc_n(g, v); a = poa_arc_a(g, v);
for (k = 0; k < a_n; k++) { for (k = 0; k < a_n; k++) {
if(a[k].v == w) break; if(a[k].v == w) break;
} }
if(k >= a_n) { if(k >= a_n) {
push_poa_arch_0(g, src, des); push_poa_arch_0(g, src, des, str_id, str_src, str_des);
} else { } else {
a[k].ul++; a[k].ul++;
v = des<<1; v^=1; v = des<<1; v^=1;
@@ -3704,6 +3744,14 @@ void update_poa_arch_0(poa_g_t *g, uint32_t src, uint32_t des)
} }
assert(k < a_n); assert(k < a_n);
a[k].ul++; a[k].ul++;
kv_pushp(emap_t, g->e_idx, &em);
em->pge = src; em->pge <<= 32; em->pge += des;
em->ule = str_src; em->ule <<= 32; em->ule += str_des;
em->ulid = str_id;
// assert((g->seq.a[em->pge>>32].nid^(debug_is_rev?1:0)) == ((uint32_t)debug_str->a[em->ule>>32]));
// assert((g->seq.a[(uint32_t)em->pge].nid^(debug_is_rev?1:0)) == ((uint32_t)debug_str->a[(uint32_t)em->ule]));
} }
} }
@@ -3719,33 +3767,40 @@ void append_integer_seq_frag(ma_ug_t *ug, uc_block_t *raw, poa_g_t *g, int64_t g
if(g_beg < 0 && g_end >= 0) {///add nodes to the left end if(g_beg < 0 && g_end >= 0) {///add nodes to the left end
assert(str_occ >= 1); assert(str_occ >= 1);
update_poa_nid_occ(ug, raw, g, g_end, str, (is_rev?(0):(str_occ-1)), is_rev, str_id, str_off); update_poa_nid_occ(ug, raw, g, g_end, str, (is_rev?(0):(str_occ-1)), is_rev);
if(str_occ < 2) return; if(str_occ < 2) return;
insert_poa_nodes_0(ug, raw, g, (is_rev?(str+1):(str)), str_occ-1, is_rev, str_id, str_off); insert_poa_nodes_0(ug, raw, g, (is_rev?(str+1):(str)), str_occ-1, is_rev, str_id, str_off+(is_rev?(1):(0)));
push_poa_arch_0(g, g->seq.n-1, g_end); push_poa_arch_0(g, g->seq.n-1, g_end, str_id, str_off + (is_rev?(1):(str_occ-2)),
str_off + (is_rev?(0):(str_occ-1)));
return; return;
} }
if(g_beg >= 0 && g_end < 0) {///add nodes to the right end if(g_beg >= 0 && g_end < 0) {///add nodes to the right end
assert(str_occ >= 1); assert(str_occ >= 1);
update_poa_nid_occ(ug, raw, g, g_beg, str, (is_rev?(str_occ-1):(0)), is_rev, str_id, str_off); update_poa_nid_occ(ug, raw, g, g_beg, str, (is_rev?(str_occ-1):(0)), is_rev);
if(str_occ < 2) return; if(str_occ < 2) return;
nid = g->seq.n;///backup nid = g->seq.n;///backup
insert_poa_nodes_0(ug, raw, g, (is_rev?(str):(str+1)), str_occ-1, is_rev, str_id, str_off); insert_poa_nodes_0(ug, raw, g, (is_rev?(str):(str+1)), str_occ-1, is_rev, str_id, str_off+(is_rev?(0):(1)));
push_poa_arch_0(g, g_beg, nid); push_poa_arch_0(g, g_beg, nid, str_id, str_off + (is_rev?(str_occ-1):(0)),
str_off + (is_rev?(str_occ-2):(1)));
return; return;
} }
if(g_beg >= 0 && g_end >= 0) {///add nodes to the middle if(g_beg >= 0 && g_end >= 0) {///add nodes to the middle
assert(str_occ >= 2); assert(str_occ >= 2);
update_poa_nid_occ(ug, raw, g, g_beg, str, (is_rev?(str_occ-1):(0)), is_rev, str_id, str_off); update_poa_nid_occ(ug, raw, g, g_beg, str, (is_rev?(str_occ-1):(0)), is_rev);
update_poa_nid_occ(ug, raw, g, g_end, str, (is_rev?(0):(str_occ-1)), is_rev, str_id, str_off); update_poa_nid_occ(ug, raw, g, g_end, str, (is_rev?(0):(str_occ-1)), is_rev);
if(str_occ > 2) {///insert new nodes if(str_occ > 2) {///insert new nodes
nid = g->seq.n;///backup nid = g->seq.n;///backup
insert_poa_nodes_0(ug, raw, g, str+1, str_occ-2, is_rev, str_id, str_off); insert_poa_nodes_0(ug, raw, g, str+1, str_occ-2, is_rev, str_id, str_off+1);
push_poa_arch_0(g, g_beg, nid); push_poa_arch_0(g, g->seq.n-1, g_end); push_poa_arch_0(g, g_beg, nid, str_id, str_off + (is_rev?(str_occ-1):(0)),
str_off + (is_rev?(str_occ-2):(1)));
push_poa_arch_0(g, g->seq.n-1, g_end, str_id, str_off + (is_rev?(1):(str_occ-2)),
str_off + (is_rev?(0):(str_occ-1)));
} else { } else {
update_poa_arch_0(g, g_beg, g_end);///add an edge between g_beg and g_end ///add an edge between g_beg and g_end
update_poa_arch_0(g, g_beg, g_end, str_id, str_off + (is_rev?(str_occ-1):(0)),
str_off + (is_rev?(0):(str_occ-1)));
} }
} }
} }
@@ -4032,7 +4087,7 @@ ul_chain_t *idx, int64_t idx_n, int64_t qid, integer_t *buf)
int64_t k, tid, is_rev; int64_t k, tid, is_rev;
reset_poa_g_t(g); reset_poa_g_t(g);
append_unmatch_integer_seq(g, ug, ul_idx->a[qid].bb.a, &(str[qid]), 0, str[qid].cn, 0, qid); append_unmatch_integer_seq(g, ug, ul_idx->a[qid].bb.a, &(str[qid]), 0, str[qid].cn, 0, qid, 0);
clean_poa_g_t(g); topo_srt_gen(g); clean_poa_g_t(g); topo_srt_gen(g);
for (k = 0; k < idx_n; k++) { for (k = 0; k < idx_n; k++) {
@@ -4268,6 +4323,213 @@ void poa_cns_chain(poa_g_t *g, all_ul_t *ul_idx, ma_ug_t *ug, ul_str_t *str, ul_
gen_cns_by_poa(g); gen_cns_by_poa(g);
} }
uint64_t cal_forward_dis(asg_t *g, uc_block_t *a, uint32_t s, uint32_t e)
{
uint32_t i, li = (uint32_t)-1, v, w, nv, z; int64_t l; asg_arc_t *av;
for(i = s, l = 0, v = w = (uint32_t)-1; i != (uint32_t)-1 && i <= e; i = a[i].aidx) {
w = (((uint32_t)(a[i].hid))<<1)|((uint32_t)(a[i].rev));
if(v != (uint32_t)-1) {
av = asg_arc_a(g, v); nv = asg_arc_n(g, v);
for (z = 0; z < nv; z++) {
if(av[z].del) continue;
if(av[z].v == w) break;
}
if(z < nv) {//found
l += (uint32_t)av[z].ul;
} else {
l += a[i].pdis + g->seq[v>>1].len - g->seq[w>>1].len;
}
}
v = w; li = i;
}
assert(li == e);
if(l < 0) l = 0;
return l;
}
uint64_t cal_integer_match_dis(ma_ug_t *ug, uc_block_t *a, int64_t k_0, int64_t k_1, int64_t is_rev, uint32_t *is_g_connect)
{
uint32_t i, k;
assert((is_rev && k_1 < k_0) || ((!is_rev) && k_1 > k_0)); (*is_g_connect) = 0;
if(is_rev) {
i = k_0; k = k_1;
} else {
i = k_1; k = k_0;
}
uint32_t li, lk, pk, bi = i; int64_t l;
for (li = i, l = 0; i != (uint32_t)-1 && i >= k; i = a[i].pidx) {
li = i; if(a[i].pidx != (uint32_t)-1 && i > k) l += a[i].pdis;
}
if(is_rev) l = cal_forward_dis(ug->g, a, li, bi);
if(li == k) {///direct path
(*is_g_connect) = 1;
return l;
}
i = li;
assert(i > k); pk = k;
for (lk = k; k != (uint32_t)-1 && k <= i; k = a[k].aidx) lk = k;
if(!is_rev) {
for (k = lk; k != (uint32_t)-1 && k != pk; k = a[k].pidx) l += a[k].pdis;
} else {
l += cal_forward_dis(ug->g, a, pk, lk);
}
if(l < 0) l = 0;
k = lk;
assert(i > k);
return l + normlize_gdis(ug, &(a[i]), &(a[k]), is_rev);
}
uint64_t cal_integer_most_dis(uint64_t *a, uint64_t a_n, double cluster_rate)
{
if(a_n <= 0) return (uint64_t)-1;
// fprintf(stderr, "\n[M::%s::] a_n::%lu\n", __func__, a_n);
uint64_t k, l, i, m, r_an = a_n, max_m, max_i, cc, cd, nd; int64_t z;
for (k = 1, l = m = max_m = 0, max_i = (uint64_t)-1; k <= a_n; k++) {
a[k-1] <<= 1; a[k-1] >>= 1;
// fprintf(stderr, "[k->%lu] d::%lu, rev::%lu\n", k-1, a[k-1]>>1, a[k-1]&1);
if(k == a_n || (a[k]>>1) != (a[l]>>1)) {
for (i = l; i < k; i++) {
if(!(a[i]&1)) break;
}
a[m] = a[l]; a[m] >>= 1; a[m] <<= 1;
///if all integer sequence are mapped reversely
if(i >= k) a[m] += 1;
a[m] |= ((uint64_t)(k-l))<<32;
if((k-l) > max_m) {
max_m = k - l; max_i = m;
} else if((k-l) == max_m && i < k) {///i < k means this distance is supported by forward sequences
max_m = k - l; max_i = m;
}
l = k; m++;
}
}
a_n = m; assert(a_n > 0);
// fprintf(stderr, "[M::%s::] m::%lu\n", __func__, m);
if(max_m > 0 && max_m > (r_an>>1)) {
// fprintf(stderr, "[M::%s::] dis::%u\n", __func__, ((uint32_t)a[max_i])>>1);
return ((uint32_t)a[max_i])>>1;
}
for (k = 0, max_m = 0, max_i = (uint64_t)-1; k < a_n; k++) {
cd = (((uint32_t)a[k])>>1); z = k;
// fprintf(stderr, "[mk->%lu] cd::%lu\n", k, cd);
for (cc = cd, z--; z >= 0; z--) {
nd = (((uint32_t)a[z])>>1); assert(nd < cd);
if(((cd-nd) > (nd*cluster_rate)) && ((cd-nd) > 512)) break;
cc += (a[z]>>32);
}
for (i = k+1; i < a_n; i++) {
nd = (((uint32_t)a[i])>>1); assert(nd > cd);
if(((nd-cd) > (nd*cluster_rate)) && ((nd-cd) > 512)) break;
cc += (a[i]>>32);
}
if(cc > max_m) {
max_m = cc; max_i = k;
} else if(cc == max_m && (!(a[k]&1))) {///means this distance is supported by forward sequences
max_m = cc; max_i = k;
}
}
k = max_i;
cd = (((uint32_t)a[k])>>1); z = k;
for (max_m = cd, max_i = k, z--; z >= 0; z--) {
nd = (((uint32_t)a[z])>>1); assert(nd < cd);
if(((cd-nd) > (nd*cluster_rate)) && ((cd-nd) > 512)) break;
cc = (a[z]>>32);
if(cc > max_m) {
max_m = cc; max_i = z;
} else if(cc == max_m && (!(a[z]&1))) {///means this distance is supported by forward sequences
max_m = cc; max_i = z;
}
}
for (i = k+1; i < a_n; i++) {
nd = (((uint32_t)a[i])>>1); assert(nd > cd);
if(((nd-cd) > (nd*cluster_rate)) && ((nd-cd) > 512)) break;
cc = (a[i]>>32);
if(cc > max_m) {
max_m = cc; max_i = i;
} else if(cc == max_m && (!(a[i]&1))) {///means this distance is supported by forward sequences
max_m = cc; max_i = i;
}
}
// fprintf(stderr, "[M::%s::] dis::%u\n", __func__, ((uint32_t)a[max_i])>>1);
return ((uint32_t)a[max_i])>>1;
}
void update_raw_integer_seq(poa_g_t *pg, ma_ug_t *ug, uint32_t *cns_seq, uint32_t cns_occ, all_ul_t *ul_idx, ul_str_t *str, uint32_t qid, integer_t *buf, ul_chain_t *idx_a, uint64_t idx_n)
{
if(cns_occ <= 0) return;
radix_sort_emap_t_srt(pg->e_idx.a, pg->e_idx.a + pg->e_idx.n);
kv_resize(uint64_t, buf->u, cns_occ); buf->u.n = cns_occ - 1; memset(buf->u.a, 0, sizeof(*(buf->u.a)*buf->u.n));
uint64_t *arc_idx = buf->u.a, arc_idx_n = buf->u.n, x; uint64_t k, l, i, n = pg->e_idx.n, fe = cns_occ - 1;
for (k = 1, l = 0; k <= n && fe > 0; k++) {
if(k == n || pg->e_idx.a[k].pge != pg->e_idx.a[l].pge) {
if(k > l) {
for (i = 0; i < arc_idx_n; i++) {
x = (cns_seq[i]>>1); x <<= 32; x += (cns_seq[i+1]>>1);
if(x == pg->e_idx.a[l].pge) {
arc_idx[i] = l; arc_idx[i] <<= 32; arc_idx[i] += k; fe--;
break;
}
}
}
l = k;
}
}
assert(fe == 0);
// for (k = 0; k < pg->e_idx.n; k++) {
// assert((pg->seq.a[pg->e_idx.a[k].pge>>32].nid>>1) ==
// (((uint32_t)str[pg->e_idx.a[k].ulid].a[pg->e_idx.a[k].ule>>32])>>1));
// assert((pg->seq.a[(uint32_t)pg->e_idx.a[k].pge].nid>>1) ==
// (((uint32_t)str[pg->e_idx.a[k].ulid].a[(uint32_t)pg->e_idx.a[k].ule])>>1));
// assert(((pg->seq.a[pg->e_idx.a[k].pge>>32].nid&1)^(((uint32_t)str[pg->e_idx.a[k].ulid].a[pg->e_idx.a[k].ule>>32])&1)) ==
// ((pg->seq.a[(uint32_t)pg->e_idx.a[k].pge].nid&1)^(((uint32_t)str[pg->e_idx.a[k].ulid].a[(uint32_t)pg->e_idx.a[k].ule])&1)));
// }
uint32_t e_s, e_e, is_rev, is_g_connect, con_occ; emap_t *g_arc; uint64_t t, dd;
if(cns_occ > 0) {
t = qid; t <<= 32; t |= ((uint64_t)(0xffffffff));
kv_push(uint64_t, buf->res_dump, t);
t = pg->seq.a[cns_seq[0]>>1].nid; t |= ((uint64_t)(0xffffffff00000000));
kv_push(uint64_t, buf->res_dump, t);
}
for (k = 0; k < arc_idx_n; k++) {
// csn_v = pg->seq.a[cns_seq[k]>>1].nid; cns_w = pg->seq.a[cns_seq[k+1]>>1].nid;
e_s = arc_idx[k]>>32; e_e = (uint32_t)arc_idx[k]; assert(e_e > e_s);
buf->o.n = 0; kv_resize(uint64_t, buf->o, e_e - e_s); con_occ = 0;
for (i = e_s; i < e_e; i++) {
g_arc = &(pg->e_idx.a[i]);
assert((g_arc->pge>>32) == (cns_seq[k]>>1) && ((uint32_t)g_arc->pge) == (cns_seq[k+1]>>1));
is_rev = ((g_arc->ule>>32) > ((uint32_t)g_arc->ule)?1:0);
assert((pg->seq.a[g_arc->pge>>32].nid^(is_rev?1:0)) == ((uint32_t)str[g_arc->ulid].a[g_arc->ule>>32]));
assert((pg->seq.a[(uint32_t)g_arc->pge].nid^(is_rev?1:0)) == ((uint32_t)str[g_arc->ulid].a[(uint32_t)g_arc->ule]));
dd = cal_integer_match_dis(ug, ul_idx->a[g_arc->ulid].bb.a, str[g_arc->ulid].a[g_arc->ule>>32]>>32,
str[g_arc->ulid].a[(uint32_t)g_arc->ule]>>32, is_rev, &is_g_connect);
dd <<= 1; if(is_rev) dd += 1;
if(is_g_connect) {
con_occ++; buf->o.a[buf->o.n] = dd;
} else {
buf->o.a[buf->o.n] = dd; buf->o.a[buf->o.n] |= ((uint64_t)(0x8000000000000000));
}
buf->o.n++;
}
radix_sort_srt64(buf->o.a, buf->o.a + buf->o.n);
if(con_occ > 0) buf->o.n = con_occ;
dd = cal_integer_most_dis(buf->o.a, buf->o.n, 0.08);
t = pg->seq.a[cns_seq[k+1]>>1].nid; t |= ((uint64_t)(dd<<32));
if(con_occ > 0) t |= ((uint64_t)(0x8000000000000000));
kv_push(uint64_t, buf->res_dump, t);
}
}
void integer_candidate(ul_resolve_t *uidx, integer_t *buf, uint32_t qid, uint32_t is_hom) void integer_candidate(ul_resolve_t *uidx, integer_t *buf, uint32_t qid, uint32_t is_hom)
{ {
// if(qid != 281) return; // if(qid != 281) return;
@@ -4385,6 +4647,8 @@ void integer_candidate(ul_resolve_t *uidx, integer_t *buf, uint32_t qid, uint32_
// integer_phase(str_idx->str.a, buf, buf->sc.a, buf->sc.n, buf->b.a, qid); // integer_phase(str_idx->str.a, buf, buf->sc.a, buf->sc.n, buf->b.a, qid);
// radix_sort_ul_chain_t_srt(buf->sc.a, buf->sc.a + buf->sc.n); // radix_sort_ul_chain_t_srt(buf->sc.a, buf->sc.a + buf->sc.n);
o = NULL; o_n = 0;
update_raw_integer_seq(&(buf->pg), ug, buf->pg.srt_b.res.a, buf->pg.srt_b.res.n, uidx->idx, str_idx->str.a, qid, buf, buf->sc.a, buf->sc.n);
} }