7 typedef struct __linkbuf_t {
10 struct __linkbuf_t *next;
13 /* --- BEGIN: Memory pool */
20 static mempool_t *mp_init()
23 mp = (mempool_t*)calloc(1, sizeof(mempool_t));
26 static void mp_destroy(mempool_t *mp)
29 for (k = 0; k < mp->n; ++k) {
30 free(mp->buf[k]->b.data);
36 static inline lbnode_t *mp_alloc(mempool_t *mp)
39 if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t));
40 else return mp->buf[--mp->n];
42 static inline void mp_free(mempool_t *mp, lbnode_t *p)
44 --mp->cnt; p->next = 0; // clear lbnode_t::next here
45 if (mp->n == mp->max) {
46 mp->max = mp->max? mp->max<<1 : 256;
47 mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max);
52 /* --- END: Memory pool */
54 /* --- BEGIN: Auxiliary functions */
56 static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
60 bam1_core_t *c = &b->core;
61 uint32_t x = c->pos, y = 0;
62 int ret = 1, is_restart = 1, first_op, last_op;
64 if (c->flag&BAM_FUNMAP) return 0; // unmapped read
65 assert(x <= pos); // otherwise a bug
66 p->qpos = -1; p->indel = 0; p->is_del = p->is_head = p->is_tail = 0;
67 first_op = bam1_cigar(b)[0] & BAM_CIGAR_MASK;
68 last_op = bam1_cigar(b)[c->n_cigar-1] & BAM_CIGAR_MASK;
69 for (k = 0; k < c->n_cigar; ++k) {
70 int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation
71 int l = bam1_cigar(b)[k] >> BAM_CIGAR_SHIFT; // length
72 if (op == BAM_CMATCH) { // NOTE: this assumes the first and the last operation MUST BE a match or a clip
73 if (x + l > pos) { // overlap with pos
74 p->indel = p->is_del = 0;
75 p->qpos = y + (pos - x);
76 if (x == pos && is_restart && first_op != BAM_CDEL) p->is_head = 1;
77 if (x + l - 1 == pos) { // come to the end of a match
78 int has_next_match = 0;
80 for (i = k + 1; i < c->n_cigar; ++i) {
81 uint32_t cigar = bam1_cigar(b)[i];
82 int opi = cigar&BAM_CIGAR_MASK;
83 if (opi == BAM_CMATCH) {
86 } else if (opi == BAM_CSOFT_CLIP || opi == BAM_CREF_SKIP || opi == BAM_CHARD_CLIP) break;
88 if (!has_next_match && last_op != BAM_CDEL) p->is_tail = 1;
89 if (k < c->n_cigar - 1 && has_next_match) { // there are additional operation(s)
90 uint32_t cigar = bam1_cigar(b)[k+1]; // next CIGAR
91 int op_next = cigar&BAM_CIGAR_MASK; // next CIGAR operation
92 if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
93 else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
94 else if (op_next == BAM_CPAD && k + 2 < c->n_cigar) { // no working for adjacent padding
95 cigar = bam1_cigar(b)[k+2]; op_next = cigar&BAM_CIGAR_MASK;
96 if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
97 else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
103 } else if (op == BAM_CDEL) { // then set ->is_del
104 if (k == 0 && x == pos) p->is_head = 1;
105 else if (x + l - 1 == pos && k == c->n_cigar - 1) p->is_tail = 1;
107 p->indel = 0; p->is_del = 1;
111 } else if (op == BAM_CREF_SKIP) x += l;
112 else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
113 if (is_restart) is_restart ^= (op == BAM_CMATCH);
114 else is_restart ^= (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP);
116 if (op == BAM_CREF_SKIP) ret = 0; // then do not put it into pileup at all
120 assert(x > pos); // otherwise a bug
124 /* --- END: Auxiliary functions */
132 lbnode_t *head, *tail, *dummy;
133 int32_t tid, pos, max_tid, max_pos;
134 int is_eof, flag_mask, max_plp, error;
136 // for the "auto" interface only
142 bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
145 iter = calloc(1, sizeof(struct __bam_plp_t));
146 iter->mp = mp_init();
147 iter->head = iter->tail = mp_alloc(iter->mp);
148 iter->dummy = mp_alloc(iter->mp);
149 iter->max_tid = iter->max_pos = -1;
150 iter->flag_mask = BAM_DEF_MASK;
154 iter->b = bam_init1();
159 void bam_plp_destroy(bam_plp_t iter)
161 mp_free(iter->mp, iter->dummy);
162 mp_free(iter->mp, iter->head);
163 if (iter->mp->cnt != 0)
164 fprintf(stderr, "[bam_plp_destroy] memory leak: %d. Continue anyway.\n", iter->mp->cnt);
165 mp_destroy(iter->mp);
166 if (iter->b) bam_destroy1(iter->b);
171 const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
173 if (iter->error) { *_n_plp = -1; return 0; }
175 if (iter->is_eof && iter->head->next == 0) return 0;
176 while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) {
179 // write iter->plp at iter->pos
180 iter->dummy->next = iter->head;
181 for (p = iter->head, q = iter->dummy; p->next; q = p, p = p->next) {
182 if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove
183 q->next = p->next; mp_free(iter->mp, p); p = q;
184 } else if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup
185 if (n_plp == iter->max_plp) { // then double the capacity
186 iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256;
187 iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp);
189 iter->plp[n_plp].b = &p->b;
190 if (resolve_cigar(iter->plp + n_plp, iter->pos)) ++n_plp; // skip the read if we are looking at ref-skip
193 iter->head = iter->dummy->next; // dummy->next may be changed
194 *_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos;
195 // update iter->tid and iter->pos
196 if (iter->head->next) {
197 if (iter->tid > iter->head->b.core.tid) {
198 fprintf(stderr, "[%s] unsorted input. Pileup aborts.\n", __func__);
204 if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence
205 iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference
206 } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid
207 iter->pos = iter->head->beg; // jump to the next position
208 } else ++iter->pos; // scan contiguously
210 if (n_plp) return iter->plp;
211 if (iter->is_eof && iter->head->next == 0) break;
216 int bam_plp_push(bam_plp_t iter, const bam1_t *b)
218 if (iter->error) return -1;
220 if (b->core.tid < 0) return 0;
221 if (b->core.flag & iter->flag_mask) return 0;
222 bam_copy1(&iter->tail->b, b);
223 iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
224 if (b->core.tid < iter->max_tid) {
225 fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
229 if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) {
230 fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
234 iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg;
235 if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) {
236 iter->tail->next = mp_alloc(iter->mp);
237 iter->tail = iter->tail->next;
239 } else iter->is_eof = 1;
243 const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
245 const bam_pileup1_t *plp;
246 if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; }
247 if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
250 if (iter->is_eof) return 0;
251 while (iter->func(iter->data, iter->b) >= 0) {
252 if (bam_plp_push(iter, iter->b) < 0) {
256 if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
258 bam_plp_push(iter, 0);
259 if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
264 void bam_plp_reset(bam_plp_t iter)
267 iter->max_tid = iter->max_pos = -1;
268 iter->tid = iter->pos = 0;
270 for (p = iter->head; p->next;) {
272 mp_free(iter->mp, p);
275 iter->head = iter->tail;
278 void bam_plp_set_mask(bam_plp_t iter, int mask)
280 iter->flag_mask = mask < 0? BAM_DEF_MASK : (BAM_FUNMAP | mask);
287 int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
293 buf = bam_plbuf_init(func, func_data);
294 bam_plbuf_set_mask(buf, mask);
295 while ((ret = bam_read1(fp, b)) >= 0)
296 bam_plbuf_push(b, buf);
297 bam_plbuf_push(0, buf);
298 bam_plbuf_destroy(buf);
303 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask)
305 bam_plp_set_mask(buf->iter, mask);
308 void bam_plbuf_reset(bam_plbuf_t *buf)
310 bam_plp_reset(buf->iter);
313 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
316 buf = calloc(1, sizeof(bam_plbuf_t));
317 buf->iter = bam_plp_init(0, 0);
323 void bam_plbuf_destroy(bam_plbuf_t *buf)
325 bam_plp_destroy(buf->iter);
329 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
331 int ret, n_plp, tid, pos;
332 const bam_pileup1_t *plp;
333 ret = bam_plp_push(buf->iter, b);
334 if (ret < 0) return ret;
335 while ((plp = bam_plp_next(buf->iter, &tid, &pos, &n_plp)) != 0)
336 buf->func(tid, pos, n_plp, plp, buf->data);
344 struct __bam_mplp_t {
349 const bam_pileup1_t **plp;
352 bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data)
356 iter = calloc(1, sizeof(struct __bam_mplp_t));
357 iter->pos = calloc(n, 8);
358 iter->n_plp = calloc(n, sizeof(int));
359 iter->plp = calloc(n, sizeof(void*));
360 iter->iter = calloc(n, sizeof(void*));
362 iter->min = (uint64_t)-1;
363 for (i = 0; i < n; ++i) {
364 iter->iter[i] = bam_plp_init(func, data[i]);
365 iter->pos[i] = iter->min;
370 void bam_mplp_destroy(bam_mplp_t iter)
373 for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]);
374 free(iter->iter); free(iter->pos); free(iter->n_plp); free(iter->plp);
378 int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp)
381 uint64_t new_min = (uint64_t)-1;
382 for (i = 0; i < iter->n; ++i) {
383 if (iter->pos[i] == iter->min) {
385 iter->plp[i] = bam_plp_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]);
386 iter->pos[i] = (uint64_t)tid<<32 | pos;
388 if (iter->plp[i] && iter->pos[i] < new_min) new_min = iter->pos[i];
391 if (new_min == (uint64_t)-1) return 0;
392 *_tid = new_min>>32; *_pos = (uint32_t)new_min;
393 for (i = 0; i < iter->n; ++i) {
394 if (iter->pos[i] == iter->min) { // FIXME: valgrind reports "uninitialised value(s) at this line"
395 n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i];
397 } else n_plp[i] = 0, plp[i] = 0;