samtools/bam_pileup.c.pysam.c

   1 #include "pysam.h"
   2
   3 #include <stdio.h>
   4 #include <stdlib.h>
   5 #include <ctype.h>
   6 #include <assert.h>
   7 #include "sam.h"
   8
   9 typedef struct {
  10         int k, x, y, end;
  11 } cstate_t;
  12
  13 static cstate_t g_cstate_null = { -1, 0, 0, 0 };
  14
  15 typedef struct __linkbuf_t {
  16         bam1_t b;
  17         uint32_t beg, end;
  18         cstate_t s;
  19         struct __linkbuf_t *next;
  20 } lbnode_t;
  21
  22 /* --- BEGIN: Memory pool */
  23
  24 typedef struct {
  25         int cnt, n, max;
  26         lbnode_t **buf;
  27 } mempool_t;
  28
  29 static mempool_t *mp_init()
  30 {
  31         mempool_t *mp;
  32         mp = (mempool_t*)calloc(1, sizeof(mempool_t));
  33         return mp;
  34 }
  35 static void mp_destroy(mempool_t *mp)
  36 {
  37         int k;
  38         for (k = 0; k < mp->n; ++k) {
  39                 free(mp->buf[k]->b.data);
  40                 free(mp->buf[k]);
  41         }
  42         free(mp->buf);
  43         free(mp);
  44 }
  45 static inline lbnode_t *mp_alloc(mempool_t *mp)
  46 {
  47         ++mp->cnt;
  48         if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t));
  49         else return mp->buf[--mp->n];
  50 }
  51 static inline void mp_free(mempool_t *mp, lbnode_t *p)
  52 {
  53         --mp->cnt; p->next = 0; // clear lbnode_t::next here
  54         if (mp->n == mp->max) {
  55                 mp->max = mp->max? mp->max<<1 : 256;
  56                 mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max);
  57         }
  58         mp->buf[mp->n++] = p;
  59 }
  60
  61 /* --- END: Memory pool */
  62
  63 /* --- BEGIN: Auxiliary functions */
  64
  65 /* s->k: the index of the CIGAR operator that has just been processed.
  66    s->x: the reference coordinate of the start of s->k
  67    s->y: the query coordiante of the start of s->k
  68  */
  69 static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s)
  70 {
  71 #define _cop(c) ((c)&BAM_CIGAR_MASK)
  72 #define _cln(c) ((c)>>BAM_CIGAR_SHIFT)
  73
  74         bam1_t *b = p->b;
  75         bam1_core_t *c = &b->core;
  76         uint32_t *cigar = bam1_cigar(b);
  77         int k, is_head = 0;
  78         // determine the current CIGAR operation
  79 //      fprintf(pysamerr, "%s\tpos=%d\tend=%d\t(%d,%d,%d)\n", bam1_qname(b), pos, s->end, s->k, s->x, s->y);
  80         if (s->k == -1) { // never processed
  81                 is_head = 1;
  82                 if (c->n_cigar == 1) { // just one operation, save a loop
  83                         if (_cop(cigar[0]) == BAM_CMATCH) s->k = 0, s->x = c->pos, s->y = 0;
  84                 } else { // find the first match or deletion
  85                         for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
  86                                 int op = _cop(cigar[k]);
  87                                 int l = _cln(cigar[k]);
  88                                 if (op == BAM_CMATCH || op == BAM_CDEL) break;
  89                                 else if (op == BAM_CREF_SKIP) s->x += l;
  90                                 else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
  91                         }
  92                         assert(k < c->n_cigar);
  93                         s->k = k;
  94                 }
  95         } else { // the read has been processed before
  96                 int op, l = _cln(cigar[s->k]);
  97                 if (pos - s->x >= l) { // jump to the next operation
  98                         assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case
  99                         op = _cop(cigar[s->k+1]);
 100                         if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP) { // jump to the next without a loop
 101                                 if (_cop(cigar[s->k]) == BAM_CMATCH) s->y += l;
 102                                 s->x += l;
 103                                 ++s->k;
 104                         } else { // find the next M/D/N
 105                                 if (_cop(cigar[s->k]) == BAM_CMATCH) s->y += l;
 106                                 s->x += l;
 107                                 for (k = s->k + 1; k < c->n_cigar; ++k) {
 108                                         op = _cop(cigar[k]), l = _cln(cigar[k]);
 109                                         if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP) break;
 110                                         else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
 111                                 }
 112                                 s->k = k;
 113                         }
 114                         assert(s->k < c->n_cigar); // otherwise a bug
 115                 } // else, do nothing
 116         }
 117         { // collect pileup information
 118                 int op, l;
 119                 op = _cop(cigar[s->k]); l = _cln(cigar[s->k]);
 120                 p->is_del = p->indel = p->is_refskip = 0;
 121                 if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation
 122                         int op2 = _cop(cigar[s->k+1]);
 123                         int l2 = _cln(cigar[s->k+1]);
 124                         if (op2 == BAM_CDEL) p->indel = -(int)l2;
 125                         else if (op2 == BAM_CINS) p->indel = l2;
 126                         else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding
 127                                 int l3 = 0;
 128                                 for (k = s->k + 2; k < c->n_cigar; ++k) {
 129                                         op2 = _cop(cigar[k]); l2 = _cln(cigar[k]);
 130                                         if (op2 == BAM_CINS) l3 += l2;
 131                                         else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP) break;
 132                                 }
 133                                 if (l3 > 0) p->indel = l3;
 134                         }
 135                 }
 136                 if (op == BAM_CMATCH) {
 137                         p->qpos = s->y + (pos - s->x);
 138                 } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
 139                         p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!!
 140                         p->is_refskip = (op == BAM_CREF_SKIP);
 141                 } // cannot be other operations; otherwise a bug
 142                 p->is_head = (pos == c->pos); p->is_tail = (pos == s->end);
 143         }
 144         return 1;
 145 }
 146
 147 /* --- END: Auxiliary functions */
 148
 149 /*******************
 150  * pileup iterator *
 151  *******************/
 152
 153 struct __bam_plp_t {
 154         mempool_t *mp;
 155         lbnode_t *head, *tail, *dummy;
 156         int32_t tid, pos, max_tid, max_pos;
 157         int is_eof, flag_mask, max_plp, error, maxcnt;
 158         bam_pileup1_t *plp;
 159         // for the "auto" interface only
 160         bam1_t *b;
 161         bam_plp_auto_f func;
 162         void *data;
 163 };
 164
 165 bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
 166 {
 167         bam_plp_t iter;
 168         iter = calloc(1, sizeof(struct __bam_plp_t));
 169         iter->mp = mp_init();
 170         iter->head = iter->tail = mp_alloc(iter->mp);
 171         iter->dummy = mp_alloc(iter->mp);
 172         iter->max_tid = iter->max_pos = -1;
 173         iter->flag_mask = BAM_DEF_MASK;
 174         iter->maxcnt = 8000;
 175         if (func) {
 176                 iter->func = func;
 177                 iter->data = data;
 178                 iter->b = bam_init1();
 179         }
 180         return iter;
 181 }
 182
 183 void bam_plp_destroy(bam_plp_t iter)
 184 {
 185         mp_free(iter->mp, iter->dummy);
 186         mp_free(iter->mp, iter->head);
 187         if (iter->mp->cnt != 0)
 188                 fprintf(pysamerr, "[bam_plp_destroy] memory leak: %d. Continue anyway.\n", iter->mp->cnt);
 189         mp_destroy(iter->mp);
 190         if (iter->b) bam_destroy1(iter->b);
 191         free(iter->plp);
 192         free(iter);
 193 }
 194
 195 const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
 196 {
 197         if (iter->error) { *_n_plp = -1; return 0; }
 198         *_n_plp = 0;
 199         if (iter->is_eof && iter->head->next == 0) return 0;
 200         while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) {
 201                 int n_plp = 0;
 202                 lbnode_t *p, *q;
 203                 // write iter->plp at iter->pos
 204                 iter->dummy->next = iter->head;
 205                 for (p = iter->head, q = iter->dummy; p->next; q = p, p = p->next) {
 206                         if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove
 207                                 q->next = p->next; mp_free(iter->mp, p); p = q;
 208                         } else if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup
 209                                 if (n_plp == iter->max_plp) { // then double the capacity
 210                                         iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256;
 211                                         iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp);
 212                                 }
 213                                 iter->plp[n_plp].b = &p->b;
 214                                 if (resolve_cigar2(iter->plp + n_plp, iter->pos, &p->s)) ++n_plp; // actually always true...
 215                         }
 216                 }
 217                 iter->head = iter->dummy->next; // dummy->next may be changed
 218                 *_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos;
 219                 // update iter->tid and iter->pos
 220                 if (iter->head->next) {
 221                         if (iter->tid > iter->head->b.core.tid) {
 222                                 fprintf(pysamerr, "[%s] unsorted input. Pileup aborts.\n", __func__);
 223                                 iter->error = 1;
 224                                 *_n_plp = -1;
 225                                 return 0;
 226                         }
 227                 }
 228                 if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence
 229                         iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference
 230                 } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid
 231                         iter->pos = iter->head->beg; // jump to the next position
 232                 } else ++iter->pos; // scan contiguously
 233                 // return
 234                 if (n_plp) return iter->plp;
 235                 if (iter->is_eof && iter->head->next == 0) break;
 236         }
 237         return 0;
 238 }
 239
 240 int bam_plp_push(bam_plp_t iter, const bam1_t *b)
 241 {
 242         if (iter->error) return -1;
 243         if (b) {
 244                 if (b->core.tid < 0) return 0;
 245                 if (b->core.flag & iter->flag_mask) return 0;
 246                 if (iter->tid == b->core.tid && iter->pos == b->core.pos && iter->mp->cnt > iter->maxcnt) return 0;
 247                 bam_copy1(&iter->tail->b, b);
 248                 iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
 249                 iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t
 250                 if (b->core.tid < iter->max_tid) {
 251                         fprintf(pysamerr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
 252                         iter->error = 1;
 253                         return -1;
 254                 }
 255                 if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) {
 256                         fprintf(pysamerr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
 257                         iter->error = 1;
 258                         return -1;
 259                 }
 260                 iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg;
 261                 if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) {
 262                         iter->tail->next = mp_alloc(iter->mp);
 263                         iter->tail = iter->tail->next;
 264                 }
 265         } else iter->is_eof = 1;
 266         return 0;
 267 }
 268
 269 const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
 270 {
 271         const bam_pileup1_t *plp;
 272         if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; }
 273         if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
 274         else { // no pileup line can be obtained; read alignments
 275                 *_n_plp = 0;
 276                 if (iter->is_eof) return 0;
 277                 while (iter->func(iter->data, iter->b) >= 0) {
 278                         if (bam_plp_push(iter, iter->b) < 0) {
 279                                 *_n_plp = -1;
 280                                 return 0;
 281                         }
 282                         if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
 283                         // otherwise no pileup line can be returned; read the next alignment.
 284                 }
 285                 bam_plp_push(iter, 0);
 286                 if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
 287                 return 0;
 288         }
 289 }
 290
 291 void bam_plp_reset(bam_plp_t iter)
 292 {
 293         lbnode_t *p, *q;
 294         iter->max_tid = iter->max_pos = -1;
 295         iter->tid = iter->pos = 0;
 296         iter->is_eof = 0;
 297         for (p = iter->head; p->next;) {
 298                 q = p->next;
 299                 mp_free(iter->mp, p);
 300                 p = q;
 301         }
 302         iter->head = iter->tail;
 303 }
 304
 305 void bam_plp_set_mask(bam_plp_t iter, int mask)
 306 {
 307         iter->flag_mask = mask < 0? BAM_DEF_MASK : (BAM_FUNMAP | mask);
 308 }
 309
 310 void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt)
 311 {
 312         iter->maxcnt = maxcnt;
 313 }
 314
 315 /*****************
 316  * callback APIs *
 317  *****************/
 318
 319 int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
 320 {
 321         bam_plbuf_t *buf;
 322         int ret;
 323         bam1_t *b;
 324         b = bam_init1();
 325         buf = bam_plbuf_init(func, func_data);
 326         bam_plbuf_set_mask(buf, mask);
 327         while ((ret = bam_read1(fp, b)) >= 0)
 328                 bam_plbuf_push(b, buf);
 329         bam_plbuf_push(0, buf);
 330         bam_plbuf_destroy(buf);
 331         bam_destroy1(b);
 332         return 0;
 333 }
 334
 335 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask)
 336 {
 337         bam_plp_set_mask(buf->iter, mask);
 338 }
 339
 340 void bam_plbuf_reset(bam_plbuf_t *buf)
 341 {
 342         bam_plp_reset(buf->iter);
 343 }
 344
 345 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
 346 {
 347         bam_plbuf_t *buf;
 348         buf = calloc(1, sizeof(bam_plbuf_t));
 349         buf->iter = bam_plp_init(0, 0);
 350         buf->func = func;
 351         buf->data = data;
 352         return buf;
 353 }
 354
 355 void bam_plbuf_destroy(bam_plbuf_t *buf)
 356 {
 357         bam_plp_destroy(buf->iter);
 358         free(buf);
 359 }
 360
 361 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
 362 {
 363         int ret, n_plp, tid, pos;
 364         const bam_pileup1_t *plp;
 365         ret = bam_plp_push(buf->iter, b);
 366         if (ret < 0) return ret;
 367         while ((plp = bam_plp_next(buf->iter, &tid, &pos, &n_plp)) != 0)
 368                 buf->func(tid, pos, n_plp, plp, buf->data);
 369         return 0;
 370 }
 371
 372 /***********
 373  * mpileup *
 374  ***********/
 375
 376 struct __bam_mplp_t {
 377         int n;
 378         uint64_t min, *pos;
 379         bam_plp_t *iter;
 380         int *n_plp;
 381         const bam_pileup1_t **plp;
 382 };
 383
 384 bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data)
 385 {
 386         int i;
 387         bam_mplp_t iter;
 388         iter = calloc(1, sizeof(struct __bam_mplp_t));
 389         iter->pos = calloc(n, 8);
 390         iter->n_plp = calloc(n, sizeof(int));
 391         iter->plp = calloc(n, sizeof(void*));
 392         iter->iter = calloc(n, sizeof(void*));
 393         iter->n = n;
 394         iter->min = (uint64_t)-1;
 395         for (i = 0; i < n; ++i) {
 396                 iter->iter[i] = bam_plp_init(func, data[i]);
 397                 iter->pos[i] = iter->min;
 398         }
 399         return iter;
 400 }
 401
 402 void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt)
 403 {
 404         int i;
 405         for (i = 0; i < iter->n; ++i)
 406                 iter->iter[i]->maxcnt = maxcnt;
 407 }
 408
 409 void bam_mplp_destroy(bam_mplp_t iter)
 410 {
 411         int i;
 412         for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]);
 413         free(iter->iter); free(iter->pos); free(iter->n_plp); free(iter->plp);
 414         free(iter);
 415 }
 416
 417 int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp)
 418 {
 419         int i, ret = 0;
 420         uint64_t new_min = (uint64_t)-1;
 421         for (i = 0; i < iter->n; ++i) {
 422                 if (iter->pos[i] == iter->min) {
 423                         int tid, pos;
 424                         iter->plp[i] = bam_plp_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]);
 425                         iter->pos[i] = (uint64_t)tid<<32 | pos;
 426                 }
 427                 if (iter->plp[i] && iter->pos[i] < new_min) new_min = iter->pos[i];
 428         }
 429         iter->min = new_min;
 430         if (new_min == (uint64_t)-1) return 0;
 431         *_tid = new_min>>32; *_pos = (uint32_t)new_min;
 432         for (i = 0; i < iter->n; ++i) {
 433                 if (iter->pos[i] == iter->min) { // FIXME: valgrind reports "uninitialised value(s) at this line"
 434                         n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i];
 435                         ++ret;
 436                 } else n_plp[i] = 0, plp[i] = 0;
 437         }
 438         return ret;
 439 }