Find file
Fetching contributors…
Cannot retrieve contributors at this time
265 lines (244 sloc) 8.86 KB
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "bwtgap.h"
#include "bwtaln.h"
#define STATE_M 0
#define STATE_I 1
#define STATE_D 2
#define aln_score(m,o,e,p) ((m)*(p)->s_mm + (o)*(p)->s_gapo + (e)*(p)->s_gape)
gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt)
{
int i;
gap_stack_t *stack;
stack = (gap_stack_t*)calloc(1, sizeof(gap_stack_t));
stack->n_stacks = aln_score(max_mm+1, max_gapo+1, max_gape+1, opt);
stack->stacks = (gap_stack1_t*)calloc(stack->n_stacks, sizeof(gap_stack1_t));
for (i = 0; i != stack->n_stacks; ++i) {
gap_stack1_t *p = stack->stacks + i;
p->m_entries = 4;
p->stack = (gap_entry_t*)calloc(p->m_entries, sizeof(gap_entry_t));
}
return stack;
}
void gap_destroy_stack(gap_stack_t *stack)
{
int i;
for (i = 0; i != stack->n_stacks; ++i) free(stack->stacks[i].stack);
free(stack->stacks);
free(stack);
}
static void gap_reset_stack(gap_stack_t *stack)
{
int i;
for (i = 0; i != stack->n_stacks; ++i)
stack->stacks[i].n_entries = 0;
stack->best = stack->n_stacks;
stack->n_entries = 0;
}
static inline void gap_push(gap_stack_t *stack, int a, int i, bwtint_t k, bwtint_t l, int n_mm, int n_gapo, int n_gape,
int state, int is_diff, const gap_opt_t *opt)
{
int score;
gap_entry_t *p;
gap_stack1_t *q;
score = aln_score(n_mm, n_gapo, n_gape, opt);
q = stack->stacks + score;
if (q->n_entries == q->m_entries) {
q->m_entries <<= 1;
q->stack = (gap_entry_t*)realloc(q->stack, sizeof(gap_entry_t) * q->m_entries);
}
p = q->stack + q->n_entries;
p->info = (u_int32_t)score<<21 | a<<20 | i; p->k = k; p->l = l;
p->n_mm = n_mm; p->n_gapo = n_gapo; p->n_gape = n_gape; p->state = state;
if (is_diff) p->last_diff_pos = i;
++(q->n_entries);
++(stack->n_entries);
if (stack->best > score) stack->best = score;
}
static inline void gap_pop(gap_stack_t *stack, gap_entry_t *e)
{
gap_stack1_t *q;
q = stack->stacks + stack->best;
*e = q->stack[q->n_entries - 1];
--(q->n_entries);
--(stack->n_entries);
if (q->n_entries == 0 && stack->n_entries) { // reset best
int i;
for (i = stack->best + 1; i < stack->n_stacks; ++i)
if (stack->stacks[i].n_entries != 0) break;
stack->best = i;
} else if (stack->n_entries == 0) stack->best = stack->n_stacks;
}
static inline void gap_shadow(int x, int len, bwtint_t max, int last_diff_pos, bwt_width_t *w)
{
int i, j;
for (i = j = 0; i < last_diff_pos; ++i) {
if (w[i].w > x) w[i].w -= x;
else if (w[i].w == x) {
w[i].bid = 1;
w[i].w = max - (++j);
} // else should not happen
}
}
static inline int int_log2(uint32_t v)
{
int c = 0;
if (v & 0xffff0000u) { v >>= 16; c |= 16; }
if (v & 0xff00) { v >>= 8; c |= 8; }
if (v & 0xf0) { v >>= 4; c |= 4; }
if (v & 0xc) { v >>= 2; c |= 2; }
if (v & 0x2) c |= 1;
return c;
}
bwt_aln1_t *bwt_match_gap(bwt_t *const bwts[2], int len, const ubyte_t *seq[2], bwt_width_t *w[2],
bwt_width_t *seed_w[2], const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack)
{
int best_score = aln_score(opt->max_diff+1, opt->max_gapo+1, opt->max_gape+1, opt);
int best_diff = opt->max_diff + 1, max_diff = opt->max_diff;
int best_cnt = 0;
int max_entries = 0, j, _j, n_aln, m_aln;
bwt_aln1_t *aln;
m_aln = 4; n_aln = 0;
aln = (bwt_aln1_t*)calloc(m_aln, sizeof(bwt_aln1_t));
// check whether there are too many N
for (j = _j = 0; j < len; ++j)
if (seq[0][j] > 3) ++_j;
if (_j > max_diff) {
*_n_aln = n_aln;
return aln;
}
//for (j = 0; j != len; ++j) printf("#0 %d: [%d,%u]\t[%d,%u]\n", j, w[0][j].bid, w[0][j].w, w[1][j].bid, w[1][j].w);
gap_reset_stack(stack); // reset stack
gap_push(stack, 0, len, 0, bwts[0]->seq_len, 0, 0, 0, 0, 0, opt);
gap_push(stack, 1, len, 0, bwts[0]->seq_len, 0, 0, 0, 0, 0, opt);
while (stack->n_entries) {
gap_entry_t e;
int a, i, m, m_seed = 0, hit_found, allow_diff, allow_M, tmp;
bwtint_t k, l, cnt_k[4], cnt_l[4], occ;
const bwt_t *bwt;
const ubyte_t *str;
const bwt_width_t *seed_width = 0;
bwt_width_t *width;
if (max_entries < stack->n_entries) max_entries = stack->n_entries;
if (stack->n_entries > opt->max_entries) break;
gap_pop(stack, &e); // get the best entry
k = e.k; l = e.l; // SA interval
a = e.info>>20&1; i = e.info&0xffff; // strand, length
if (!(opt->mode & BWA_MODE_NONSTOP) && e.info>>21 > best_score + opt->s_mm) break; // no need to proceed
m = max_diff - (e.n_mm + e.n_gapo);
if (opt->mode & BWA_MODE_GAPE) m -= e.n_gape;
if (m < 0) continue;
bwt = bwts[1-a]; str = seq[a]; width = w[a];
if (seed_w) { // apply seeding
seed_width = seed_w[a];
m_seed = opt->max_seed_diff - (e.n_mm + e.n_gapo);
if (opt->mode & BWA_MODE_GAPE) m_seed -= e.n_gape;
}
//printf("#1\t[%d,%d,%d,%c]\t[%d,%d,%d]\t[%u,%u]\t[%u,%u]\t%d\n", stack->n_entries, a, i, "MID"[e.state], e.n_mm, e.n_gapo, e.n_gape, width[i-1].bid, width[i-1].w, k, l, e.last_diff_pos);
if (i > 0 && m < width[i-1].bid) continue;
// check whether a hit is found
hit_found = 0;
if (i == 0) hit_found = 1;
else if (m == 0 && (e.state == STATE_M || (opt->mode&BWA_MODE_GAPE) || e.n_gape == opt->max_gape)) { // no diff allowed
if (bwt_match_exact_alt(bwt, i, str, &k, &l)) hit_found = 1;
else continue; // no hit, skip
}
if (hit_found) { // action for found hits
int score = aln_score(e.n_mm, e.n_gapo, e.n_gape, opt);
int do_add = 1;
//printf("#2 hits found: %d:(%u,%u)\n", e.n_mm+e.n_gapo, k, l);
if (n_aln == 0) {
best_score = score;
best_diff = e.n_mm + e.n_gapo;
if (opt->mode & BWA_MODE_GAPE) best_diff += e.n_gape;
if (!(opt->mode & BWA_MODE_NONSTOP))
max_diff = (best_diff + 1 > opt->max_diff)? opt->max_diff : best_diff + 1; // top2 behaviour
}
if (score == best_score) best_cnt += l - k + 1;
else if (best_cnt > opt->max_top2) break; // top2b behaviour
if (e.n_gapo) { // check whether the hit has been found. this may happen when a gap occurs in a tandem repeat
for (j = 0; j != n_aln; ++j)
if (aln[j].k == k && aln[j].l == l) break;
if (j < n_aln) do_add = 0;
}
if (do_add) { // append
bwt_aln1_t *p;
gap_shadow(l - k + 1, len, bwt->seq_len, e.last_diff_pos, width);
if (n_aln == m_aln) {
m_aln <<= 1;
aln = (bwt_aln1_t*)realloc(aln, m_aln * sizeof(bwt_aln1_t));
memset(aln + m_aln/2, 0, m_aln/2*sizeof(bwt_aln1_t));
}
p = aln + n_aln;
p->n_mm = e.n_mm; p->n_gapo = e.n_gapo; p->n_gape = e.n_gape; p->a = a;
p->k = k; p->l = l;
p->score = score;
++n_aln;
}
continue;
}
--i;
bwt_2occ4(bwt, k - 1, l, cnt_k, cnt_l); // retrieve Occ values
occ = l - k + 1;
// test whether diff is allowed
allow_diff = allow_M = 1;
if (i > 0) {
int ii = i - (len - opt->seed_len);
if (width[i-1].bid > m-1) allow_diff = 0;
else if (width[i-1].bid == m-1 && width[i].bid == m-1 && width[i-1].w == width[i].w) allow_M = 0;
if (seed_w && ii > 0) {
if (seed_width[ii-1].bid > m_seed-1) allow_diff = 0;
else if (seed_width[ii-1].bid == m_seed-1 && seed_width[ii].bid == m_seed-1
&& seed_width[ii-1].w == seed_width[ii].w) allow_M = 0;
}
}
// indels
tmp = (opt->mode & BWA_MODE_LOGGAP)? int_log2(e.n_gape + e.n_gapo)/2+1 : e.n_gapo + e.n_gape;
if (allow_diff && i >= opt->indel_end_skip + tmp && len - i >= opt->indel_end_skip + tmp) {
if (e.state == STATE_M) { // gap open
if (e.n_gapo < opt->max_gapo) { // gap open is allowed
// insertion
gap_push(stack, a, i, k, l, e.n_mm, e.n_gapo + 1, e.n_gape, STATE_I, 1, opt);
// deletion
for (j = 0; j != 4; ++j) {
k = bwt->L2[j] + cnt_k[j] + 1;
l = bwt->L2[j] + cnt_l[j];
if (k <= l) gap_push(stack, a, i + 1, k, l, e.n_mm, e.n_gapo + 1, e.n_gape, STATE_D, 1, opt);
}
}
} else if (e.state == STATE_I) { // extention of an insertion
if (e.n_gape < opt->max_gape) // gap extention is allowed
gap_push(stack, a, i, k, l, e.n_mm, e.n_gapo, e.n_gape + 1, STATE_I, 1, opt);
} else if (e.state == STATE_D) { // extention of a deletion
if (e.n_gape < opt->max_gape) { // gap extention is allowed
if (e.n_gape + e.n_gapo < max_diff || occ < opt->max_del_occ) {
for (j = 0; j != 4; ++j) {
k = bwt->L2[j] + cnt_k[j] + 1;
l = bwt->L2[j] + cnt_l[j];
if (k <= l) gap_push(stack, a, i + 1, k, l, e.n_mm, e.n_gapo, e.n_gape + 1, STATE_D, 1, opt);
}
}
}
}
}
// mismatches
if (allow_diff && allow_M) { // mismatch is allowed
for (j = 1; j <= 4; ++j) {
int c = (str[i] + j) & 3;
int is_mm = (j != 4 || str[i] > 3);
k = bwt->L2[c] + cnt_k[c] + 1;
l = bwt->L2[c] + cnt_l[c];
if (k <= l) gap_push(stack, a, i, k, l, e.n_mm + is_mm, e.n_gapo, e.n_gape, STATE_M, is_mm, opt);
}
} else if (str[i] < 4) { // try exact match only
int c = str[i] & 3;
k = bwt->L2[c] + cnt_k[c] + 1;
l = bwt->L2[c] + cnt_l[c];
if (k <= l) gap_push(stack, a, i, k, l, e.n_mm, e.n_gapo, e.n_gape, STATE_M, 0, opt);
}
}
*_n_aln = n_aln;
//fprintf(stderr, "max_entries = %d\n", max_entries);
return aln;
}