comparison bwa-0.6.2/bwtsw2_core.c @ 2:a294fbfcb1db draft default tip

Uploaded BWA
author ashvark
date Fri, 18 Jul 2014 07:55:59 -0400
parents dd1186b11b3b
children
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1:a9636dc1e99a 2:a294fbfcb1db
1 #include <stdlib.h>
2 #include <string.h>
3 #include <stdio.h>
4 #include <sys/resource.h>
5 #include <assert.h>
6 #include "bwt_lite.h"
7 #include "bwtsw2.h"
8 #include "bwt.h"
9 #include "kvec.h"
10
11 typedef struct {
12 bwtint_t k, l;
13 } qintv_t;
14
15 #define qintv_eq(a, b) ((a).k == (b).k && (a).l == (b).l)
16 #define qintv_hash(a) ((a).k>>7^(a).l<<17)
17
18 #include "khash.h"
19 KHASH_INIT(qintv, qintv_t, uint64_t, 1, qintv_hash, qintv_eq)
20 KHASH_MAP_INIT_INT64(64, uint64_t)
21
22 #define MINUS_INF -0x3fffffff
23 #define MASK_LEVEL 0.90f
24
25 struct __mempool_t;
26 static void mp_destroy(struct __mempool_t*);
27 typedef struct {
28 bwtint_t qk, ql;
29 int I, D, G;
30 uint32_t pj:2, qlen:30;
31 int tlen;
32 int ppos, upos;
33 int cpos[4];
34 } bsw2cell_t;
35
36 #include "ksort.h"
37 KSORT_INIT_GENERIC(int)
38 #define __hitG_lt(a, b) (((a).G + ((int)(a).n_seeds<<2)) > (b).G + ((int)(b).n_seeds<<2))
39 KSORT_INIT(hitG, bsw2hit_t, __hitG_lt)
40
41 static const bsw2cell_t g_default_cell = { 0, 0, MINUS_INF, MINUS_INF, MINUS_INF, 0, 0, 0, -1, -1, {-1, -1, -1, -1} };
42
43 typedef struct {
44 int n, max;
45 uint32_t tk, tl; // this is fine
46 bsw2cell_t *array;
47 } bsw2entry_t, *bsw2entry_p;
48
49 /* --- BEGIN: Stack operations --- */
50 typedef struct {
51 int n_pending;
52 kvec_t(bsw2entry_p) stack0, pending;
53 struct __mempool_t *pool;
54 } bsw2stack_t;
55
56 #define stack_isempty(s) (kv_size(s->stack0) == 0 && s->n_pending == 0)
57 static void stack_destroy(bsw2stack_t *s) { mp_destroy(s->pool); kv_destroy(s->stack0); kv_destroy(s->pending); free(s); }
58 inline static void stack_push0(bsw2stack_t *s, bsw2entry_p e) { kv_push(bsw2entry_p, s->stack0, e); }
59 inline static bsw2entry_p stack_pop(bsw2stack_t *s)
60 {
61 assert(!(kv_size(s->stack0) == 0 && s->n_pending != 0));
62 return kv_pop(s->stack0);
63 }
64 /* --- END: Stack operations --- */
65
66 /* --- BEGIN: memory pool --- */
67 typedef struct __mempool_t {
68 int cnt; // if cnt!=0, then there must be memory leak
69 kvec_t(bsw2entry_p) pool;
70 } mempool_t;
71 inline static bsw2entry_p mp_alloc(mempool_t *mp)
72 {
73 ++mp->cnt;
74 if (kv_size(mp->pool) == 0) return (bsw2entry_t*)calloc(1, sizeof(bsw2entry_t));
75 else return kv_pop(mp->pool);
76 }
77 inline static void mp_free(mempool_t *mp, bsw2entry_p e)
78 {
79 --mp->cnt; e->n = 0;
80 kv_push(bsw2entry_p, mp->pool, e);
81 }
82 static void mp_destroy(struct __mempool_t *mp)
83 {
84 int i;
85 for (i = 0; i != kv_size(mp->pool); ++i) {
86 free(kv_A(mp->pool, i)->array);
87 free(kv_A(mp->pool, i));
88 }
89 kv_destroy(mp->pool);
90 free(mp);
91 }
92 /* --- END: memory pool --- */
93
94 /* --- BEGIN: utilities --- */
95 static khash_t(64) *bsw2_connectivity(const bwtl_t *b)
96 {
97 khash_t(64) *h;
98 uint32_t k, l, cntk[4], cntl[4]; // this is fine
99 uint64_t x;
100 khiter_t iter;
101 int j, ret;
102 kvec_t(uint64_t) stack;
103
104 kv_init(stack);
105 h = kh_init(64);
106 kh_resize(64, h, b->seq_len * 4);
107 x = b->seq_len;
108 kv_push(uint64_t, stack, x);
109 while (kv_size(stack)) {
110 x = kv_pop(stack);
111 k = x>>32; l = (uint32_t)x;
112 bwtl_2occ4(b, k-1, l, cntk, cntl);
113 for (j = 0; j != 4; ++j) {
114 k = b->L2[j] + cntk[j] + 1;
115 l = b->L2[j] + cntl[j];
116 if (k > l) continue;
117 x = (uint64_t)k << 32 | l;
118 iter = kh_put(64, h, x, &ret);
119 if (ret) { // if not present
120 kh_value(h, iter) = 1;
121 kv_push(uint64_t, stack, x);
122 } else ++kh_value(h, iter);
123 }
124 }
125 kv_destroy(stack);
126 //fprintf(stderr, "[bsw2_connectivity] %u nodes in the DAG\n", kh_size(h));
127 return h;
128 }
129 // pick up top T matches at a node
130 static void cut_tail(bsw2entry_t *u, int T, bsw2entry_t *aux)
131 {
132 int i, *a, n, x;
133 if (u->n <= T) return;
134 if (aux->max < u->n) {
135 aux->max = u->n;
136 aux->array = (bsw2cell_t*)realloc(aux->array, aux->max * sizeof(bsw2cell_t));
137 }
138 a = (int*)aux->array;
139 for (i = n = 0; i != u->n; ++i)
140 if (u->array[i].ql && u->array[i].G > 0)
141 a[n++] = -u->array[i].G;
142 if (n <= T) return;
143 x = -ks_ksmall(int, n, a, T);
144 n = 0;
145 for (i = 0; i < u->n; ++i) {
146 bsw2cell_t *p = u->array + i;
147 if (p->G == x) ++n;
148 if (p->G < x || (p->G == x && n >= T)) {
149 p->qk = p->ql = 0; p->G = 0;
150 if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -1;
151 }
152 }
153 }
154 // remove duplicated cells
155 static inline void remove_duplicate(bsw2entry_t *u, khash_t(qintv) *hash)
156 {
157 int i, ret, j;
158 khiter_t k;
159 qintv_t key;
160 kh_clear(qintv, hash);
161 for (i = 0; i != u->n; ++i) {
162 bsw2cell_t *p = u->array + i;
163 if (p->ql == 0) continue;
164 key.k = p->qk; key.l = p->ql;
165 k = kh_put(qintv, hash, key, &ret);
166 j = -1;
167 if (ret == 0) {
168 if ((uint32_t)kh_value(hash, k) >= p->G) j = i;
169 else {
170 j = kh_value(hash, k)>>32;
171 kh_value(hash, k) = (uint64_t)i<<32 | p->G;
172 }
173 } else kh_value(hash, k) = (uint64_t)i<<32 | p->G;
174 if (j >= 0) {
175 p = u->array + j;
176 p->qk = p->ql = 0; p->G = 0;
177 if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -3;
178 }
179 }
180 }
181 // merge two entries
182 static void merge_entry(const bsw2opt_t * __restrict opt, bsw2entry_t *u, bsw2entry_t *v, bwtsw2_t *b)
183 {
184 int i;
185 if (u->n + v->n >= u->max) {
186 u->max = u->n + v->n;
187 u->array = (bsw2cell_t*)realloc(u->array, u->max * sizeof(bsw2cell_t));
188 }
189 for (i = 0; i != v->n; ++i) {
190 bsw2cell_t *p = v->array + i;
191 if (p->ppos >= 0) p->ppos += u->n;
192 if (p->cpos[0] >= 0) p->cpos[0] += u->n;
193 if (p->cpos[1] >= 0) p->cpos[1] += u->n;
194 if (p->cpos[2] >= 0) p->cpos[2] += u->n;
195 if (p->cpos[3] >= 0) p->cpos[3] += u->n;
196 }
197 memcpy(u->array + u->n, v->array, v->n * sizeof(bsw2cell_t));
198 u->n += v->n;
199 }
200
201 static inline bsw2cell_t *push_array_p(bsw2entry_t *e)
202 {
203 if (e->n == e->max) {
204 e->max = e->max? e->max<<1 : 256;
205 e->array = (bsw2cell_t*)realloc(e->array, sizeof(bsw2cell_t) * e->max);
206 }
207 return e->array + e->n;
208 }
209
210 static inline double time_elapse(const struct rusage *curr, const struct rusage *last)
211 {
212 long t1 = (curr->ru_utime.tv_sec - last->ru_utime.tv_sec) + (curr->ru_stime.tv_sec - last->ru_stime.tv_sec);
213 long t2 = (curr->ru_utime.tv_usec - last->ru_utime.tv_usec) + (curr->ru_stime.tv_usec - last->ru_stime.tv_usec);
214 return (double)t1 + t2 * 1e-6;
215 }
216 /* --- END: utilities --- */
217
218 /* --- BEGIN: processing partial hits --- */
219 static void save_hits(const bwtl_t *bwt, int thres, bsw2hit_t *hits, bsw2entry_t *u)
220 {
221 int i;
222 uint32_t k; // this is fine
223 for (i = 0; i < u->n; ++i) {
224 bsw2cell_t *p = u->array + i;
225 if (p->G < thres) continue;
226 for (k = u->tk; k <= u->tl; ++k) {
227 int beg, end;
228 bsw2hit_t *q = 0;
229 beg = bwt->sa[k]; end = beg + p->tlen;
230 if (p->G > hits[beg*2].G) {
231 hits[beg*2+1] = hits[beg*2];
232 q = hits + beg * 2;
233 } else if (p->G > hits[beg*2+1].G) q = hits + beg * 2 + 1;
234 if (q) {
235 q->k = p->qk; q->l = p->ql; q->len = p->qlen; q->G = p->G;
236 q->beg = beg; q->end = end; q->G2 = q->k == q->l? 0 : q->G;
237 q->flag = q->n_seeds = 0;
238 }
239 }
240 }
241 }
242 /* "narrow hits" are node-to-node hits that have a high score and
243 * are not so repetitive (|SA interval|<=IS). */
244 static void save_narrow_hits(const bwtl_t *bwtl, bsw2entry_t *u, bwtsw2_t *b1, int t, int IS)
245 {
246 int i;
247 for (i = 0; i < u->n; ++i) {
248 bsw2hit_t *q;
249 bsw2cell_t *p = u->array + i;
250 if (p->G >= t && p->ql - p->qk + 1 <= IS) { // good narrow hit
251 if (b1->max == b1->n) {
252 b1->max = b1->max? b1->max<<1 : 4;
253 b1->hits = realloc(b1->hits, b1->max * sizeof(bsw2hit_t));
254 }
255 q = &b1->hits[b1->n++];
256 q->k = p->qk; q->l = p->ql;
257 q->len = p->qlen;
258 q->G = p->G; q->G2 = 0;
259 q->beg = bwtl->sa[u->tk]; q->end = q->beg + p->tlen;
260 q->flag = 0;
261 // delete p
262 p->qk = p->ql = 0; p->G = 0;
263 if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -3;
264 }
265 }
266 }
267 /* after this, "narrow SA hits" will be expanded and the coordinates
268 * will be obtained and stored in b->hits[*].k. */
269 int bsw2_resolve_duphits(const bntseq_t *bns, const bwt_t *bwt, bwtsw2_t *b, int IS)
270 {
271 int i, j, n, is_rev;
272 if (b->n == 0) return 0;
273 if (bwt && bns) { // convert to chromosomal coordinates if requested
274 int old_n = b->n;
275 bsw2hit_t *old_hits = b->hits;
276 for (i = n = 0; i < b->n; ++i) { // compute the memory to allocated
277 bsw2hit_t *p = old_hits + i;
278 if (p->l - p->k + 1 <= IS) n += p->l - p->k + 1;
279 else if (p->G > 0) ++n;
280 }
281 b->n = b->max = n;
282 b->hits = calloc(b->max, sizeof(bsw2hit_t));
283 for (i = j = 0; i < old_n; ++i) {
284 bsw2hit_t *p = old_hits + i;
285 if (p->l - p->k + 1 <= IS) { // the hit is no so repetitive
286 bwtint_t k;
287 if (p->G == 0 && p->k == 0 && p->l == 0 && p->len == 0) continue;
288 for (k = p->k; k <= p->l; ++k) {
289 b->hits[j] = *p;
290 b->hits[j].k = bns_depos(bns, bwt_sa(bwt, k), &is_rev);
291 b->hits[j].l = 0;
292 b->hits[j].is_rev = is_rev;
293 if (is_rev) b->hits[j].k -= p->len - 1;
294 ++j;
295 }
296 } else if (p->G > 0) {
297 b->hits[j] = *p;
298 b->hits[j].k = bns_depos(bns, bwt_sa(bwt, p->k), &is_rev);
299 b->hits[j].l = 0;
300 b->hits[j].flag |= 1;
301 b->hits[j].is_rev = is_rev;
302 if (is_rev) b->hits[j].k -= p->len - 1;
303 ++j;
304 }
305 }
306 free(old_hits);
307 }
308 for (i = j = 0; i < b->n; ++i) // squeeze out empty elements
309 if (b->hits[i].G) b->hits[j++] = b->hits[i];
310 b->n = j;
311 ks_introsort(hitG, b->n, b->hits);
312 for (i = 1; i < b->n; ++i) {
313 bsw2hit_t *p = b->hits + i;
314 for (j = 0; j < i; ++j) {
315 bsw2hit_t *q = b->hits + j;
316 int compatible = 1;
317 if (p->is_rev != q->is_rev) continue; // hits from opposite strands are not duplicates
318 if (p->l == 0 && q->l == 0) {
319 int qol = (p->end < q->end? p->end : q->end) - (p->beg > q->beg? p->beg : q->beg); // length of query overlap
320 if (qol < 0) qol = 0;
321 if ((float)qol / (p->end - p->beg) > MASK_LEVEL || (float)qol / (q->end - q->beg) > MASK_LEVEL) {
322 int64_t tol = (int64_t)(p->k + p->len < q->k + q->len? p->k + p->len : q->k + q->len)
323 - (int64_t)(p->k > q->k? p->k : q->k); // length of target overlap
324 if ((double)tol / p->len > MASK_LEVEL || (double)tol / q->len > MASK_LEVEL)
325 compatible = 0;
326 }
327 }
328 if (!compatible) {
329 p->G = 0;
330 if (q->G2 < p->G2) q->G2 = p->G2;
331 break;
332 }
333 }
334 }
335 n = i;
336 for (i = j = 0; i < n; ++i) {
337 if (b->hits[i].G == 0) continue;
338 if (i != j) b->hits[j++] = b->hits[i];
339 else ++j;
340 }
341 b->n = j;
342 return b->n;
343 }
344
345 int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level)
346 {
347 int i, j, n;
348 if (b->n == 0) return 0;
349 ks_introsort(hitG, b->n, b->hits);
350 { // choose a random one
351 int G0 = b->hits[0].G;
352 for (i = 1; i < b->n; ++i)
353 if (b->hits[i].G != G0) break;
354 j = (int)(i * drand48());
355 if (j) {
356 bsw2hit_t tmp;
357 tmp = b->hits[0]; b->hits[0] = b->hits[j]; b->hits[j] = tmp;
358 }
359 }
360 for (i = 1; i < b->n; ++i) {
361 bsw2hit_t *p = b->hits + i;
362 int all_compatible = 1;
363 if (p->G == 0) break;
364 for (j = 0; j < i; ++j) {
365 bsw2hit_t *q = b->hits + j;
366 int64_t tol = 0;
367 int qol, compatible = 0;
368 float fol;
369 if (q->G == 0) continue;
370 qol = (p->end < q->end? p->end : q->end) - (p->beg > q->beg? p->beg : q->beg);
371 if (qol < 0) qol = 0;
372 if (p->l == 0 && q->l == 0) {
373 tol = (int64_t)(p->k + p->len < q->k + q->len? p->k + p->len : q->k + q->len)
374 - (p->k > q->k? p->k : q->k);
375 if (tol < 0) tol = 0;
376 }
377 fol = (float)qol / (p->end - p->beg < q->end - q->beg? p->end - p->beg : q->end - q->beg);
378 if (fol < mask_level || (tol > 0 && qol < p->end - p->beg && qol < q->end - q->beg)) compatible = 1;
379 if (!compatible) {
380 if (q->G2 < p->G) q->G2 = p->G;
381 all_compatible = 0;
382 }
383 }
384 if (!all_compatible) p->G = 0;
385 }
386 n = i;
387 for (i = j = 0; i < n; ++i) {
388 if (b->hits[i].G == 0) continue;
389 if (i != j) b->hits[j++] = b->hits[i];
390 else ++j;
391 }
392 b->n = j;
393 return j;
394 }
395 /* --- END: processing partial hits --- */
396
397 /* --- BEGIN: global mem pool --- */
398 bsw2global_t *bsw2_global_init()
399 {
400 bsw2global_t *pool;
401 bsw2stack_t *stack;
402 pool = calloc(1, sizeof(bsw2global_t));
403 stack = calloc(1, sizeof(bsw2stack_t));
404 stack->pool = (mempool_t*)calloc(1, sizeof(mempool_t));
405 pool->stack = (void*)stack;
406 return pool;
407 }
408
409 void bsw2_global_destroy(bsw2global_t *pool)
410 {
411 stack_destroy((bsw2stack_t*)pool->stack);
412 free(pool->aln_mem);
413 free(pool);
414 }
415 /* --- END: global mem pool --- */
416
417 static inline int fill_cell(const bsw2opt_t *o, int match_score, bsw2cell_t *c[4])
418 {
419 int G = c[3]? c[3]->G + match_score : MINUS_INF;
420 if (c[1]) {
421 c[0]->I = c[1]->I > c[1]->G - o->q? c[1]->I - o->r : c[1]->G - o->qr;
422 if (c[0]->I > G) G = c[0]->I;
423 } else c[0]->I = MINUS_INF;
424 if (c[2]) {
425 c[0]->D = c[2]->D > c[2]->G - o->q? c[2]->D - o->r : c[2]->G - o->qr;
426 if (c[0]->D > G) G = c[0]->D;
427 } else c[0]->D = MINUS_INF;
428 return(c[0]->G = G);
429 }
430
431 static void init_bwtsw2(const bwtl_t *target, const bwt_t *query, bsw2stack_t *s)
432 {
433 bsw2entry_t *u;
434 bsw2cell_t *x;
435
436 u = mp_alloc(s->pool);
437 u->tk = 0; u->tl = target->seq_len;
438 x = push_array_p(u);
439 *x = g_default_cell;
440 x->G = 0; x->qk = 0; x->ql = query->seq_len;
441 u->n++;
442 stack_push0(s, u);
443 }
444 /* On return, ret[1] keeps not-so-repetitive hits (narrow SA hits); ret[0] keeps all hits (right?) */
445 bwtsw2_t **bsw2_core(const bntseq_t *bns, const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool)
446 {
447 bsw2stack_t *stack = (bsw2stack_t*)pool->stack;
448 bwtsw2_t *b, *b1, **b_ret;
449 int i, j, score_mat[16], *heap, heap_size, n_tot = 0;
450 struct rusage curr, last;
451 khash_t(qintv) *rhash;
452 khash_t(64) *chash;
453
454 // initialize connectivity hash (chash)
455 chash = bsw2_connectivity(target);
456 // calculate score matrix
457 for (i = 0; i != 4; ++i)
458 for (j = 0; j != 4; ++j)
459 score_mat[i<<2|j] = (i == j)? opt->a : -opt->b;
460 // initialize other variables
461 rhash = kh_init(qintv);
462 init_bwtsw2(target, query, stack);
463 heap_size = opt->z;
464 heap = calloc(heap_size, sizeof(int));
465 // initialize the return struct
466 b = (bwtsw2_t*)calloc(1, sizeof(bwtsw2_t));
467 b->n = b->max = target->seq_len * 2;
468 b->hits = calloc(b->max, sizeof(bsw2hit_t));
469 b1 = (bwtsw2_t*)calloc(1, sizeof(bwtsw2_t));
470 b_ret = calloc(2, sizeof(void*));
471 b_ret[0] = b; b_ret[1] = b1;
472 // initialize timer
473 getrusage(0, &last);
474 // the main loop: traversal of the DAG
475 while (!stack_isempty(stack)) {
476 int old_n, tj;
477 bsw2entry_t *v;
478 uint32_t tcntk[4], tcntl[4];
479 bwtint_t k, l;
480
481 v = stack_pop(stack); old_n = v->n;
482 n_tot += v->n;
483
484 for (i = 0; i < v->n; ++i) { // test max depth and band width
485 bsw2cell_t *p = v->array + i;
486 if (p->ql == 0) continue;
487 if (p->tlen - (int)p->qlen > opt->bw || (int)p->qlen - p->tlen > opt->bw) {
488 p->qk = p->ql = 0;
489 if (p->ppos >= 0) v->array[p->ppos].cpos[p->pj] = -5;
490 }
491 }
492
493 // get Occ for the DAG
494 bwtl_2occ4(target, v->tk - 1, v->tl, tcntk, tcntl);
495 for (tj = 0; tj != 4; ++tj) { // descend to the children
496 bwtint_t qcntk[4], qcntl[4];
497 int qj, *curr_score_mat = score_mat + tj * 4;
498 khiter_t iter;
499 bsw2entry_t *u;
500
501 k = target->L2[tj] + tcntk[tj] + 1;
502 l = target->L2[tj] + tcntl[tj];
503 if (k > l) continue;
504 // update counter
505 iter = kh_get(64, chash, (uint64_t)k<<32 | l);
506 --kh_value(chash, iter);
507 // initialization
508 u = mp_alloc(stack->pool);
509 u->tk = k; u->tl = l;
510 memset(heap, 0, sizeof(int) * opt->z);
511 // loop through all the nodes in v
512 for (i = 0; i < v->n; ++i) {
513 bsw2cell_t *p = v->array + i, *x, *c[4]; // c[0]=>current, c[1]=>I, c[2]=>D, c[3]=>G
514 int is_added = 0;
515 if (p->ql == 0) continue; // deleted node
516 c[0] = x = push_array_p(u);
517 x->G = MINUS_INF;
518 p->upos = x->upos = -1;
519 if (p->ppos >= 0) { // parent has been visited
520 c[1] = (v->array[p->ppos].upos >= 0)? u->array + v->array[p->ppos].upos : 0;
521 c[3] = v->array + p->ppos; c[2] = p;
522 if (fill_cell(opt, curr_score_mat[p->pj], c) > 0) { // then update topology at p and x
523 x->ppos = v->array[p->ppos].upos; // the parent pos in u
524 p->upos = u->n++; // the current pos in u
525 if (x->ppos >= 0) u->array[x->ppos].cpos[p->pj] = p->upos; // the child pos of its parent in u
526 is_added = 1;
527 }
528 } else {
529 x->D = p->D > p->G - opt->q? p->D - opt->r : p->G - opt->qr;
530 if (x->D > 0) {
531 x->G = x->D;
532 x->I = MINUS_INF; x->ppos = -1;
533 p->upos = u->n++;
534 is_added = 1;
535 }
536 }
537 if (is_added) { // x has been added to u->array. fill the remaining variables
538 x->cpos[0] = x->cpos[1] = x->cpos[2] = x->cpos[3] = -1;
539 x->pj = p->pj; x->qk = p->qk; x->ql = p->ql; x->qlen = p->qlen; x->tlen = p->tlen + 1;
540 if (x->G > -heap[0]) {
541 heap[0] = -x->G;
542 ks_heapadjust(int, 0, heap_size, heap);
543 }
544 }
545 if ((x->G > opt->qr && x->G >= -heap[0]) || i < old_n) { // good node in u, or in v
546 if (p->cpos[0] == -1 || p->cpos[1] == -1 || p->cpos[2] == -1 || p->cpos[3] == -1) {
547 bwt_2occ4(query, p->qk - 1, p->ql, qcntk, qcntl);
548 for (qj = 0; qj != 4; ++qj) { // descend to the prefix trie
549 if (p->cpos[qj] != -1) continue; // this node will be visited later
550 k = query->L2[qj] + qcntk[qj] + 1;
551 l = query->L2[qj] + qcntl[qj];
552 if (k > l) { p->cpos[qj] = -2; continue; }
553 x = push_array_p(v);
554 p = v->array + i; // p may not point to the correct position after realloc
555 x->G = x->I = x->D = MINUS_INF;
556 x->qk = k; x->ql = l; x->pj = qj; x->qlen = p->qlen + 1; x->ppos = i; x->tlen = p->tlen;
557 x->cpos[0] = x->cpos[1] = x->cpos[2] = x->cpos[3] = -1;
558 p->cpos[qj] = v->n++;
559 } // ~for(qj)
560 } // ~if(p->cpos[])
561 } // ~if
562 } // ~for(i)
563 if (u->n) save_hits(target, opt->t, b->hits, u);
564 { // push u to the stack (or to the pending array)
565 uint32_t cnt, pos;
566 cnt = (uint32_t)kh_value(chash, iter);
567 pos = kh_value(chash, iter)>>32;
568 if (pos) { // something in the pending array, then merge
569 bsw2entry_t *w = kv_A(stack->pending, pos-1);
570 if (u->n) {
571 if (w->n < u->n) { // swap
572 w = u; u = kv_A(stack->pending, pos-1); kv_A(stack->pending, pos-1) = w;
573 }
574 merge_entry(opt, w, u, b);
575 }
576 if (cnt == 0) { // move from pending to stack0
577 remove_duplicate(w, rhash);
578 save_narrow_hits(target, w, b1, opt->t, opt->is);
579 cut_tail(w, opt->z, u);
580 stack_push0(stack, w);
581 kv_A(stack->pending, pos-1) = 0;
582 --stack->n_pending;
583 }
584 mp_free(stack->pool, u);
585 } else if (cnt) { // the first time
586 if (u->n) { // push to the pending queue
587 ++stack->n_pending;
588 kv_push(bsw2entry_p, stack->pending, u);
589 kh_value(chash, iter) = (uint64_t)kv_size(stack->pending)<<32 | cnt;
590 } else mp_free(stack->pool, u);
591 } else { // cnt == 0, then push to the stack
592 bsw2entry_t *w = mp_alloc(stack->pool);
593 save_narrow_hits(target, u, b1, opt->t, opt->is);
594 cut_tail(u, opt->z, w);
595 mp_free(stack->pool, w);
596 stack_push0(stack, u);
597 }
598 }
599 } // ~for(tj)
600 mp_free(stack->pool, v);
601 } // while(top)
602 getrusage(0, &curr);
603 for (i = 0; i < 2; ++i)
604 for (j = 0; j < b_ret[i]->n; ++j)
605 b_ret[i]->hits[j].n_seeds = 0;
606 bsw2_resolve_duphits(bns, query, b, opt->is);
607 bsw2_resolve_duphits(bns, query, b1, opt->is);
608 //fprintf(stderr, "stats: %.3lf sec; %d elems\n", time_elapse(&curr, &last), n_tot);
609 // free
610 free(heap);
611 kh_destroy(qintv, rhash);
612 kh_destroy(64, chash);
613 stack->pending.n = stack->stack0.n = 0;
614 return b_ret;
615 }