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rcut.cpp
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#define __STDC_LIMIT_MACROS
#include <stdint.h>
#include <stdlib.h>
#include "rcut.h"
#include "Purge_Dups.h"
#include "Correct.h"
#include "ksort.h"
#include "kthread.h"
#include "hic.h"
#define VERBOSE_CUT 0
#define mc_edge_key(e) ((e).x)
KRADIX_SORT_INIT(mce, mc_edge_t, mc_edge_key, member_size(mc_edge_t, x))
#define mb_edge_key(e) ((e).x)
KRADIX_SORT_INIT(mbe, mb_edge_t, mb_edge_key, member_size(mb_edge_t, x))
#define mc_generic_key(x) (x)
KRADIX_SORT_INIT(mc64, uint64_t, mc_generic_key, 8)
KRADIX_SORT_INIT(mc32, uint32_t, mc_generic_key, 4)
#define pt_a(x, id) ((x).ma.a + ((x).idx.a[(id)]>>32))
#define pt_n(x, id) ((uint32_t)((x).idx.a[(id)]))
#define ma_x(z) (((z).x>>32))
#define ma_y(z) (((uint32_t)((z).x)))
#define mcb_pat(x, id) (&((x).m.a[(id)-1]))
#define mcp_de(x, id, m) ((x).z[((id)<<(x).hapN)+(m)])
uint8_t bit_filed[8] = {1, 2, 4, 8, 16, 32, 64, 128};
#define is_bit_set(id, a) ((a)[(id)>>3]&bit_filed[(id)&7])
typedef struct {
int32_t max_iter;
int32_t n_perturb;
int32_t n_b_perturb;
int32_t n_s_perturb;
double f_perturb;
uint64_t seed;
} mc_opt_t;
typedef struct {
t_w_t z[2];
} mc_pairsc_t;
typedef struct {
uint64_t x; // RNG
uint32_t cc_off, cc_size;
kvec_t(uint64_t) cc_edge;
uint32_t *cc_node;
uint32_t *bfs, *bfs_mark;
mc_pairsc_t *z, *z_opt;///keep scores to nodes(1) and nodes(-1)
int8_t *s, *s_opt;
uint8_t *f;
} mc_svaux_t;
typedef struct {
uint64_t x; // RNG
uint32_t cc_off, cc_size;
kvec_t(uint64_t) cc_edge;
uint32_t *cc_node;
uint32_t *bfs, *bfs_mark;
mb_node_t *u, *u_opt;///keep status
uint8_t *f;
} mb_svaux_t;
typedef struct{
uint64_t chain_id, bid, uid;
}mc_bp_iter;
typedef struct{
uint32_t chain_id;
uint32_t f_bid;
uint32_t f_uid;
uint32_t l_bid;
uint32_t l_uid;
uint32_t id;
t_w_t w;
}mc_bp_res;
typedef struct{
size_t n, m;
uint8_t *a;
}bits_p;
typedef struct{
bubble_type* b_b;
uint64_t *idx, idx_n, occ, n_thread;
mc_bp_res *res;
uint8_t *lock;
mc_svaux_t *b_aux;
mc_match_t *ma;
bits_p *vis;
}mc_bp_t;
typedef struct {
uint64_t x; // RNG
uint32_t cc_off, cc_size;
kvec_t(uint32_t) cc_node;
kvec_t(uint32_t) bfs;
///share
uint32_t *bfs_mark;
mc_pairsc_t *z, *z_opt;///keep scores to nodes(1) and nodes(-1)
int8_t *s, *s_opt;
} mc_svaux_t_s;
typedef struct {
kvec_t(mc_svaux_t_s) bs;
kvec_t(uint64_t) cc_edge;
uint32_t *bfs_mark;
mc_pairsc_t *z, *z_opt;///keep scores to nodes(1) and nodes(-1)
int8_t *s, *s_opt;
uint32_t n_t, n_g;
} mc_svaux_t_mul;
void mc_opt_init(mc_opt_t *opt, int32_t n_perturb, double f_perturb, uint64_t seed)
{
memset(opt, 0, sizeof(mc_opt_t));
opt->n_perturb = n_perturb;
opt->f_perturb = f_perturb;
opt->max_iter = 1000;
opt->seed = seed;
opt->n_s_perturb = n_perturb;
opt->n_b_perturb = n_perturb*0.5;
}
void mc_merge_dup(mc_g_t *mg) // MUST BE sorted
{
uint32_t i, j, k, st;
w_t w;
for (st = 0, i = 1, k = 0; i <= mg->e->ma.n; ++i) {
if (i == mg->e->ma.n || mg->e->ma.a[i].x != mg->e->ma.a[st].x) {
if (i - st > 1) {
for (j = st, w = 0; j < i; ++j) {
w += mg->e->ma.a[j].w;
}
mg->e->ma.a[k] = mg->e->ma.a[st];
mg->e->ma.a[k++].w = w;
} else mg->e->ma.a[k++] = mg->e->ma.a[st];
st = i;
}
}
mg->e->ma.n = k;
}
void mb_merge_dup(mb_g_t *mbg) // MUST BE sorted
{
uint32_t i, j, k, st;
t_w_t w[4];
for (st = 0, i = 1, k = 0; i <= mbg->e->ma.n; ++i) {
if (i == mbg->e->ma.n || mbg->e->ma.a[i].x != mbg->e->ma.a[st].x) {
if (i - st > 1) {
w[0] = w[1] = w[2] = w[3] = 0;
for (j = st; j < i; ++j) {
w[0] += mbg->e->ma.a[j].w[0];
w[1] += mbg->e->ma.a[j].w[1];
w[2] += mbg->e->ma.a[j].w[2];
w[3] += mbg->e->ma.a[j].w[3];
}
mbg->e->ma.a[k] = mbg->e->ma.a[st];
mbg->e->ma.a[k].w[0] = w[0];
mbg->e->ma.a[k].w[1] = w[1];
mbg->e->ma.a[k].w[2] = w[2];
mbg->e->ma.a[k].w[3] = w[3];
k++;
} else mbg->e->ma.a[k++] = mbg->e->ma.a[st];
st = i;
}
}
mbg->e->ma.n = k;
}
static void mc_edges_idx(mc_match_t *ma)
{
uint32_t st, i;
kv_resize(uint64_t, ma->idx, ma->n_seq);
ma->idx.n = ma->n_seq;
memset(ma->idx.a, 0, ma->idx.n*sizeof(uint64_t));
for (st = 0, i = 1; i <= ma->ma.n; ++i)
if (i == ma->ma.n || (ma->ma.a[i].x>>32) != (ma->ma.a[st].x>>32))
ma->idx.a[ma->ma.a[st].x>>32] = (uint64_t)st << 32 | (i - st), st = i;
}
static void mb_edges_idx(mb_match_t *ma)
{
uint32_t st, i;
kv_resize(uint64_t, ma->idx, ma->n_seq);
ma->idx.n = ma->n_seq;
memset(ma->idx.a, 0, ma->idx.n*sizeof(uint64_t));
for (st = 0, i = 1; i <= ma->ma.n; ++i)
if (i == ma->ma.n || (ma->ma.a[i].x>>32) != (ma->ma.a[st].x>>32))
ma->idx.a[ma->ma.a[st].x>>32] = (uint64_t)st << 32 | (i - st), st = i;
}
mc_g_t *init_mc_g_t(ma_ug_t *ug, asg_t *read_g, int8_t *s, uint32_t renew_s)
{
mc_g_t *p = NULL; CALLOC(p, 1);
p->ug = ug;
p->rg = read_g;
kv_init(p->s);
if(s)
{
p->s.a = s;
p->s.n = ug->g->n_seq;
p->s.m = 0;
if(renew_s) memset(p->s.a, 0, p->s.n);
}
else
{
CALLOC(p->s.a, ug->g->n_seq);
p->s.n = p->s.m = ug->g->n_seq;
}
return p;
}
static mc_edge_t *get_mc_edge(const mc_match_t *ma, uint32_t sid1, uint32_t sid2)
{
mc_edge_t *o = pt_a(*ma, sid1);
uint32_t n = pt_n(*ma, sid1), k;
for (k = 0; k < n; ++k)
if (((uint32_t)o[k].x) == sid2)
return &(o[k]);
return NULL;
}
static mb_edge_t *get_mb_edge(const mb_match_t *ma, uint32_t sid1, uint32_t sid2)
{
mb_edge_t *o = pt_a(*ma, sid1);
uint32_t n = pt_n(*ma, sid1), k;
for (k = 0; k < n; ++k)
if (((uint32_t)o[k].x) == sid2)
return &(o[k]);
return NULL;
}
uint32_t mb_edges_symm(mb_match_t *ma);
uint32_t debug_mb_edges_symm(mb_match_t *ma)
{
uint32_t i, n = 0;
mb_edge_t *t = NULL, *m = NULL;
for (i = 0; i < ma->ma.n; ++i) {
m = &ma->ma.a[i];
if (ma_x(*m) == ma_y(*m))
{
fprintf(stderr, "ERROR-0-::%s\n", __func__);
continue;
}
t = get_mb_edge(ma, ma_y(*m), ma_x(*m));
if(!t)
{
fprintf(stderr, "ERROR-1-::%s\n", __func__);
continue;
}
if(m->w[0] != t->w[0])
{
fprintf(stderr, "\nERROR-2-::%s\n", __func__);
fprintf(stderr, "ma_x(*m): %lu, ma_y(*m): %u\n", ma_x(*m), ma_y(*m));
// fprintf(stderr, "m->w[0]: %ld, m->w[1]: %ld, m->w[2]: %ld, m->w[3]: %ld\n",
// m->w[0], m->w[1], m->w[2], m->w[3]);
// fprintf(stderr, "t->w[0]: %ld, t->w[1]: %ld, t->w[2]: %ld, t->w[3]: %ld\n",
// t->w[0], t->w[1], t->w[2], t->w[3]);
fprintf(stderr, "m->w[0]: %f, m->w[1]: %f, m->w[2]: %f, m->w[3]: %f\n",
m->w[0], m->w[1], m->w[2], m->w[3]);
fprintf(stderr, "t->w[0]: %f, t->w[1]: %f, t->w[2]: %f, t->w[3]: %f\n",
t->w[0], t->w[1], t->w[2], t->w[3]);
}
if(m->w[3] != t->w[3])
{
fprintf(stderr, "\nERROR-3-::%s\n", __func__);
fprintf(stderr, "ma_x(*m): %lu, ma_y(*m): %u\n", ma_x(*m), ma_y(*m));
// fprintf(stderr, "m->w[0]: %ld, m->w[1]: %ld, m->w[2]: %ld, m->w[3]: %ld\n",
// m->w[0], m->w[1], m->w[2], m->w[3]);
// fprintf(stderr, "t->w[0]: %ld, t->w[1]: %ld, t->w[2]: %ld, t->w[3]: %ld\n",
// t->w[0], t->w[1], t->w[2], t->w[3]);
fprintf(stderr, "m->w[0]: %f, m->w[1]: %f, m->w[2]: %f, m->w[3]: %f\n",
m->w[0], m->w[1], m->w[2], m->w[3]);
fprintf(stderr, "t->w[0]: %f, t->w[1]: %f, t->w[2]: %f, t->w[3]: %f\n",
t->w[0], t->w[1], t->w[2], t->w[3]);
}
if(m->w[1] != t->w[2])
{
fprintf(stderr, "\nERROR-4-::%s\n", __func__);
fprintf(stderr, "ma_x(*m): %lu, ma_y(*m): %u\n", ma_x(*m), ma_y(*m));
// fprintf(stderr, "m->w[0]: %ld, m->w[1]: %ld, m->w[2]: %ld, m->w[3]: %ld\n",
// m->w[0], m->w[1], m->w[2], m->w[3]);
// fprintf(stderr, "t->w[0]: %ld, t->w[1]: %ld, t->w[2]: %ld, t->w[3]: %ld\n",
// t->w[0], t->w[1], t->w[2], t->w[3]);
fprintf(stderr, "m->w[0]: %f, m->w[1]: %f, m->w[2]: %f, m->w[3]: %f\n",
m->w[0], m->w[1], m->w[2], m->w[3]);
fprintf(stderr, "t->w[0]: %f, t->w[1]: %f, t->w[2]: %f, t->w[3]: %f\n",
t->w[0], t->w[1], t->w[2], t->w[3]);
}
if(m->w[2] != t->w[1])
{
fprintf(stderr, "\nERROR-5-::%s\n", __func__);
fprintf(stderr, "ma_x(*m): %lu, ma_y(*m): %u\n", ma_x(*m), ma_y(*m));
// fprintf(stderr, "m->w[0]: %ld, m->w[1]: %ld, m->w[2]: %ld, m->w[3]: %ld\n",
// m->w[0], m->w[1], m->w[2], m->w[3]);
// fprintf(stderr, "t->w[0]: %ld, t->w[1]: %ld, t->w[2]: %ld, t->w[3]: %ld\n",
// t->w[0], t->w[1], t->w[2], t->w[3]);
fprintf(stderr, "m->w[0]: %f, m->w[1]: %f, m->w[2]: %f, m->w[3]: %f\n",
m->w[0], m->w[1], m->w[2], m->w[3]);
fprintf(stderr, "t->w[0]: %f, t->w[1]: %f, t->w[2]: %f, t->w[3]: %f\n",
t->w[0], t->w[1], t->w[2], t->w[3]);
}
}
return n;
}
inline void decode_mb_node(mb_g_t *mbg, uint32_t id, uint32_t **a0, uint32_t *n0, mc_node_t *s0,
uint32_t **a1, uint32_t *n1, mc_node_t *s1)
{
if(a0) (*a0) = mbg->u->bid.a + mbg->u->u.a[id].a[0];
if(n0) (*n0) = mbg->u->u.a[id].occ[0];
if(s0) (*s0) = mbg->u->u.a[id].s[0];
if(a1) (*a1) = mbg->u->bid.a + mbg->u->u.a[id].a[1];
if(n1) (*n1) = mbg->u->u.a[id].occ[1];
if(s1) (*s1) = mbg->u->u.a[id].s[1];
}
uint64_t *mb_nodes_core(kv_u_trans_t *ref, mc_match_t* ma, uint32_t occ, uint32_t *fg, kvec_t_u32_warp *sk)
{
uint32_t i, x, y;
uint64_t *group;
u_trans_t *o = NULL;
for (i = 0; i < occ; ++i)
fg[i] = (uint32_t)-1;
// connected componets
for (i = 0; i < occ; ++i) {
if (fg[i] != (uint32_t)-1) continue;
if (pt_n(*ma, i) == 0)
{
fg[i] = i;///group id
continue;
}
sk->a.n = 0;
kv_push(uint32_t, sk->a, i);
while (sk->a.n > 0) {
uint32_t k, j, st, n, t;
sk->a.n--;
k = sk->a.a[sk->a.n];
fg[k] = i;///group id
o = u_trans_a(*ref, k);
n = u_trans_n(*ref, k);
for (st = 0, j = 1; j <= n; ++j)
{
if(j == n || o[j].tn != o[st].tn)
{
t = o[st].tn;
if ((pt_n(*ma, t) != 0) && (fg[t] == (uint32_t)-1))
{
kv_push(uint32_t, sk->a, t);
}
st = j;
}
}
}
}
// precalculate the size of each group
CALLOC(group, occ);
for (i = 0; i < occ; ++i)
group[i] = (uint64_t)fg[i] << 32 | i;
radix_sort_mc64(group, group + occ);
for (i = 1, x = y = 0; i <= occ; ++i) {
if (i == occ || group[i]>>32 != group[x]>>32) {
uint32_t j;
for (j = x; j < i; ++j)
group[j] = (uint64_t)y << 32 | (uint32_t)group[j];///(group id)|first element in this group
++y, x = i;
}
}
return group;
}
void assgin_mb_node(mb_nodes_t *x, kv_u_trans_t *ref, mc_match_t* ma, uint32_t *fg, kvec_t_u32_warp *sk, uint64_t *cc, uint32_t cc_off, uint32_t cc_size)
{
uint32_t i, v, n, st, j, t, pass, uid;
u_trans_t *o = NULL;
mb_node_t *p = NULL;
for (i = 0; i < cc_size; ++i)
{
v = (uint32_t)cc[cc_off + i];///node id
fg[v] = (uint32_t)-1;
}
sk->a.n = 0;
v = (uint32_t)cc[cc_off];
kv_push(uint32_t, sk->a, v);
fg[v] = 0;
pass = 1;
while (sk->a.n > 0)
{
sk->a.n--;
v = sk->a.a[sk->a.n];
if(pt_n(*ma, v) == 0) continue;
o = u_trans_a(*ref, v);
n = u_trans_n(*ref, v);
for (st = 0, j = 1; j <= n; ++j)
{
if(j == n || o[j].tn != o[st].tn)
{
t = o[st].tn;
if (pt_n(*ma, t) == 0)
{
st = j;
continue;
}
if (fg[t] == (uint32_t)-1)///uncolor
{
fg[t] = 1 - fg[v];
kv_push(uint32_t, sk->a, t);
}
else if(fg[t] == fg[v]) ///color
{
pass = 0;
break;
}
st = j;
}
}
if(pass == 0) break;
}
if(pass)
{
uid = x->u.n;
kv_pushp(mb_node_t, x->u, &p);
p->z[0] = p->z[1] = p->z[2] = p->z[3] = 0;
p->s[0] = p->s[1] = 0;
p->occ[0] = p->occ[1] = 0;
for (i = 0, p->a[0] = x->bid.n; i < cc_size; ++i)
{
v = (uint32_t)cc[cc_off + i];///node id
if(fg[v] == 0)
{
kv_push(uint32_t, x->bid, v);
p->occ[0]++;
x->idx.a[v] = (uid<<1);
}
}
for (i = 0, p->a[1] = x->bid.n; i < cc_size; ++i)
{
v = (uint32_t)cc[cc_off + i];///node id
if(fg[v] == 1)
{
kv_push(uint32_t, x->bid, v);
p->occ[1]++;
x->idx.a[v] = (uid<<1) + 1;
}
}
}
else
{
for (i = 0; i < cc_size; ++i)
{
v = (uint32_t)cc[cc_off + i];///node id
uid = x->u.n;
kv_pushp(mb_node_t, x->u, &p);
p->z[0] = p->z[1] = p->z[2] = p->z[3] = 0;
p->s[0] = p->s[1] = 0;
p->occ[0] = p->occ[1] = 0;
p->a[0] = x->bid.n;
kv_push(uint32_t, x->bid, v);
p->occ[0]++;
x->idx.a[v] = (uid<<1);
p->a[1] = x->bid.n;
}
}
}
void debug_mb_nodes(mb_nodes_t *x, kv_u_trans_t *ref, mc_match_t* ma)
{
uint32_t i, k, bid, ori, *a = NULL, a_n, v;
for (i = 0; i < x->idx.n; i++)
{
if(x->idx.a[i] == (uint32_t)-1)
{
fprintf(stderr, "ERROR-0-::%s\n", __func__);
continue;
}
bid = x->idx.a[i]>>1; ori = x->idx.a[i] & 1;
a = x->bid.a + x->u.a[bid].a[ori];
a_n = x->u.a[bid].occ[ori];
for (k = 0; k < a_n; k++)
{
if(a[k] == i) break;
}
if(k >= a_n) fprintf(stderr, "ERROR-1-::%s\n", __func__);
}
uint32_t *tt[2], t_n[2], o_n, m, t, found;
int8_t *vis = NULL; CALLOC(vis, x->idx.n);
u_trans_t *o = NULL;
for (i = 0; i < x->u.n; i++)///each block
{
tt[0] = x->bid.a + x->u.a[i].a[0];
t_n[0] = x->u.a[i].occ[0];
tt[1] = x->bid.a + x->u.a[i].a[1];
t_n[1] = x->u.a[i].occ[1];
if(t_n[0] == 1 && t_n[1] == 0) continue;
for (k = 0; k < t_n[0]; k++)
{
vis[tt[0][k]] = 1;
}
for (k = 0; k < t_n[1]; k++)
{
vis[tt[1][k]] = -1;
}
for (k = 0; k < t_n[0]; k++)
{
v = tt[0][k];
o = u_trans_a(*ref, v);
o_n = u_trans_n(*ref, v);
found = 0;
for (m = 0; m < o_n; m++)
{
t = o[m].tn;
if (pt_n(*ma, t) == 0) continue;
if (vis[t] != -1) fprintf(stderr, "ERROR-2-::%s\n", __func__);
else found = 1;
}
if(found == 0) fprintf(stderr, "ERROR-2-*::%s\n", __func__);
}
for (k = 0; k < t_n[1]; k++)
{
v = tt[1][k];
o = u_trans_a(*ref, v);
o_n = u_trans_n(*ref, v);
found = 0;
for (m = 0; m < o_n; m++)
{
t = o[m].tn;
if (pt_n(*ma, t) == 0) continue;
if (vis[t] != 1) fprintf(stderr, "ERROR-3-::%s\n", __func__);
else found = 1;
}
if(found == 0) fprintf(stderr, "ERROR-3-*::%s\n", __func__);
}
for (k = 0; k < t_n[0]; k++)
{
vis[tt[0][k]] = 0;
}
for (k = 0; k < t_n[1]; k++)
{
vis[tt[1][k]] = 0;
}
}
free(vis);
}
mb_nodes_t *update_mb_nodes_t(kv_u_trans_t *ref, mc_match_t* ma, uint32_t occ)
{
uint32_t i, st;
uint64_t *cc = NULL;
mb_nodes_t *x = NULL; CALLOC(x, 1);
x->bid.n = x->u.n = x->idx.n = 0;
kv_resize(uint32_t, x->idx, occ);
x->idx.n = occ;
memset(x->idx.a, -1, sizeof(uint32_t)*x->idx.n);
kvec_t_u32_warp stack; kv_init(stack.a);
uint32_t *flag = NULL; MALLOC(flag, occ);
cc = mb_nodes_core(ref, ma, occ, flag, &stack);
for (st = 0, i = 1; i <= occ; ++i) {
if (i == occ || cc[st]>>32 != cc[i]>>32) {
assgin_mb_node(x, ref, ma, flag, &stack, cc, st, i - st);
st = i;
}
}
free(cc); free(flag);
kv_destroy(stack.a);
/*******************************for debug************************************/
// debug_mb_nodes(x, ref, ma);
/*******************************for debug************************************/
return x;
}
mb_g_t *init_mb_g_t(mc_match_t* e, kv_u_trans_t *ref, uint32_t is_sys)
{
mc_edge_t *o = NULL;
uint32_t i, k, m, n, a_n[2], *a[2], qn, tn, qb, tb;
mb_edge_t *t = NULL;
mb_g_t *p = NULL; CALLOC(p, 1);
p->u = update_mb_nodes_t(ref, e, e->n_seq);
p->e = NULL; CALLOC(p->e, 1);
p->e->n_seq = p->u->u.n;
kv_init(p->e->ma); kv_init(p->e->idx);
for (i = 0; i < p->u->u.n; i++)///each block
{
qb = i;
p->u->u.a[i].s[0] = p->u->u.a[i].s[1] = 0;
decode_mb_node(p, i, &(a[0]), &(a_n[0]), NULL, &(a[1]), &(a_n[1]), NULL);
for (k = 0; k < a_n[0]; k++)
{
qn = a[0][k];
o = pt_a(*e, qn);
n = pt_n(*e, qn);
for (m = 0; m < n; m++)
{
tn = ma_y(o[m]);
tb = p->u->idx.a[tn]>>1;
if(tb == qb)
{
continue;
}
kv_pushp(mb_edge_t, p->e->ma, &t);
t->x = (uint64_t)qb << 32 | tb;
t->w[0] = t->w[1] = t->w[2] = t->w[3] = 0;
t->w[p->u->idx.a[tn]&1] = o[m].w;
}
}
for (k = 0; k < a_n[1]; k++)
{
qn = a[1][k];
o = pt_a(*e, qn);
n = pt_n(*e, qn);
for (m = 0; m < n; m++)
{
tn = ma_y(o[m]);
tb = p->u->idx.a[tn]>>1;
if(tb == qb)
{
continue;
}
kv_pushp(mb_edge_t, p->e->ma, &t);
t->x = (uint64_t)qb << 32 | tb;
t->w[0] = t->w[1] = t->w[2] = t->w[3] = 0;
t->w[(p->u->idx.a[tn]&1)+2] = o[m].w;
}
}
}
radix_sort_mbe(p->e->ma.a, p->e->ma.a + p->e->ma.n);
mb_merge_dup(p); // MUST BE sorted
mb_edges_idx(p->e);
/*******************************for debug************************************/
// debug_mb_edges_symm(p->e);
/*******************************for debug************************************/
if(is_sys) mb_edges_symm(p->e);
return p;
}
void destory_mc_g_t(mc_g_t **p)
{
if(!p || !(*p)) return;
if((*p)->s.m == 0) (*p)->s.a = NULL;
kv_destroy((*p)->s);
if((*p)->e)
{
kv_destroy((*p)->e->idx);
kv_destroy((*p)->e->ma);
free((*p)->e->cc);
free((*p)->e);
}
free((*p));
}
void destory_mb_g_t(mb_g_t **p)
{
if(!p || !(*p)) return;
kv_destroy((*p)->e->idx);
kv_destroy((*p)->e->ma);
free((*p)->e->cc);
free((*p)->e);
kv_destroy((*p)->u->bid);
kv_destroy((*p)->u->idx);
kv_destroy((*p)->u->u);
free((*p)->u);
free((*p));
}
static void ks_shuffle_uint32_t(size_t n, uint32_t a[], uint64_t *x)
{
size_t i, j;
for (i = n; i > 1; --i) {
uint32_t tmp;
j = (size_t)(kr_drand_r(x) * i);
tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp;
}
}
static void normalize_mc_edge(mc_edge_t *a, mc_edge_t *b)
{
if(a->w >= b->w)
{
b->x = (uint32_t)a->x;
b->x <<= 32;
b->x |= (a->x>>32);
b->w = a->w;
}
else
{
a->x = (uint32_t)b->x;
a->x <<= 32;
a->x |= (b->x>>32);
a->w = b->w;
}
}
uint32_t mc_edges_symm(mc_match_t *ma)
{
uint8_t *del = NULL;
uint32_t i, k, n = 0;
mc_edge_t *t = NULL, *m = NULL;
CALLOC(del, ma->ma.n);
for (i = 0; i < ma->ma.n; ++i) {
m = &ma->ma.a[i];
if (ma_x(*m) == ma_y(*m))
{
del[i] = 1, ++n;///self overlap
continue;
}
t = get_mc_edge(ma, ma_y(*m), ma_x(*m));
if(!t)
{
del[i] = 1, ++n;///self overlap
continue;
}
normalize_mc_edge(m, t);
}
if (n > 0) {
for (i = k = 0; i < ma->ma.n; ++i)
if (!del[i]) ma->ma.a[k++] = ma->ma.a[i];
ma->ma.n = k;
mc_edges_idx(ma);
}
free(del);
return n;
}
static void normalize_mb_edge(mb_edge_t *a, mb_edge_t *b)
{
if(a->w >= b->w)
{
b->x = (uint32_t)a->x;
b->x <<= 32;
b->x |= (a->x>>32);
b->w[0] = a->w[0];
b->w[3] = a->w[3];
b->w[1] = a->w[2];
b->w[2] = a->w[1];
}
else
{
a->x = (uint32_t)b->x;
a->x <<= 32;
a->x |= (b->x>>32);
a->w[0] = b->w[0];
a->w[3] = b->w[3];
a->w[1] = b->w[2];
a->w[2] = b->w[1];
}
}
uint32_t mb_edges_symm(mb_match_t *ma)
{
uint8_t *del = NULL;
uint32_t i, k, n = 0;
mb_edge_t *t = NULL, *m = NULL;
CALLOC(del, ma->ma.n);
for (i = 0; i < ma->ma.n; ++i) {
m = &ma->ma.a[i];
if (ma_x(*m) == ma_y(*m))
{
del[i] = 1, ++n;///self overlap
continue;
}
t = get_mb_edge(ma, ma_y(*m), ma_x(*m));
if(!t)
{
del[i] = 1, ++n;///self overlap
continue;
}
normalize_mb_edge(m, t);
}
if (n > 0) {
for (i = k = 0; i < ma->ma.n; ++i)
if (!del[i]) ma->ma.a[k++] = ma->ma.a[i];
ma->ma.n = k;
mb_edges_idx(ma);
}
free(del);
return n;
}
void debug_mc_interval_t(mc_interval_t *p, uint32_t p_n, uint32_t *p_idx, ma_ug_t *ug, asg_t *rg,
trans_chain* t_ch)
{
fprintf(stderr, "0----------[M::%s]----------\n", __func__);
uint32_t i, offset, v, sid, eid, spos, epos, p_status, p_uid, occ;
ma_utg_t *u = NULL;
mc_interval_t *a = NULL, *t = NULL;
for (v = 0; v < ug->u.n; v++)
{
a = p + p_idx[v];
occ = p_idx[v+1] - p_idx[v];
for (i = 0; i < occ; i++)
{
if(a[i].uID != v) fprintf(stderr, "ERROR-s\n");
}
}
for (v = 0, p_status = (uint32_t)-1, p_uid = (uint32_t)-1; v < p_n; v++)
{
t = &(p[v]);
sid = t->nS;
eid = t->nE;
spos = t->bS;
epos = t->bE;
if(p_uid == t->uID && p_status == t->hs)
{
fprintf(stderr, "ERROR-a\n");
}
p_status = t->hs;
p_uid = t->uID;
u = &(ug->u.a[t->uID]);
for (i = offset = 0; i < u->n; i++)
{
if(i == sid)
{
if(spos != offset)
{
fprintf(stderr, "ERROR-b\n");
}
}
if(i == eid)
{
if(epos != (offset+rg->seq[u->a[i]>>33].len - 1))
{
fprintf(stderr, "ERROR-c, real end: %u\n",
(uint32_t)(offset+rg->seq[u->a[i]>>33].len - 1));
}
}
offset += (uint32_t)u->a[i];
if(i >= sid && i <= eid)
{
if(t_ch->ir_het[u->a[i]>>33] != t->hs)
{
fprintf(stderr, "ERROR-d: is_r_het: %u, h_status: %u\n", t_ch->ir_het[u->a[i]>>33], t->hs);
}
}
}
}
}
double get_w_scale(kv_u_trans_t *ta)
{
uint32_t i, max_w_i, min_w_i;
double max_w = 0, min_w = 0, w;
max_w_i = min_w_i = (uint32_t)-1;
for (i = 0; i < ta->n; ++i)
{
if(ta->a[i].del) continue;
if(ta->a[i].nw == 0) continue;
w = (ta->a[i].nw >= 0? ta->a[i].nw:-ta->a[i].nw);
if(max_w_i == (uint32_t)-1 || max_w < w) max_w = w, max_w_i = i;
if(min_w_i == (uint32_t)-1 || min_w > w) min_w = w, min_w_i = i;
}
if(max_w_i == (uint32_t)-1 || min_w_i == (uint32_t)-1) return 1;
if(min_w > 1.1) return 1;
double sc_max = (double)(1<<30), sc_min = 1.1;
return MIN(sc_max/max_w, sc_min/min_w) + sc_min;
}
void update_mc_edges(mc_g_t *mg, hap_overlaps_list* ha, kv_u_trans_t *ta, trans_chain* t_ch, double f_rate, uint32_t is_sys)
{
uint32_t v, i, k, qn, tn, qs, qe, ts, te, occ, as, ae, l, offset, l_pos;
uint64_t hetLen, homLen, oLen;
mc_interval_t *a = NULL;
mc_edge_t *ma = NULL;
asg_t* nsg = mg->ug->g;
ma_utg_t *u = NULL;
mc_interval_t *t = NULL;
kvec_t(mc_interval_t) p; kv_init(p);
kvec_t(uint32_t) p_idx; kv_init(p_idx);
if(t_ch)
{
kv_push(uint32_t, p_idx, 0);
for (v = 0; v < nsg->n_seq; v++)
{
u = &(mg->ug->u.a[v]);
for (k = 1, l = 0, offset = 0, l_pos = 0; k <= u->n; ++k)
{
if (k == u->n || t_ch->ir_het[u->a[k]>>33] != t_ch->ir_het[u->a[l]>>33])
{
kv_pushp(mc_interval_t, p, &t);
t->uID = v;
t->hs = t_ch->ir_het[u->a[l]>>33];
t->bS = l_pos;
t->bE = offset + mg->rg->seq[u->a[k-1]>>33].len - 1;
t->nS = l;
t->nE = k - 1;
l = k;
l_pos = offset + (uint32_t)u->a[k-1];
}
offset += (uint32_t)u->a[k-1];
}
kv_push(uint32_t, p_idx, p.n);
}
///debug_mc_interval_t(p.a, p.n, p_idx.a, mg->ug, mg->rg, t_ch);
}
if(!mg->e)
{
CALLOC(mg->e, 1);
mg->e->n_seq = mg->ug->g->n_seq;
kv_init(mg->e->idx); kv_init(mg->e->ma);
}
if(ha)
{
for (v = 0; v < ha->num; v++)
{
for (i = 0; i < ha->x[v].a.n; i++)
{
if(ha->x[v].a.a[i].score <= 0) continue;
if(ha->x[v].a.a[i].xUid == ha->x[v].a.a[i].yUid) continue;
if(p.n > 0 && p_idx.n > 0)
{
/*****************qn*****************/
qn = ha->x[v].a.a[i].xUid;
qs = ha->x[v].a.a[i].x_beg_pos;
qe = ha->x[v].a.a[i].x_end_pos - 1;
a = p.a + p_idx.a[qn];
occ = p_idx.a[qn+1] - p_idx.a[qn];
for (k = 0, hetLen = 0, homLen = 0; k < occ; k++)
{
as = a[k].bS;
ae = a[k].bE;
oLen = ((MIN(qe, ae) >= MAX(qs, as))? MIN(qe, ae) - MAX(qs, as) + 1 : 0);
if(homLen + hetLen > 0 && oLen == 0) break;
if(oLen == 0) continue;
if(a[k].hs == N_HET)
{
homLen += oLen;
}
else if(asm_opt.polyploidy <= 2 && (a[k].hs&P_HET))///if(asm_opt.polyploidy <= 2 && (a[k].hs&S_HET))
{