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 #ifdef USE_MALLOC_WRAPPERS
12 # include "malloc_wrap.h"
13 #endif
14
15 typedef struct {
16 bwtint_t k, l;
17 } qintv_t;
18
19 #define qintv_eq(a, b) ((a).k == (b).k && (a).l == (b).l)
20 #define qintv_hash(a) ((a).k>>7^(a).l<<17)
21
22 #include "khash.h"
23 KHASH_INIT(qintv, qintv_t, uint64_t, 1, qintv_hash, qintv_eq)
24 KHASH_MAP_INIT_INT64(64, uint64_t)
25
26 #define MINUS_INF -0x3fffffff
27 #define MASK_LEVEL 0.90f
28
29 struct __mempool_t;
30 static void mp_destroy(struct __mempool_t*);
31 typedef struct {
32 bwtint_t qk, ql;
33 int I, D, G;
34 uint32_t pj:2, qlen:30;
35 int tlen;
36 int ppos, upos;
37 int cpos[4];
38 } bsw2cell_t;
39
40 #include "ksort.h"
41 KSORT_INIT_GENERIC(int)
42 #define __hitG_lt(a, b) (((a).G + ((int)(a).n_seeds<<2)) > (b).G + ((int)(b).n_seeds<<2))
43 KSORT_INIT(hitG, bsw2hit_t, __hitG_lt)
44
45 static const bsw2cell_t g_default_cell = { 0, 0, MINUS_INF, MINUS_INF, MINUS_INF, 0, 0, 0, -1, -1, {-1, -1, -1, -1} };
46
47 typedef struct {
48 int n, max;
49 uint32_t tk, tl; // this is fine
50 bsw2cell_t *array;
51 } bsw2entry_t, *bsw2entry_p;
52
53 /* --- BEGIN: Stack operations --- */
54 typedef struct {
55 int n_pending;
56 kvec_t(bsw2entry_p) stack0, pending;
57 struct __mempool_t *pool;
58 } bsw2stack_t;
59
60 #define stack_isempty(s) (kv_size(s->stack0) == 0 && s->n_pending == 0)
stack_destroy(bsw2stack_t * s)61 static void stack_destroy(bsw2stack_t *s) { mp_destroy(s->pool); kv_destroy(s->stack0); kv_destroy(s->pending); free(s); }
stack_push0(bsw2stack_t * s,bsw2entry_p e)62 inline static void stack_push0(bsw2stack_t *s, bsw2entry_p e) { kv_push(bsw2entry_p, s->stack0, e); }
stack_pop(bsw2stack_t * s)63 inline static bsw2entry_p stack_pop(bsw2stack_t *s)
64 {
65 assert(!(kv_size(s->stack0) == 0 && s->n_pending != 0));
66 return kv_pop(s->stack0);
67 }
68 /* --- END: Stack operations --- */
69
70 /* --- BEGIN: memory pool --- */
71 typedef struct __mempool_t {
72 int cnt; // if cnt!=0, then there must be memory leak
73 kvec_t(bsw2entry_p) pool;
74 } mempool_t;
mp_alloc(mempool_t * mp)75 inline static bsw2entry_p mp_alloc(mempool_t *mp)
76 {
77 ++mp->cnt;
78 if (kv_size(mp->pool) == 0) return (bsw2entry_t*)calloc(1, sizeof(bsw2entry_t));
79 else return kv_pop(mp->pool);
80 }
mp_free(mempool_t * mp,bsw2entry_p e)81 inline static void mp_free(mempool_t *mp, bsw2entry_p e)
82 {
83 --mp->cnt; e->n = 0;
84 kv_push(bsw2entry_p, mp->pool, e);
85 }
mp_destroy(struct __mempool_t * mp)86 static void mp_destroy(struct __mempool_t *mp)
87 {
88 int i;
89 for (i = 0; i != kv_size(mp->pool); ++i) {
90 free(kv_A(mp->pool, i)->array);
91 free(kv_A(mp->pool, i));
92 }
93 kv_destroy(mp->pool);
94 free(mp);
95 }
96 /* --- END: memory pool --- */
97
98 /* --- BEGIN: utilities --- */
bsw2_connectivity(const bwtl_t * b)99 static khash_t(64) *bsw2_connectivity(const bwtl_t *b)
100 {
101 khash_t(64) *h;
102 uint32_t k, l, cntk[4], cntl[4]; // this is fine
103 uint64_t x;
104 khiter_t iter;
105 int j, ret;
106 kvec_t(uint64_t) stack;
107
108 kv_init(stack);
109 h = kh_init(64);
110 kh_resize(64, h, b->seq_len * 4);
111 x = b->seq_len;
112 kv_push(uint64_t, stack, x);
113 while (kv_size(stack)) {
114 x = kv_pop(stack);
115 k = x>>32; l = (uint32_t)x;
116 bwtl_2occ4(b, k-1, l, cntk, cntl);
117 for (j = 0; j != 4; ++j) {
118 k = b->L2[j] + cntk[j] + 1;
119 l = b->L2[j] + cntl[j];
120 if (k > l) continue;
121 x = (uint64_t)k << 32 | l;
122 iter = kh_put(64, h, x, &ret);
123 if (ret) { // if not present
124 kh_value(h, iter) = 1;
125 kv_push(uint64_t, stack, x);
126 } else ++kh_value(h, iter);
127 }
128 }
129 kv_destroy(stack);
130 //fprintf(stderr, "[bsw2_connectivity] %u nodes in the DAG\n", kh_size(h));
131 return h;
132 }
133 // pick up top T matches at a node
cut_tail(bsw2entry_t * u,int T,bsw2entry_t * aux)134 static void cut_tail(bsw2entry_t *u, int T, bsw2entry_t *aux)
135 {
136 int i, *a, n, x;
137 if (u->n <= T) return;
138 if (aux->max < u->n) {
139 aux->max = u->n;
140 aux->array = (bsw2cell_t*)realloc(aux->array, aux->max * sizeof(bsw2cell_t));
141 }
142 a = (int*)aux->array;
143 for (i = n = 0; i != u->n; ++i)
144 if (u->array[i].ql && u->array[i].G > 0)
145 a[n++] = -u->array[i].G;
146 if (n <= T) return;
147 x = -ks_ksmall(int, n, a, T);
148 n = 0;
149 for (i = 0; i < u->n; ++i) {
150 bsw2cell_t *p = u->array + i;
151 if (p->G == x) ++n;
152 if (p->G < x || (p->G == x && n >= T)) {
153 p->qk = p->ql = 0; p->G = 0;
154 if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -1;
155 }
156 }
157 }
158 // remove duplicated cells
remove_duplicate(bsw2entry_t * u,khash_t (qintv)* hash)159 static inline void remove_duplicate(bsw2entry_t *u, khash_t(qintv) *hash)
160 {
161 int i, ret, j;
162 khiter_t k;
163 qintv_t key;
164 kh_clear(qintv, hash);
165 for (i = 0; i != u->n; ++i) {
166 bsw2cell_t *p = u->array + i;
167 if (p->ql == 0) continue;
168 key.k = p->qk; key.l = p->ql;
169 k = kh_put(qintv, hash, key, &ret);
170 j = -1;
171 if (ret == 0) {
172 if ((uint32_t)kh_value(hash, k) >= p->G) j = i;
173 else {
174 j = kh_value(hash, k)>>32;
175 kh_value(hash, k) = (uint64_t)i<<32 | p->G;
176 }
177 } else kh_value(hash, k) = (uint64_t)i<<32 | p->G;
178 if (j >= 0) {
179 p = u->array + j;
180 p->qk = p->ql = 0; p->G = 0;
181 if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -3;
182 }
183 }
184 }
185 // merge two entries
merge_entry(const bsw2opt_t * __restrict opt,bsw2entry_t * u,bsw2entry_t * v,bwtsw2_t * b)186 static void merge_entry(const bsw2opt_t * __restrict opt, bsw2entry_t *u, bsw2entry_t *v, bwtsw2_t *b)
187 {
188 int i;
189 if (u->n + v->n >= u->max) {
190 u->max = u->n + v->n;
191 u->array = (bsw2cell_t*)realloc(u->array, u->max * sizeof(bsw2cell_t));
192 }
193 for (i = 0; i != v->n; ++i) {
194 bsw2cell_t *p = v->array + i;
195 if (p->ppos >= 0) p->ppos += u->n;
196 if (p->cpos[0] >= 0) p->cpos[0] += u->n;
197 if (p->cpos[1] >= 0) p->cpos[1] += u->n;
198 if (p->cpos[2] >= 0) p->cpos[2] += u->n;
199 if (p->cpos[3] >= 0) p->cpos[3] += u->n;
200 }
201 memcpy(u->array + u->n, v->array, v->n * sizeof(bsw2cell_t));
202 u->n += v->n;
203 }
204
push_array_p(bsw2entry_t * e)205 static inline bsw2cell_t *push_array_p(bsw2entry_t *e)
206 {
207 if (e->n == e->max) {
208 e->max = e->max? e->max<<1 : 256;
209 e->array = (bsw2cell_t*)realloc(e->array, sizeof(bsw2cell_t) * e->max);
210 }
211 return e->array + e->n;
212 }
213
time_elapse(const struct rusage * curr,const struct rusage * last)214 static inline double time_elapse(const struct rusage *curr, const struct rusage *last)
215 {
216 long t1 = (curr->ru_utime.tv_sec - last->ru_utime.tv_sec) + (curr->ru_stime.tv_sec - last->ru_stime.tv_sec);
217 long t2 = (curr->ru_utime.tv_usec - last->ru_utime.tv_usec) + (curr->ru_stime.tv_usec - last->ru_stime.tv_usec);
218 return (double)t1 + t2 * 1e-6;
219 }
220 /* --- END: utilities --- */
221
222 /* --- BEGIN: processing partial hits --- */
save_hits(const bwtl_t * bwt,int thres,bsw2hit_t * hits,bsw2entry_t * u)223 static void save_hits(const bwtl_t *bwt, int thres, bsw2hit_t *hits, bsw2entry_t *u)
224 {
225 int i;
226 uint32_t k; // this is fine
227 for (i = 0; i < u->n; ++i) {
228 bsw2cell_t *p = u->array + i;
229 if (p->G < thres) continue;
230 for (k = u->tk; k <= u->tl; ++k) {
231 int beg, end;
232 bsw2hit_t *q = 0;
233 beg = bwt->sa[k]; end = beg + p->tlen;
234 if (p->G > hits[beg*2].G) {
235 hits[beg*2+1] = hits[beg*2];
236 q = hits + beg * 2;
237 } else if (p->G > hits[beg*2+1].G) q = hits + beg * 2 + 1;
238 if (q) {
239 q->k = p->qk; q->l = p->ql; q->len = p->qlen; q->G = p->G;
240 q->beg = beg; q->end = end; q->G2 = q->k == q->l? 0 : q->G;
241 q->flag = q->n_seeds = 0;
242 }
243 }
244 }
245 }
246 /* "narrow hits" are node-to-node hits that have a high score and
247 * are not so repetitive (|SA interval|<=IS). */
save_narrow_hits(const bwtl_t * bwtl,bsw2entry_t * u,bwtsw2_t * b1,int t,int IS)248 static void save_narrow_hits(const bwtl_t *bwtl, bsw2entry_t *u, bwtsw2_t *b1, int t, int IS)
249 {
250 int i;
251 for (i = 0; i < u->n; ++i) {
252 bsw2hit_t *q;
253 bsw2cell_t *p = u->array + i;
254 if (p->G >= t && p->ql - p->qk + 1 <= IS) { // good narrow hit
255 if (b1->max == b1->n) {
256 b1->max = b1->max? b1->max<<1 : 4;
257 b1->hits = realloc(b1->hits, b1->max * sizeof(bsw2hit_t));
258 }
259 q = &b1->hits[b1->n++];
260 q->k = p->qk; q->l = p->ql;
261 q->len = p->qlen;
262 q->G = p->G; q->G2 = 0;
263 q->beg = bwtl->sa[u->tk]; q->end = q->beg + p->tlen;
264 q->flag = 0;
265 // delete p
266 p->qk = p->ql = 0; p->G = 0;
267 if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -3;
268 }
269 }
270 }
271 /* after this, "narrow SA hits" will be expanded and the coordinates
272 * will be obtained and stored in b->hits[*].k. */
bsw2_resolve_duphits(const bntseq_t * bns,const bwt_t * bwt,bwtsw2_t * b,int IS)273 int bsw2_resolve_duphits(const bntseq_t *bns, const bwt_t *bwt, bwtsw2_t *b, int IS)
274 {
275 int i, j, n, is_rev;
276 if (b->n == 0) return 0;
277 if (bwt && bns) { // convert to chromosomal coordinates if requested
278 int old_n = b->n;
279 bsw2hit_t *old_hits = b->hits;
280 for (i = n = 0; i < b->n; ++i) { // compute the memory to allocated
281 bsw2hit_t *p = old_hits + i;
282 if (p->l - p->k + 1 <= IS) n += p->l - p->k + 1;
283 else if (p->G > 0) ++n;
284 }
285 b->n = b->max = n;
286 b->hits = calloc(b->max, sizeof(bsw2hit_t));
287 for (i = j = 0; i < old_n; ++i) {
288 bsw2hit_t *p = old_hits + i;
289 if (p->l - p->k + 1 <= IS) { // the hit is no so repetitive
290 bwtint_t k;
291 if (p->G == 0 && p->k == 0 && p->l == 0 && p->len == 0) continue;
292 for (k = p->k; k <= p->l; ++k) {
293 b->hits[j] = *p;
294 b->hits[j].k = bns_depos(bns, bwt_sa(bwt, k), &is_rev);
295 b->hits[j].l = 0;
296 b->hits[j].is_rev = is_rev;
297 if (is_rev) b->hits[j].k -= p->len - 1;
298 ++j;
299 }
300 } else if (p->G > 0) {
301 b->hits[j] = *p;
302 b->hits[j].k = bns_depos(bns, bwt_sa(bwt, p->k), &is_rev);
303 b->hits[j].l = 0;
304 b->hits[j].flag |= 1;
305 b->hits[j].is_rev = is_rev;
306 if (is_rev) b->hits[j].k -= p->len - 1;
307 ++j;
308 }
309 }
310 free(old_hits);
311 }
312 for (i = j = 0; i < b->n; ++i) // squeeze out empty elements
313 if (b->hits[i].G) b->hits[j++] = b->hits[i];
314 b->n = j;
315 ks_introsort(hitG, b->n, b->hits);
316 for (i = 1; i < b->n; ++i) {
317 bsw2hit_t *p = b->hits + i;
318 for (j = 0; j < i; ++j) {
319 bsw2hit_t *q = b->hits + j;
320 int compatible = 1;
321 if (p->is_rev != q->is_rev) continue; // hits from opposite strands are not duplicates
322 if (p->l == 0 && q->l == 0) {
323 int qol = (p->end < q->end? p->end : q->end) - (p->beg > q->beg? p->beg : q->beg); // length of query overlap
324 if (qol < 0) qol = 0;
325 if ((float)qol / (p->end - p->beg) > MASK_LEVEL || (float)qol / (q->end - q->beg) > MASK_LEVEL) {
326 int64_t tol = (int64_t)(p->k + p->len < q->k + q->len? p->k + p->len : q->k + q->len)
327 - (int64_t)(p->k > q->k? p->k : q->k); // length of target overlap
328 if ((double)tol / p->len > MASK_LEVEL || (double)tol / q->len > MASK_LEVEL)
329 compatible = 0;
330 }
331 }
332 if (!compatible) {
333 p->G = 0;
334 if (q->G2 < p->G2) q->G2 = p->G2;
335 break;
336 }
337 }
338 }
339 n = i;
340 for (i = j = 0; i < n; ++i) {
341 if (b->hits[i].G == 0) continue;
342 if (i != j) b->hits[j++] = b->hits[i];
343 else ++j;
344 }
345 b->n = j;
346 return b->n;
347 }
348
bsw2_resolve_query_overlaps(bwtsw2_t * b,float mask_level)349 int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level)
350 {
351 int i, j, n;
352 if (b->n == 0) return 0;
353 ks_introsort(hitG, b->n, b->hits);
354 { // choose a random one
355 int G0 = b->hits[0].G;
356 for (i = 1; i < b->n; ++i)
357 if (b->hits[i].G != G0) break;
358 j = (int)(i * drand48());
359 if (j) {
360 bsw2hit_t tmp;
361 tmp = b->hits[0]; b->hits[0] = b->hits[j]; b->hits[j] = tmp;
362 }
363 }
364 for (i = 1; i < b->n; ++i) {
365 bsw2hit_t *p = b->hits + i;
366 int all_compatible = 1;
367 if (p->G == 0) break;
368 for (j = 0; j < i; ++j) {
369 bsw2hit_t *q = b->hits + j;
370 int64_t tol = 0;
371 int qol, compatible = 0;
372 float fol;
373 if (q->G == 0) continue;
374 qol = (p->end < q->end? p->end : q->end) - (p->beg > q->beg? p->beg : q->beg);
375 if (qol < 0) qol = 0;
376 if (p->l == 0 && q->l == 0) {
377 tol = (int64_t)(p->k + p->len < q->k + q->len? p->k + p->len : q->k + q->len)
378 - (p->k > q->k? p->k : q->k);
379 if (tol < 0) tol = 0;
380 }
381 fol = (float)qol / (p->end - p->beg < q->end - q->beg? p->end - p->beg : q->end - q->beg);
382 if (fol < mask_level || (tol > 0 && qol < p->end - p->beg && qol < q->end - q->beg)) compatible = 1;
383 if (!compatible) {
384 if (q->G2 < p->G) q->G2 = p->G;
385 all_compatible = 0;
386 }
387 }
388 if (!all_compatible) p->G = 0;
389 }
390 n = i;
391 for (i = j = 0; i < n; ++i) {
392 if (b->hits[i].G == 0) continue;
393 if (i != j) b->hits[j++] = b->hits[i];
394 else ++j;
395 }
396 b->n = j;
397 return j;
398 }
399 /* --- END: processing partial hits --- */
400
401 /* --- BEGIN: global mem pool --- */
bsw2_global_init()402 bsw2global_t *bsw2_global_init()
403 {
404 bsw2global_t *pool;
405 bsw2stack_t *stack;
406 pool = calloc(1, sizeof(bsw2global_t));
407 stack = calloc(1, sizeof(bsw2stack_t));
408 stack->pool = (mempool_t*)calloc(1, sizeof(mempool_t));
409 pool->stack = (void*)stack;
410 return pool;
411 }
412
bsw2_global_destroy(bsw2global_t * pool)413 void bsw2_global_destroy(bsw2global_t *pool)
414 {
415 stack_destroy((bsw2stack_t*)pool->stack);
416 free(pool->aln_mem);
417 free(pool);
418 }
419 /* --- END: global mem pool --- */
420
fill_cell(const bsw2opt_t * o,int match_score,bsw2cell_t * c[4])421 static inline int fill_cell(const bsw2opt_t *o, int match_score, bsw2cell_t *c[4])
422 {
423 int G = c[3]? c[3]->G + match_score : MINUS_INF;
424 if (c[1]) {
425 c[0]->I = c[1]->I > c[1]->G - o->q? c[1]->I - o->r : c[1]->G - o->qr;
426 if (c[0]->I > G) G = c[0]->I;
427 } else c[0]->I = MINUS_INF;
428 if (c[2]) {
429 c[0]->D = c[2]->D > c[2]->G - o->q? c[2]->D - o->r : c[2]->G - o->qr;
430 if (c[0]->D > G) G = c[0]->D;
431 } else c[0]->D = MINUS_INF;
432 return(c[0]->G = G);
433 }
434
init_bwtsw2(const bwtl_t * target,const bwt_t * query,bsw2stack_t * s)435 static void init_bwtsw2(const bwtl_t *target, const bwt_t *query, bsw2stack_t *s)
436 {
437 bsw2entry_t *u;
438 bsw2cell_t *x;
439
440 u = mp_alloc(s->pool);
441 u->tk = 0; u->tl = target->seq_len;
442 x = push_array_p(u);
443 *x = g_default_cell;
444 x->G = 0; x->qk = 0; x->ql = query->seq_len;
445 u->n++;
446 stack_push0(s, u);
447 }
448 /* On return, ret[1] keeps not-so-repetitive hits (narrow SA hits); ret[0] keeps all hits (right?) */
bsw2_core(const bntseq_t * bns,const bsw2opt_t * opt,const bwtl_t * target,const bwt_t * query,bsw2global_t * pool)449 bwtsw2_t **bsw2_core(const bntseq_t *bns, const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool)
450 {
451 bsw2stack_t *stack = (bsw2stack_t*)pool->stack;
452 bwtsw2_t *b, *b1, **b_ret;
453 int i, j, score_mat[16], *heap, heap_size, n_tot = 0;
454 struct rusage curr, last;
455 khash_t(qintv) *rhash;
456 khash_t(64) *chash;
457
458 // initialize connectivity hash (chash)
459 chash = bsw2_connectivity(target);
460 // calculate score matrix
461 for (i = 0; i != 4; ++i)
462 for (j = 0; j != 4; ++j)
463 score_mat[i<<2|j] = (i == j)? opt->a : -opt->b;
464 // initialize other variables
465 rhash = kh_init(qintv);
466 init_bwtsw2(target, query, stack);
467 heap_size = opt->z;
468 heap = calloc(heap_size, sizeof(int));
469 // initialize the return struct
470 b = (bwtsw2_t*)calloc(1, sizeof(bwtsw2_t));
471 b->n = b->max = target->seq_len * 2;
472 b->hits = calloc(b->max, sizeof(bsw2hit_t));
473 b1 = (bwtsw2_t*)calloc(1, sizeof(bwtsw2_t));
474 b_ret = calloc(2, sizeof(void*));
475 b_ret[0] = b; b_ret[1] = b1;
476 // initialize timer
477 getrusage(0, &last);
478 // the main loop: traversal of the DAG
479 while (!stack_isempty(stack)) {
480 int old_n, tj;
481 bsw2entry_t *v;
482 uint32_t tcntk[4], tcntl[4];
483 bwtint_t k, l;
484
485 v = stack_pop(stack); old_n = v->n;
486 n_tot += v->n;
487
488 for (i = 0; i < v->n; ++i) { // test max depth and band width
489 bsw2cell_t *p = v->array + i;
490 if (p->ql == 0) continue;
491 if (p->tlen - (int)p->qlen > opt->bw || (int)p->qlen - p->tlen > opt->bw) {
492 p->qk = p->ql = 0;
493 if (p->ppos >= 0) v->array[p->ppos].cpos[p->pj] = -5;
494 }
495 }
496
497 // get Occ for the DAG
498 bwtl_2occ4(target, v->tk - 1, v->tl, tcntk, tcntl);
499 for (tj = 0; tj != 4; ++tj) { // descend to the children
500 bwtint_t qcntk[4], qcntl[4];
501 int qj, *curr_score_mat = score_mat + tj * 4;
502 khiter_t iter;
503 bsw2entry_t *u;
504
505 k = target->L2[tj] + tcntk[tj] + 1;
506 l = target->L2[tj] + tcntl[tj];
507 if (k > l) continue;
508 // update counter
509 iter = kh_get(64, chash, (uint64_t)k<<32 | l);
510 --kh_value(chash, iter);
511 // initialization
512 u = mp_alloc(stack->pool);
513 u->tk = k; u->tl = l;
514 memset(heap, 0, sizeof(int) * opt->z);
515 // loop through all the nodes in v
516 for (i = 0; i < v->n; ++i) {
517 bsw2cell_t *p = v->array + i, *x, *c[4]; // c[0]=>current, c[1]=>I, c[2]=>D, c[3]=>G
518 int is_added = 0;
519 if (p->ql == 0) continue; // deleted node
520 c[0] = x = push_array_p(u);
521 x->G = MINUS_INF;
522 p->upos = x->upos = -1;
523 if (p->ppos >= 0) { // parent has been visited
524 c[1] = (v->array[p->ppos].upos >= 0)? u->array + v->array[p->ppos].upos : 0;
525 c[3] = v->array + p->ppos; c[2] = p;
526 if (fill_cell(opt, curr_score_mat[p->pj], c) > 0) { // then update topology at p and x
527 x->ppos = v->array[p->ppos].upos; // the parent pos in u
528 p->upos = u->n++; // the current pos in u
529 if (x->ppos >= 0) u->array[x->ppos].cpos[p->pj] = p->upos; // the child pos of its parent in u
530 is_added = 1;
531 }
532 } else {
533 x->D = p->D > p->G - opt->q? p->D - opt->r : p->G - opt->qr;
534 if (x->D > 0) {
535 x->G = x->D;
536 x->I = MINUS_INF; x->ppos = -1;
537 p->upos = u->n++;
538 is_added = 1;
539 }
540 }
541 if (is_added) { // x has been added to u->array. fill the remaining variables
542 x->cpos[0] = x->cpos[1] = x->cpos[2] = x->cpos[3] = -1;
543 x->pj = p->pj; x->qk = p->qk; x->ql = p->ql; x->qlen = p->qlen; x->tlen = p->tlen + 1;
544 if (x->G > -heap[0]) {
545 heap[0] = -x->G;
546 ks_heapadjust(int, 0, heap_size, heap);
547 }
548 }
549 if ((x->G > opt->qr && x->G >= -heap[0]) || i < old_n) { // good node in u, or in v
550 if (p->cpos[0] == -1 || p->cpos[1] == -1 || p->cpos[2] == -1 || p->cpos[3] == -1) {
551 bwt_2occ4(query, p->qk - 1, p->ql, qcntk, qcntl);
552 for (qj = 0; qj != 4; ++qj) { // descend to the prefix trie
553 if (p->cpos[qj] != -1) continue; // this node will be visited later
554 k = query->L2[qj] + qcntk[qj] + 1;
555 l = query->L2[qj] + qcntl[qj];
556 if (k > l) { p->cpos[qj] = -2; continue; }
557 x = push_array_p(v);
558 p = v->array + i; // p may not point to the correct position after realloc
559 x->G = x->I = x->D = MINUS_INF;
560 x->qk = k; x->ql = l; x->pj = qj; x->qlen = p->qlen + 1; x->ppos = i; x->tlen = p->tlen;
561 x->cpos[0] = x->cpos[1] = x->cpos[2] = x->cpos[3] = -1;
562 p->cpos[qj] = v->n++;
563 } // ~for(qj)
564 } // ~if(p->cpos[])
565 } // ~if
566 } // ~for(i)
567 if (u->n) save_hits(target, opt->t, b->hits, u);
568 { // push u to the stack (or to the pending array)
569 uint32_t cnt, pos;
570 cnt = (uint32_t)kh_value(chash, iter);
571 pos = kh_value(chash, iter)>>32;
572 if (pos) { // something in the pending array, then merge
573 bsw2entry_t *w = kv_A(stack->pending, pos-1);
574 if (u->n) {
575 if (w->n < u->n) { // swap
576 w = u; u = kv_A(stack->pending, pos-1); kv_A(stack->pending, pos-1) = w;
577 }
578 merge_entry(opt, w, u, b);
579 }
580 if (cnt == 0) { // move from pending to stack0
581 remove_duplicate(w, rhash);
582 save_narrow_hits(target, w, b1, opt->t, opt->is);
583 cut_tail(w, opt->z, u);
584 stack_push0(stack, w);
585 kv_A(stack->pending, pos-1) = 0;
586 --stack->n_pending;
587 }
588 mp_free(stack->pool, u);
589 } else if (cnt) { // the first time
590 if (u->n) { // push to the pending queue
591 ++stack->n_pending;
592 kv_push(bsw2entry_p, stack->pending, u);
593 kh_value(chash, iter) = (uint64_t)kv_size(stack->pending)<<32 | cnt;
594 } else mp_free(stack->pool, u);
595 } else { // cnt == 0, then push to the stack
596 bsw2entry_t *w = mp_alloc(stack->pool);
597 save_narrow_hits(target, u, b1, opt->t, opt->is);
598 cut_tail(u, opt->z, w);
599 mp_free(stack->pool, w);
600 stack_push0(stack, u);
601 }
602 }
603 } // ~for(tj)
604 mp_free(stack->pool, v);
605 } // while(top)
606 getrusage(0, &curr);
607 for (i = 0; i < 2; ++i)
608 for (j = 0; j < b_ret[i]->n; ++j)
609 b_ret[i]->hits[j].n_seeds = 0;
610 bsw2_resolve_duphits(bns, query, b, opt->is);
611 bsw2_resolve_duphits(bns, query, b1, opt->is);
612 //fprintf(stderr, "stats: %.3lf sec; %d elems\n", time_elapse(&curr, &last), n_tot);
613 // free
614 free(heap);
615 kh_destroy(qintv, rhash);
616 kh_destroy(64, chash);
617 stack->pending.n = stack->stack0.n = 0;
618 return b_ret;
619 }
620