bam_import.c

   1 #include <zlib.h>
   2 #include <stdio.h>
   3 #include <ctype.h>
   4 #include <string.h>
   5 #include <stdlib.h>
   6 #include <unistd.h>
   7 #include <assert.h>
   8 #include "kstring.h"
   9 #include "bam.h"
  10 #include "kseq.h"
  11 #include "khash.h"
  12
  13 KSTREAM_INIT(gzFile, gzread, 8192)
  14 KHASH_MAP_INIT_STR(ref, uint64_t)
  15
  16 void bam_init_header_hash(bam_header_t *header);
  17 void bam_destroy_header_hash(bam_header_t *header);
  18 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
  19
  20 unsigned char bam_nt16_table[256] = {
  21         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  22         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  23         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  24          1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
  25         15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
  26         15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
  27         15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
  28         15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
  29         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  30         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  31         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  32         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  33         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  34         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  35         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  36         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
  37 };
  38
  39 char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
  40
  41 struct __tamFile_t {
  42         gzFile fp;
  43         kstream_t *ks;
  44         kstring_t *str;
  45         uint64_t n_lines;
  46         int is_first;
  47 };
  48
  49 char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
  50 {
  51         char **list = 0, *s;
  52         int n = 0, dret, m = 0;
  53         gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
  54         kstream_t *ks;
  55         kstring_t *str;
  56         str = (kstring_t*)calloc(1, sizeof(kstring_t));
  57         ks = ks_init(fp);
  58         while (ks_getuntil(ks, '\n', str, &dret) > 0) {
  59                 if (n == m) {
  60                         m = m? m << 1 : 16;
  61                         list = (char**)realloc(list, m * sizeof(char*));
  62                 }
  63                 if (str->s[str->l-1] == '\r')
  64                         str->s[--str->l] = '\0';
  65                 s = list[n++] = (char*)calloc(str->l + 1, 1);
  66                 strcpy(s, str->s);
  67         }
  68         ks_destroy(ks);
  69         gzclose(fp);
  70         free(str->s); free(str);
  71         *_n = n;
  72         return list;
  73 }
  74
  75 static bam_header_t *hash2header(const kh_ref_t *hash)
  76 {
  77         bam_header_t *header;
  78         khiter_t k;
  79         header = bam_header_init();
  80         header->n_targets = kh_size(hash);
  81         header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
  82         header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
  83         for (k = kh_begin(hash); k != kh_end(hash); ++k) {
  84                 if (kh_exist(hash, k)) {
  85                         int i = (int)kh_value(hash, k);
  86                         header->target_name[i] = (char*)kh_key(hash, k);
  87                         header->target_len[i] = kh_value(hash, k)>>32;
  88                 }
  89         }
  90         bam_init_header_hash(header);
  91         return header;
  92 }
  93 bam_header_t *sam_header_read2(const char *fn)
  94 {
  95         bam_header_t *header;
  96         int c, dret, ret;
  97         gzFile fp;
  98         kstream_t *ks;
  99         kstring_t *str;
 100         kh_ref_t *hash;
 101         khiter_t k;
 102         hash = kh_init(ref);
 103         fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
 104         assert(fp);
 105         ks = ks_init(fp);
 106         str = (kstring_t*)calloc(1, sizeof(kstring_t));
 107         while (ks_getuntil(ks, 0, str, &dret) > 0) {
 108                 char *s = strdup(str->s);
 109                 int len, i;
 110                 i = kh_size(hash);
 111                 ks_getuntil(ks, 0, str, &dret);
 112                 len = atoi(str->s);
 113                 k = kh_put(ref, hash, s, &ret);
 114                 kh_value(hash, k) = (uint64_t)len<<32 | i;
 115                 if (dret != '\n')
 116                         while ((c = ks_getc(ks)) != '\n' && c != -1);
 117         }
 118         ks_destroy(ks);
 119         gzclose(fp);
 120         free(str->s); free(str);
 121         fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
 122         header = hash2header(hash);
 123         kh_destroy(ref, hash);
 124         return header;
 125 }
 126 static inline uint8_t *alloc_data(bam1_t *b, int size)
 127 {
 128         if (b->m_data < size) {
 129                 b->m_data = size;
 130                 kroundup32(b->m_data);
 131                 b->data = (uint8_t*)realloc(b->data, b->m_data);
 132         }
 133         return b->data;
 134 }
 135 static inline void parse_error(int64_t n_lines, const char * __restrict msg)
 136 {
 137         fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
 138         abort();
 139 }
 140 static inline void append_text(bam_header_t *header, kstring_t *str)
 141 {
 142         int x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
 143         kroundup32(x); kroundup32(y);
 144         if (x < y) header->text = (char*)realloc(header->text, y);
 145         strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
 146         header->l_text += str->l + 1;
 147         header->text[header->l_text] = 0;
 148 }
 149
 150 int sam_header_parse_rg(bam_header_t *h)
 151 {
 152         kstring_t *rgid, *rglib;
 153         char *p, *q, *s, *r;
 154         int n = 0;
 155
 156         // free
 157         bam_strmap_destroy(h->rg2lib); h->rg2lib = 0;
 158         if (h->l_text < 3) return 0;
 159         // parse @RG lines
 160         h->rg2lib = bam_strmap_init();
 161         rgid = calloc(1, sizeof(kstring_t));
 162         rglib = calloc(1, sizeof(kstring_t));
 163         s = h->text;
 164         while ((s = strstr(s, "@RG")) != 0) {
 165                 if (rgid->l && rglib->l) {
 166                         bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
 167                         ++n;
 168                 }
 169                 rgid->l = rglib->l = 0;
 170                 s += 3;
 171                 r = s;
 172                 if ((p = strstr(s, "ID:")) != 0) {
 173                         q = p + 3;
 174                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 175                         kputsn(q, p - q, rgid);
 176                 } else {
 177                         fprintf(stderr, "[bam_header_parse] missing ID tag in @RG lines.\n");
 178                         break;
 179                 }
 180                 if (r < p) r = p;
 181                 if ((p = strstr(s, "LB:")) != 0) {
 182                         q = p + 3;
 183                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 184                         kputsn(q, p - q, rglib);
 185                 } else {
 186                         fprintf(stderr, "[bam_header_parse] missing LB tag in @RG lines.\n");
 187                         break;
 188                 }
 189                 if (r < p) r = p;
 190                 s = r + 3;
 191         }
 192         if (rgid->l && rglib->l) {
 193                 bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
 194                 ++n;
 195         }
 196         free(rgid->s); free(rgid);
 197         free(rglib->s); free(rglib);
 198         if (n == 0) {
 199                 bam_strmap_destroy(h->rg2lib);
 200                 h->rg2lib = 0;
 201         }
 202         return n;
 203 }
 204
 205 int sam_header_parse(bam_header_t *h)
 206 {
 207         int i;
 208         char *s, *p, *q, *r;
 209
 210         // free
 211         free(h->target_len); free(h->target_name);
 212         h->n_targets = 0; h->target_len = 0; h->target_name = 0;
 213         if (h->l_text < 3) return 0;
 214         // count number of @SQ
 215         s = h->text;
 216         while ((s = strstr(s, "@SQ")) != 0) {
 217                 ++h->n_targets;
 218                 s += 3;
 219         }
 220         if (h->n_targets == 0) return 0;
 221         h->target_len = (uint32_t*)calloc(h->n_targets, 4);
 222         h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
 223         // parse @SQ lines
 224         i = 0;
 225         s = h->text;
 226         while ((s = strstr(s, "@SQ")) != 0) {
 227                 s += 3;
 228                 r = s;
 229                 if ((p = strstr(s, "SN:")) != 0) {
 230                         q = p + 3;
 231                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 232                         h->target_name[i] = (char*)calloc(p - q + 1, 1);
 233                         strncpy(h->target_name[i], q, p - q);
 234                 } else goto header_err_ret;
 235                 if (r < p) r = p;
 236                 if ((p = strstr(s, "LN:")) != 0) h->target_len[i] = strtol(p + 3, 0, 10);
 237                 else goto header_err_ret;
 238                 if (r < p) r = p;
 239                 s = r + 3;
 240                 ++i;
 241         }
 242         sam_header_parse_rg(h);
 243         return h->n_targets;
 244
 245 header_err_ret:
 246         fprintf(stderr, "[bam_header_parse] missing SN or LN tag in @SQ lines.\n");
 247         free(h->target_len); free(h->target_name);
 248         h->n_targets = 0; h->target_len = 0; h->target_name = 0;
 249         return 0;
 250 }
 251
 252 bam_header_t *sam_header_read(tamFile fp)
 253 {
 254         int ret, dret;
 255         bam_header_t *header = bam_header_init();
 256         kstring_t *str = fp->str;
 257         while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
 258                 str->s[str->l] = dret; // note that str->s is NOT null terminated!!
 259                 append_text(header, str);
 260                 if (dret != '\n') {
 261                         ret = ks_getuntil(fp->ks, '\n', str, &dret);
 262                         str->s[str->l] = '\n'; // NOT null terminated!!
 263                         append_text(header, str);
 264                 }
 265                 ++fp->n_lines;
 266         }
 267         sam_header_parse(header);
 268         bam_init_header_hash(header);
 269         fp->is_first = 1;
 270         return header;
 271 }
 272
 273 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 274 {
 275         int ret, doff, doff0, dret, z = 0;
 276         bam1_core_t *c = &b->core;
 277         kstring_t *str = fp->str;
 278         kstream_t *ks = fp->ks;
 279
 280         if (fp->is_first) {
 281                 fp->is_first = 0;
 282                 ret = str->l;
 283         } else {
 284                 do { // special consideration for empty lines
 285                         ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
 286                         if (ret >= 0) z += str->l + 1;
 287                 } while (ret == 0);
 288         }
 289         if (ret < 0) return -1;
 290         ++fp->n_lines;
 291         doff = 0;
 292
 293         { // name
 294                 c->l_qname = strlen(str->s) + 1;
 295                 memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
 296                 doff += c->l_qname;
 297         }
 298         { // flag, tid, pos, qual
 299                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->flag = atoi(str->s);
 300                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
 301                 if (c->tid < 0 && strcmp(str->s, "*")) {
 302                         if (header->n_targets == 0) {
 303                                 fprintf(stderr, "[sam_read1] missing header? Abort!\n");
 304                                 exit(1);
 305                         } else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
 306                 }
 307                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 308                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
 309                 if (ret < 0) return -2;
 310         }
 311         { // cigar
 312                 char *s, *t;
 313                 int i, op;
 314                 long x;
 315                 c->n_cigar = 0;
 316                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
 317                 z += str->l + 1;
 318                 if (str->s[0] != '*') {
 319                         for (s = str->s; *s; ++s) {
 320                                 if (isalpha(*s)) ++c->n_cigar;
 321                                 else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
 322                         }
 323                         b->data = alloc_data(b, doff + c->n_cigar * 4);
 324                         for (i = 0, s = str->s; i != c->n_cigar; ++i) {
 325                                 x = strtol(s, &t, 10);
 326                                 op = toupper(*t);
 327                                 if (op == 'M') op = BAM_CMATCH;
 328                                 else if (op == 'I') op = BAM_CINS;
 329                                 else if (op == 'D') op = BAM_CDEL;
 330                                 else if (op == 'N') op = BAM_CREF_SKIP;
 331                                 else if (op == 'S') op = BAM_CSOFT_CLIP;
 332                                 else if (op == 'H') op = BAM_CHARD_CLIP;
 333                                 else if (op == 'P') op = BAM_CPAD;
 334                                 else parse_error(fp->n_lines, "invalid CIGAR operation");
 335                                 s = t + 1;
 336                                 bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
 337                         }
 338                         if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
 339                         c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
 340                         doff += c->n_cigar * 4;
 341                 } else c->bin = bam_reg2bin(c->pos, c->pos + 1);
 342         }
 343         { // mtid, mpos, isize
 344                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 345                 c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
 346                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 347                 c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 348                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 349                 c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
 350                 if (ret < 0) return -4;
 351         }
 352         { // seq and qual
 353                 int i;
 354                 uint8_t *p;
 355                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
 356                 z += str->l + 1;
 357                 c->l_qseq = strlen(str->s);
 358                 if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
 359                         parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
 360                 p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
 361                 bzero(p, (c->l_qseq+1)/2);
 362                 for (i = 0; i < c->l_qseq; ++i)
 363                         p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
 364                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
 365                 z += str->l + 1;
 366                 if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
 367                         parse_error(fp->n_lines, "sequence and quality are inconsistent");
 368                 p += (c->l_qseq+1)/2;
 369                 if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
 370                 else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
 371                 doff += c->l_qseq + (c->l_qseq+1)/2;
 372         }
 373         doff0 = doff;
 374         if (dret != '\n' && dret != '\r') { // aux
 375                 while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
 376                         uint8_t *s, type, key[2];
 377                         z += str->l + 1;
 378                         if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
 379                                 parse_error(fp->n_lines, "missing colon in auxiliary data");
 380                         key[0] = str->s[0]; key[1] = str->s[1];
 381                         type = str->s[3];
 382                         s = alloc_data(b, doff + 3) + doff;
 383                         s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
 384                         if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
 385                                 s = alloc_data(b, doff + 2) + doff;
 386                                 *s++ = 'A'; *s = str->s[5];
 387                                 doff += 2;
 388                         } else if (type == 'I' || type == 'i') {
 389                                 long long x;
 390                                 s = alloc_data(b, doff + 5) + doff;
 391                                 x = (long long)atoll(str->s + 5);
 392                                 if (x < 0) {
 393                                         if (x >= -127) {
 394                                                 *s++ = 'c'; *(int8_t*)s = (int8_t)x;
 395                                                 s += 1; doff += 2;
 396                                         } else if (x >= -32767) {
 397                                                 *s++ = 's'; *(int16_t*)s = (int16_t)x;
 398                                                 s += 2; doff += 3;
 399                                         } else {
 400                                                 *s++ = 'i'; *(int32_t*)s = (int32_t)x;
 401                                                 s += 4; doff += 5;
 402                                                 if (x < -2147483648ll)
 403                                                         fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
 404                                                                         (long long)fp->n_lines, x);
 405                                         }
 406                                 } else {
 407                                         if (x <= 255) {
 408                                                 *s++ = 'C'; *s++ = (uint8_t)x;
 409                                                 doff += 2;
 410                                         } else if (x <= 65535) {
 411                                                 *s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
 412                                                 s += 2; doff += 3;
 413                                         } else {
 414                                                 *s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
 415                                                 s += 4; doff += 5;
 416                                                 if (x > 4294967295ll)
 417                                                         fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
 418                                                                         (long long)fp->n_lines, x);
 419                                         }
 420                                 }
 421                         } else if (type == 'f') {
 422                                 s = alloc_data(b, doff + 5) + doff;
 423                                 *s++ = 'f';
 424                                 *(float*)s = (float)atof(str->s + 5);
 425                                 s += 4; doff += 5;
 426                         } else if (type == 'd') {
 427                                 s = alloc_data(b, doff + 9) + doff;
 428                                 *s++ = 'd';
 429                                 *(float*)s = (float)atof(str->s + 9);
 430                                 s += 8; doff += 9;
 431                         } else if (type == 'Z' || type == 'H') {
 432                                 int size = 1 + (str->l - 5) + 1;
 433                                 if (type == 'H') { // check whether the hex string is valid
 434                                         int i;
 435                                         if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
 436                                         for (i = 0; i < str->l - 5; ++i) {
 437                                                 int c = toupper(str->s[5 + i]);
 438                                                 if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
 439                                                         parse_error(fp->n_lines, "invalid hex character");
 440                                         }
 441                                 }
 442                                 s = alloc_data(b, doff + size) + doff;
 443                                 *s++ = type;
 444                                 memcpy(s, str->s + 5, str->l - 5);
 445                                 s[str->l - 5] = 0;
 446                                 doff += size;
 447                         } else parse_error(fp->n_lines, "unrecognized type");
 448                         if (dret == '\n' || dret == '\r') break;
 449                 }
 450         }
 451         b->l_aux = doff - doff0;
 452         b->data_len = doff;
 453         return z;
 454 }
 455
 456 tamFile sam_open(const char *fn)
 457 {
 458         tamFile fp;
 459         fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
 460         fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
 461         fp->fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
 462         fp->ks = ks_init(fp->fp);
 463         return fp;
 464 }
 465
 466 void sam_close(tamFile fp)
 467 {
 468         if (fp) {
 469                 ks_destroy(fp->ks);
 470                 gzclose(fp->fp);
 471                 free(fp->str->s); free(fp->str);
 472                 free(fp);
 473         }
 474 }