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algo.c
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algo.c
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#include <stdlib.h>
#include <string.h>
#include "kalloc.h"
#define __STDC_LIMIT_MACROS
#include "algo.h"
#include "miniwfa.h"
/************************
* Max-scoring segments *
************************/
#include "kvec-km.h"
#define MSS_NEG_INF INT32_MIN
typedef struct {
int32_t st, en;
MG_MSS_TYPE L, R;
int32_t pre;
} msseg_aux_t;
typedef kvec_t(mg_msseg_t) msseg_v;
typedef kvec_t(msseg_aux_t) msseg_aux_v;
static void move_segs(void *km, msseg_v *ret, msseg_aux_v *seg, MG_MSS_TYPE min_sc)
{
int32_t i;
for (i = 0; i < seg->n; ++i) {
msseg_aux_t *p = &seg->a[i];
if (p->R - p->L >= min_sc) {
mg_msseg_t *q;
kv_pushp(mg_msseg_t, km, *ret, &q);
q->st = p->st, q->en = p->en, q->sc = p->R - p->L;
}
}
seg->n = 0;
}
// Reference: Ruzzo and Tompa (1999) A linear time algorithm for finding all maximal scoring subsequencs
mg_msseg_t *mg_mss_all(void *km, int32_t n, const MG_MSS_TYPE *S, MG_MSS_TYPE min_sc, MG_MSS_TYPE xdrop, int32_t *n_seg)
{
int32_t i, j;
MG_MSS_TYPE L, max;
msseg_v ret = {0,0,0};
msseg_aux_v seg = {0,0,0};
msseg_aux_t t;
kv_resize(mg_msseg_t, km, ret, 16);
kv_resize(msseg_aux_t, km, seg, 16);
for (i = 0, L = 0, max = MSS_NEG_INF; i < n;) {
if (S[i] > 0) {
int32_t k;
MG_MSS_TYPE R = L + S[i];
for (k = i + 1; k < n && S[k] > 0; ++k)
R += S[k];
if (R > max) max = R;
t.st = i, t.en = k, t.L = L, t.R = R;
while (1) {
msseg_aux_t *p;
for (j = seg.n - 1; j >= 0;) {
p = &seg.a[j];
if (p->L < t.L) break;
j = p->pre >= 0? p->pre : j - 1;
}
if (j >= 0 && seg.a[j].R < t.R) {
p = &seg.a[j];
t.st = p->st, t.L = p->L, t.pre = p->pre;
seg.n = j;
} else {
if (j < 0) {
move_segs(km, &ret, &seg, min_sc);
max = R;
}
t.pre = j;
kv_push(msseg_aux_t, km, seg, t);
break;
}
}
L = R, i = k;
} else {
if (xdrop > 0 && L + S[i] + xdrop < max) { // reset
move_segs(km, &ret, &seg, min_sc);
L = 0, max = MSS_NEG_INF;
}
L += S[i++];
}
}
move_segs(km, &ret, &seg, min_sc);
kfree(km, seg.a);
KREALLOC(km, ret.a, ret.n);
*n_seg = ret.n;
return ret.a;
}
/**************************
* Interval overlap query *
**************************/
#include <assert.h>
#include "ksort.h"
#define sort_key_intv(a) ((a).st)
KRADIX_SORT_INIT(mg_intv, mg_intv_t, sort_key_intv, 4)
int32_t mg_intv_index(int32_t n, mg_intv_t *a)
{
int32_t i, last_i, last, k;
if (n <= 0) return -1;
radix_sort_mg_intv(a, a + n);
for (i = 0; i < n; i += 2) last_i = i, last = a[i].far = a[i].en;
for (k = 1; 1LL<<k <= n; ++k) {
int64_t x = 1LL<<(k-1), i0 = (x<<1) - 1, step = x<<2;
for (i = i0; i < n; i += step) {
int32_t el = a[i - x].far;
int32_t er = i + x < n? a[i + x].far : last;
int32_t e = a[i].en;
e = e > el? e : el;
e = e > er? e : er;
a[i].far = e;
}
last_i = last_i>>k&1? last_i - x : last_i + x;
if (last_i < n && a[last_i].far > last)
last = a[last_i].far;
}
return k - 1;
}
typedef struct {
int64_t x;
int32_t k, w;
} istack_t;
int32_t mg_intv_overlap(void *km, int32_t n_a, const mg_intv_t *a, int32_t st, int32_t en, int32_t **b_, int32_t *m_b_)
{
int32_t t = 0, h, *b = *b_, m_b = *m_b_, n = 0;
istack_t stack[64], *p;
for (h = 0; 1<<h <= n_a; ++h);
--h;
p = &stack[t++];
p->k = h, p->x = (1LL<<p->k) - 1, p->w = 0; // push the root into the stack
while (t) { // stack is not empyt
istack_t z = stack[--t];
if (z.k <= 3) { // the subtree is no larger than (1<<(z.k+1))-1; do a linear scan
int32_t i, i0 = z.x >> z.k << z.k, i1 = i0 + (1LL<<(z.k+1)) - 1;
if (i1 >= n_a) i1 = n_a;
for (i = i0; i < i1 && a[i].st < en; ++i)
if (st < a[i].en) {
if (n == m_b) KEXPAND(km, b, m_b);
b[n++] = i;
}
} else if (z.w == 0) { // if left child not processed
int32_t y = z.x - (1LL<<(z.k-1));
p = &stack[t++];
p->k = z.k, p->x = z.x, p->w = 1;
if (y >= n_a || a[y].far > st) {
p = &stack[t++];
p->k = z.k - 1, p->x = y, p->w = 0; // push the left child to the stack
}
} else if (z.x < n_a && a[z.x].st < en) {
if (st < a[z.x].en) { // then z.x overlaps the query; write to the output array
if (n == m_b) KEXPAND(km, b, m_b);
b[n++] = z.x;
}
p = &stack[t++];
p->k = z.k - 1, p->x = z.x + (1LL<<(z.k-1)), p->w = 0; // push the right child
}
}
*b_ = b, *m_b_ = m_b;
return n;
}
/********************
* Global alignment *
********************/
int32_t mg_wfa_cmp(void *km, int32_t l1, const char *s1, int32_t l2, const char *s2, int32_t max_pen, int32_t *mlen, int32_t *blen)
{
mwf_opt_t opt;
mwf_rst_t r;
int32_t i;
mwf_opt_init(&opt);
opt.max_s = max_pen;
opt.flag |= MWF_F_CIGAR;
mwf_wfa_exact(km, &opt, l1, s1, l2, s2, &r);
*mlen = *blen = 0;
for (i = 0; i < r.n_cigar; ++i) {
int32_t op = r.cigar[i]&0xf, len = r.cigar[i]>>4;
*blen += len;
if (op == 7) *mlen += len;
}
kfree(km, r.cigar);
return r.s < 0? -(l1 + l2) : (l1 + l2) / 2 - r.s;
}