bam_pileup.c

   1 #include <stdio.h>
   2 #include <stdlib.h>
   3 #include <ctype.h>
   4 #include <assert.h>
   5 #include "sam.h"
   6
   7 typedef struct __linkbuf_t {
   8         bam1_t b;
   9         uint32_t beg, end;
  10         struct __linkbuf_t *next;
  11 } lbnode_t;
  12
  13 /* --- BEGIN: Memory pool */
  14
  15 typedef struct {
  16         int cnt, n, max;
  17         lbnode_t **buf;
  18 } mempool_t;
  19
  20 static mempool_t *mp_init()
  21 {
  22         mempool_t *mp;
  23         mp = (mempool_t*)calloc(1, sizeof(mempool_t));
  24         return mp;
  25 }
  26 static void mp_destroy(mempool_t *mp)
  27 {
  28         int k;
  29         for (k = 0; k < mp->n; ++k) {
  30                 free(mp->buf[k]->b.data);
  31                 free(mp->buf[k]);
  32         }
  33         free(mp->buf);
  34         free(mp);
  35 }
  36 static inline lbnode_t *mp_alloc(mempool_t *mp)
  37 {
  38         ++mp->cnt;
  39         if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t));
  40         else return mp->buf[--mp->n];
  41 }
  42 static inline void mp_free(mempool_t *mp, lbnode_t *p)
  43 {
  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);
  48         }
  49         mp->buf[mp->n++] = p;
  50 }
  51
  52 /* --- END: Memory pool */
  53
  54 /* --- BEGIN: Auxiliary functions */
  55
  56 static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
  57 {
  58         unsigned k;
  59         bam1_t *b = p->b;
  60         bam1_core_t *c = &b->core;
  61         uint32_t x = c->pos, y = 0;
  62         int ret = 1, is_restart = 1;
  63
  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         for (k = 0; k < c->n_cigar; ++k) {
  68                 int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation
  69                 int l = bam1_cigar(b)[k] >> BAM_CIGAR_SHIFT; // length
  70                 if (op == BAM_CMATCH) { // NOTE: this assumes the first and the last operation MUST BE a match or a clip
  71                         if (x + l > pos) { // overlap with pos
  72                                 p->indel = p->is_del = 0;
  73                                 p->qpos = y + (pos - x);
  74                                 if (x == pos && is_restart) p->is_head = 1;
  75                                 if (x + l - 1 == pos) { // come to the end of a match
  76                                         int has_next_match = 0;
  77                                         unsigned i;
  78                                         for (i = k + 1; i < c->n_cigar; ++i) {
  79                                                 uint32_t cigar = bam1_cigar(b)[i];
  80                                                 int opi = cigar&BAM_CIGAR_MASK;
  81                                                 if (opi == BAM_CMATCH) {
  82                                                         has_next_match = 1;
  83                                                         break;
  84                                                 } else if (opi == BAM_CSOFT_CLIP || opi == BAM_CREF_SKIP || opi == BAM_CHARD_CLIP) break;
  85                                         }
  86                                         if (!has_next_match) p->is_tail = 1;
  87                                         if (k < c->n_cigar - 1 && has_next_match) { // there are additional operation(s)
  88                                                 uint32_t cigar = bam1_cigar(b)[k+1]; // next CIGAR
  89                                                 int op_next = cigar&BAM_CIGAR_MASK; // next CIGAR operation
  90                                                 if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
  91                                                 else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
  92                                                 else if (op_next == BAM_CPAD && k + 2 < c->n_cigar) { // no working for adjacent padding
  93                                                         cigar = bam1_cigar(b)[k+2]; op_next = cigar&BAM_CIGAR_MASK;
  94                                                         if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
  95                                                         else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
  96                                                 }
  97                                         }
  98                                 }
  99                         }
 100                         x += l; y += l;
 101                 } else if (op == BAM_CDEL) { // then set ->is_del
 102                         if (x + l > pos) {
 103                                 p->indel = 0; p->is_del = 1;
 104                                 p->qpos = y + (pos - x);
 105                         }
 106                         x += l;
 107                 } else if (op == BAM_CREF_SKIP) x += l;
 108                 else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
 109                 if (is_restart) is_restart ^= (op == BAM_CMATCH);
 110                 else is_restart ^= (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP);
 111                 if (x > pos) {
 112                         if (op == BAM_CREF_SKIP) ret = 0; // then do not put it into pileup at all
 113                         break;
 114                 }
 115         }
 116         assert(x > pos); // otherwise a bug
 117         return ret;
 118 }
 119
 120 /* --- END: Auxiliary functions */
 121
 122 /*******************
 123  * pileup iterator *
 124  *******************/
 125
 126 struct __bam_plp_t {
 127         mempool_t *mp;
 128         lbnode_t *head, *tail, *dummy;
 129         int32_t tid, pos, max_tid, max_pos;
 130         int is_eof, flag_mask, max_plp, error;
 131         bam_pileup1_t *plp;
 132         // for the "auto" interface only
 133         bam1_t *b;
 134         bam_plp_auto_f func;
 135         void *data;
 136 };
 137
 138 bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
 139 {
 140         bam_plp_t iter;
 141         iter = calloc(1, sizeof(struct __bam_plp_t));
 142         iter->mp = mp_init();
 143         iter->head = iter->tail = mp_alloc(iter->mp);
 144         iter->dummy = mp_alloc(iter->mp);
 145         iter->max_tid = iter->max_pos = -1;
 146         iter->flag_mask = BAM_DEF_MASK;
 147         if (func) {
 148                 iter->func = func;
 149                 iter->data = data;
 150                 iter->b = bam_init1();
 151         }
 152         return iter;
 153 }
 154
 155 void bam_plp_destroy(bam_plp_t iter)
 156 {
 157         mp_free(iter->mp, iter->dummy);
 158         mp_free(iter->mp, iter->head);
 159         if (iter->mp->cnt != 0)
 160                 fprintf(stderr, "[bam_plp_destroy] memory leak: %d. Continue anyway.\n", iter->mp->cnt);
 161         mp_destroy(iter->mp);
 162         if (iter->b) bam_destroy1(iter->b);
 163         free(iter->plp);
 164         free(iter);
 165 }
 166
 167 const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
 168 {
 169         if (iter->error) { *_n_plp = -1; return 0; }
 170         *_n_plp = 0;
 171         if (iter->is_eof && iter->head->next == 0) return 0;
 172         while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) {
 173                 int n_plp = 0;
 174                 lbnode_t *p, *q;
 175                 // write iter->plp at iter->pos
 176                 iter->dummy->next = iter->head;
 177                 for (p = iter->head, q = iter->dummy; p->next; q = p, p = p->next) {
 178                         if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove
 179                                 q->next = p->next; mp_free(iter->mp, p); p = q;
 180                         } else if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup
 181                                 if (n_plp == iter->max_plp) { // then double the capacity
 182                                         iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256;
 183                                         iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp);
 184                                 }
 185                                 iter->plp[n_plp].b = &p->b;
 186                                 if (resolve_cigar(iter->plp + n_plp, iter->pos)) ++n_plp; // skip the read if we are looking at ref-skip
 187                         }
 188                 }
 189                 iter->head = iter->dummy->next; // dummy->next may be changed
 190                 *_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos;
 191                 // update iter->tid and iter->pos
 192                 if (iter->head->next) {
 193                         if (iter->tid > iter->head->b.core.tid) {
 194                                 fprintf(stderr, "[%s] unsorted input. Pileup aborts.\n", __func__);
 195                                 iter->error = 1;
 196                                 *_n_plp = -1;
 197                                 return 0;
 198                         }
 199                 }
 200                 if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence
 201                         iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference
 202                 } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid
 203                         iter->pos = iter->head->beg; // jump to the next position
 204                 } else ++iter->pos; // scan contiguously
 205                 // return
 206                 if (n_plp) return iter->plp;
 207                 if (iter->is_eof && iter->head->next == 0) break;
 208         }
 209         return 0;
 210 }
 211
 212 int bam_plp_push(bam_plp_t iter, const bam1_t *b)
 213 {
 214         if (iter->error) return -1;
 215         if (b) {
 216                 if (b->core.tid < 0) return 0;
 217                 if (b->core.flag & iter->flag_mask) return 0;
 218                 bam_copy1(&iter->tail->b, b);
 219                 iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
 220                 if (b->core.tid < iter->max_tid) {
 221                         fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
 222                         iter->error = 1;
 223                         return -1;
 224                 }
 225                 if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) {
 226                         fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
 227                         iter->error = 1;
 228                         return -1;
 229                 }
 230                 iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg;
 231                 if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) {
 232                         iter->tail->next = mp_alloc(iter->mp);
 233                         iter->tail = iter->tail->next;
 234                 }
 235         } else iter->is_eof = 1;
 236         return 0;
 237 }
 238
 239 const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
 240 {
 241         const bam_pileup1_t *plp;
 242         if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; }
 243         if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
 244         else {
 245                 *_n_plp = 0;
 246                 if (iter->is_eof) return 0;
 247                 while (iter->func(iter->data, iter->b) >= 0) {
 248                         if (bam_plp_push(iter, iter->b) < 0) {
 249                                 *_n_plp = -1;
 250                                 return 0;
 251                         }
 252                         if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
 253                 }
 254                 bam_plp_push(iter, 0);
 255                 if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
 256                 return 0;
 257         }
 258 }
 259
 260 void bam_plp_reset(bam_plp_t iter)
 261 {
 262         lbnode_t *p, *q;
 263         iter->max_tid = iter->max_pos = -1;
 264         iter->tid = iter->pos = 0;
 265         iter->is_eof = 0;
 266         for (p = iter->head; p->next;) {
 267                 q = p->next;
 268                 mp_free(iter->mp, p);
 269                 p = q;
 270         }
 271         iter->head = iter->tail;
 272 }
 273
 274 void bam_plp_set_mask(bam_plp_t iter, int mask)
 275 {
 276         iter->flag_mask = mask < 0? BAM_DEF_MASK : (BAM_FUNMAP | mask);
 277 }
 278
 279 /*****************
 280  * callback APIs *
 281  *****************/
 282
 283 int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
 284 {
 285         bam_plbuf_t *buf;
 286         int ret;
 287         bam1_t *b;
 288         b = bam_init1();
 289         buf = bam_plbuf_init(func, func_data);
 290         bam_plbuf_set_mask(buf, mask);
 291         while ((ret = bam_read1(fp, b)) >= 0)
 292                 bam_plbuf_push(b, buf);
 293         bam_plbuf_push(0, buf);
 294         bam_plbuf_destroy(buf);
 295         bam_destroy1(b);
 296         return 0;
 297 }
 298
 299 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask)
 300 {
 301         bam_plp_set_mask(buf->iter, mask);
 302 }
 303
 304 void bam_plbuf_reset(bam_plbuf_t *buf)
 305 {
 306         bam_plp_reset(buf->iter);
 307 }
 308
 309 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
 310 {
 311         bam_plbuf_t *buf;
 312         buf = calloc(1, sizeof(bam_plbuf_t));
 313         buf->iter = bam_plp_init(0, 0);
 314         buf->func = func;
 315         buf->data = data;
 316         return buf;
 317 }
 318
 319 void bam_plbuf_destroy(bam_plbuf_t *buf)
 320 {
 321         bam_plp_destroy(buf->iter);
 322         free(buf);
 323 }
 324
 325 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
 326 {
 327         int ret, n_plp, tid, pos;
 328         const bam_pileup1_t *plp;
 329         ret = bam_plp_push(buf->iter, b);
 330         if (ret < 0) return ret;
 331         while ((plp = bam_plp_next(buf->iter, &tid, &pos, &n_plp)) != 0)
 332                 buf->func(tid, pos, n_plp, plp, buf->data);
 333         return 0;
 334 }
 335
 336 /***********
 337  * mpileup *
 338  ***********/
 339
 340 struct __bam_mplp_t {
 341         int n;
 342         uint64_t min, *pos;
 343         bam_plp_t *iter;
 344         int *n_plp;
 345         const bam_pileup1_t **plp;
 346 };
 347
 348 bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data)
 349 {
 350         int i;
 351         bam_mplp_t iter;
 352         iter = calloc(1, sizeof(struct __bam_mplp_t));
 353         iter->pos = calloc(n, 8);
 354         iter->n_plp = calloc(n, sizeof(int));
 355         iter->plp = calloc(n, sizeof(void*));
 356         iter->iter = calloc(n, sizeof(void*));
 357         iter->n = n;
 358         iter->min = (uint64_t)-1;
 359         for (i = 0; i < n; ++i) {
 360                 iter->iter[i] = bam_plp_init(func, data[i]);
 361                 iter->pos[i] = iter->min;
 362         }
 363         return iter;
 364 }
 365
 366 void bam_mplp_destroy(bam_mplp_t iter)
 367 {
 368         int i;
 369         for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]);
 370         free(iter->iter); free(iter->pos); free(iter->n_plp); free(iter->plp);
 371         free(iter);
 372 }
 373
 374 int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp)
 375 {
 376         int i, ret = 0;
 377         uint64_t new_min = (uint64_t)-1;
 378         for (i = 0; i < iter->n; ++i) {
 379                 if (iter->pos[i] == iter->min) {
 380                         int tid, pos;
 381                         iter->plp[i] = bam_plp_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]);
 382                         iter->pos[i] = (uint64_t)tid<<32 | pos;
 383                 }
 384                 if (iter->plp[i] && iter->pos[i] < new_min) new_min = iter->pos[i];
 385         }
 386         iter->min = new_min;
 387         if (new_min == (uint64_t)-1) return 0;
 388         *_tid = new_min>>32; *_pos = (uint32_t)new_min;
 389         for (i = 0; i < iter->n; ++i) {
 390                 if (iter->pos[i] == iter->min) {
 391                         n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i];
 392                         ++ret;
 393                 } else n_plp[i] = 0, plp[i] = 0;
 394         }
 395         return ret;
 396 }