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