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;
 120         bam_pileup1_t *plp;
 121 };
 122
 123 bam_plp_t bam_plp_init(void)
 124 {
 125         bam_plp_t iter;
 126         iter = calloc(1, sizeof(struct __bam_plp_t));
 127         iter->mp = mp_init();
 128         iter->head = iter->tail = mp_alloc(iter->mp);
 129         iter->dummy = mp_alloc(iter->mp);
 130         iter->max_tid = iter->max_pos = -1;
 131         iter->flag_mask = BAM_DEF_MASK;
 132         return iter;
 133 }
 134
 135 const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_n_plp, int *_tid, int *_pos)
 136 {
 137         *_n_plp = 0;
 138         if (iter->is_eof && iter->head->next == 0) return 0;
 139         while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) {
 140                 int n_plp = 0;
 141                 lbnode_t *p, *q;
 142                 // write iter->plp at iter->pos
 143                 iter->dummy->next = iter->head;
 144                 for (p = iter->head, q = iter->dummy; p->next; q = p, p = p->next) {
 145                         if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove
 146                                 q->next = p->next; mp_free(iter->mp, p); p = q;
 147                         } else if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup
 148                                 if (n_plp == iter->max_plp) { // then double the capacity
 149                                         iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256;
 150                                         iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp);
 151                                 }
 152                                 iter->plp[n_plp].b = &p->b;
 153                                 if (resolve_cigar(iter->plp + n_plp, iter->pos)) ++n_plp; // skip the read if we are looking at ref-skip
 154                         }
 155                 }
 156                 iter->head = iter->dummy->next; // dummy->next may be changed
 157                 *_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos;
 158                 // update iter->tid and iter->pos
 159                 if (iter->head->next) {
 160                         if (iter->tid > iter->head->b.core.tid) {
 161                                 fprintf(stderr, "[%s] unsorted input. Pileup aborts.\n", __func__);
 162                                 *_n_plp = -1;
 163                                 return 0;
 164                         }
 165                 }
 166                 if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence
 167                         iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference
 168                 } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid
 169                         iter->pos = iter->head->beg; // jump to the next position
 170                 } else ++iter->pos; // scan contiguously
 171                 // return
 172                 if (n_plp) return iter->plp;
 173                 if (iter->is_eof && iter->head->next == 0) break;
 174         }
 175         return 0;
 176 }
 177
 178 int bam_plp_push(bam_plp_t iter, const bam1_t *b)
 179 {
 180         if (b) {
 181                 if (b->core.tid < 0) return 0;
 182                 if (b->core.flag & iter->flag_mask) return 0;
 183                 bam_copy1(&iter->tail->b, b);
 184                 iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
 185                 if (b->core.tid < iter->max_tid) {
 186                         fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
 187                         return -1;
 188                 }
 189                 if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) {
 190                         fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
 191                         return -1;
 192                 }
 193                 iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg;
 194                 if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) {
 195                         iter->tail->next = mp_alloc(iter->mp);
 196                         iter->tail = iter->tail->next;
 197                 }
 198         } else iter->is_eof = 1;
 199         return 0;
 200 }
 201
 202 void bam_plp_reset(bam_plp_t iter)
 203 {
 204         lbnode_t *p, *q;
 205         iter->max_tid = iter->max_pos = -1;
 206         iter->tid = iter->pos = 0;
 207         iter->is_eof = 0;
 208         for (p = iter->head; p->next;) {
 209                 q = p->next;
 210                 mp_free(iter->mp, p);
 211                 p = q;
 212         }
 213         iter->head = iter->tail;
 214 }
 215
 216 void bam_plp_set_mask(bam_plp_t iter, int mask)
 217 {
 218         iter->flag_mask = mask < 0? BAM_DEF_MASK : (BAM_FUNMAP | mask);
 219 }
 220
 221 void bam_plp_destroy(bam_plp_t iter)
 222 {
 223         mp_free(iter->mp, iter->dummy);
 224         mp_free(iter->mp, iter->head);
 225         if (iter->mp->cnt != 0)
 226                 fprintf(stderr, "[bam_plp_destroy] memory leak: %d. Continue anyway.\n", iter->mp->cnt);
 227         mp_destroy(iter->mp);
 228         free(iter->plp);
 229         free(iter);
 230 }
 231
 232 /*****************
 233  * callback APIs *
 234  *****************/
 235
 236 int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
 237 {
 238         bam_plbuf_t *buf;
 239         int ret;
 240         bam1_t *b;
 241         b = bam_init1();
 242         buf = bam_plbuf_init(func, func_data);
 243         bam_plbuf_set_mask(buf, mask);
 244         while ((ret = bam_read1(fp, b)) >= 0)
 245                 bam_plbuf_push(b, buf);
 246         bam_plbuf_push(0, buf);
 247         bam_plbuf_destroy(buf);
 248         bam_destroy1(b);
 249         return 0;
 250 }
 251
 252 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask)
 253 {
 254         bam_plp_set_mask(buf->iter, mask);
 255 }
 256
 257 void bam_plbuf_reset(bam_plbuf_t *buf)
 258 {
 259         bam_plp_reset(buf->iter);
 260 }
 261
 262 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
 263 {
 264         bam_plbuf_t *buf;
 265         buf = calloc(1, sizeof(bam_plbuf_t));
 266         buf->iter = bam_plp_init();
 267         buf->func = func;
 268         buf->data = data;
 269         return buf;
 270 }
 271
 272 void bam_plbuf_destroy(bam_plbuf_t *buf)
 273 {
 274         bam_plp_destroy(buf->iter);
 275         free(buf);
 276 }
 277
 278 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
 279 {
 280         int ret, n_plp, tid, pos;
 281         const bam_pileup1_t *plp;
 282         ret = bam_plp_push(buf->iter, b);
 283         if (ret < 0) return ret;
 284         while ((plp = bam_plp_next(buf->iter, &n_plp, &tid, &pos)) != 0)
 285                 buf->func(tid, pos, n_plp, plp, buf->data);
 286         return 0;
 287 }