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         if (h == 0) return 0;
 158         bam_strmap_destroy(h->rg2lib); h->rg2lib = 0;
 159         if (h->l_text < 3) return 0;
 160         // parse @RG lines
 161         h->rg2lib = bam_strmap_init();
 162         rgid = calloc(1, sizeof(kstring_t));
 163         rglib = calloc(1, sizeof(kstring_t));
 164         s = h->text;
 165         while ((s = strstr(s, "@RG")) != 0) {
 166                 if (rgid->l && rglib->l) {
 167                         bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
 168                         ++n;
 169                 }
 170                 rgid->l = rglib->l = 0;
 171                 s += 3;
 172                 r = s;
 173                 if ((p = strstr(s, "ID:")) != 0) {
 174                         q = p + 3;
 175                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 176                         kputsn(q, p - q, rgid);
 177                 } else {
 178                         fprintf(stderr, "[bam_header_parse] missing ID tag in @RG lines.\n");
 179                         break;
 180                 }
 181                 if (r < p) r = p;
 182                 if ((p = strstr(s, "LB:")) != 0) {
 183                         q = p + 3;
 184                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 185                         kputsn(q, p - q, rglib);
 186                 } else {
 187                         fprintf(stderr, "[bam_header_parse] missing LB tag in @RG lines.\n");
 188                         break;
 189                 }
 190                 if (r < p) r = p;
 191                 s = r + 3;
 192         }
 193         if (rgid->l && rglib->l) {
 194                 bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
 195                 ++n;
 196         }
 197         free(rgid->s); free(rgid);
 198         free(rglib->s); free(rglib);
 199         if (n == 0) {
 200                 bam_strmap_destroy(h->rg2lib);
 201                 h->rg2lib = 0;
 202         }
 203         return n;
 204 }
 205
 206 int sam_header_parse(bam_header_t *h)
 207 {
 208         int i;
 209         char *s, *p, *q, *r;
 210
 211         // free
 212         free(h->target_len); free(h->target_name);
 213         h->n_targets = 0; h->target_len = 0; h->target_name = 0;
 214         if (h->l_text < 3) return 0;
 215         // count number of @SQ
 216         s = h->text;
 217         while ((s = strstr(s, "@SQ")) != 0) {
 218                 ++h->n_targets;
 219                 s += 3;
 220         }
 221         if (h->n_targets == 0) return 0;
 222         h->target_len = (uint32_t*)calloc(h->n_targets, 4);
 223         h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
 224         // parse @SQ lines
 225         i = 0;
 226         s = h->text;
 227         while ((s = strstr(s, "@SQ")) != 0) {
 228                 s += 3;
 229                 r = s;
 230                 if ((p = strstr(s, "SN:")) != 0) {
 231                         q = p + 3;
 232                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 233                         h->target_name[i] = (char*)calloc(p - q + 1, 1);
 234                         strncpy(h->target_name[i], q, p - q);
 235                 } else goto header_err_ret;
 236                 if (r < p) r = p;
 237                 if ((p = strstr(s, "LN:")) != 0) h->target_len[i] = strtol(p + 3, 0, 10);
 238                 else goto header_err_ret;
 239                 if (r < p) r = p;
 240                 s = r + 3;
 241                 ++i;
 242         }
 243         sam_header_parse_rg(h);
 244         return h->n_targets;
 245
 246 header_err_ret:
 247         fprintf(stderr, "[bam_header_parse] missing SN or LN tag in @SQ lines.\n");
 248         free(h->target_len); free(h->target_name);
 249         h->n_targets = 0; h->target_len = 0; h->target_name = 0;
 250         return 0;
 251 }
 252
 253 bam_header_t *sam_header_read(tamFile fp)
 254 {
 255         int ret, dret;
 256         bam_header_t *header = bam_header_init();
 257         kstring_t *str = fp->str;
 258         while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
 259                 str->s[str->l] = dret; // note that str->s is NOT null terminated!!
 260                 append_text(header, str);
 261                 if (dret != '\n') {
 262                         ret = ks_getuntil(fp->ks, '\n', str, &dret);
 263                         str->s[str->l] = '\n'; // NOT null terminated!!
 264                         append_text(header, str);
 265                 }
 266                 ++fp->n_lines;
 267         }
 268         sam_header_parse(header);
 269         bam_init_header_hash(header);
 270         fp->is_first = 1;
 271         return header;
 272 }
 273
 274 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 275 {
 276         int ret, doff, doff0, dret, z = 0;
 277         bam1_core_t *c = &b->core;
 278         kstring_t *str = fp->str;
 279         kstream_t *ks = fp->ks;
 280
 281         if (fp->is_first) {
 282                 fp->is_first = 0;
 283                 ret = str->l;
 284         } else {
 285                 do { // special consideration for empty lines
 286                         ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
 287                         if (ret >= 0) z += str->l + 1;
 288                 } while (ret == 0);
 289         }
 290         if (ret < 0) return -1;
 291         ++fp->n_lines;
 292         doff = 0;
 293
 294         { // name
 295                 c->l_qname = strlen(str->s) + 1;
 296                 memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
 297                 doff += c->l_qname;
 298         }
 299         { // flag, tid, pos, qual
 300                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->flag = atoi(str->s);
 301                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
 302                 if (c->tid < 0 && strcmp(str->s, "*")) {
 303                         if (header->n_targets == 0) {
 304                                 fprintf(stderr, "[sam_read1] missing header? Abort!\n");
 305                                 exit(1);
 306                         } else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
 307                 }
 308                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 309                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
 310                 if (ret < 0) return -2;
 311         }
 312         { // cigar
 313                 char *s, *t;
 314                 int i, op;
 315                 long x;
 316                 c->n_cigar = 0;
 317                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
 318                 z += str->l + 1;
 319                 if (str->s[0] != '*') {
 320                         for (s = str->s; *s; ++s) {
 321                                 if (isalpha(*s)) ++c->n_cigar;
 322                                 else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
 323                         }
 324                         b->data = alloc_data(b, doff + c->n_cigar * 4);
 325                         for (i = 0, s = str->s; i != c->n_cigar; ++i) {
 326                                 x = strtol(s, &t, 10);
 327                                 op = toupper(*t);
 328                                 if (op == 'M') op = BAM_CMATCH;
 329                                 else if (op == 'I') op = BAM_CINS;
 330                                 else if (op == 'D') op = BAM_CDEL;
 331                                 else if (op == 'N') op = BAM_CREF_SKIP;
 332                                 else if (op == 'S') op = BAM_CSOFT_CLIP;
 333                                 else if (op == 'H') op = BAM_CHARD_CLIP;
 334                                 else if (op == 'P') op = BAM_CPAD;
 335                                 else parse_error(fp->n_lines, "invalid CIGAR operation");
 336                                 s = t + 1;
 337                                 bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
 338                         }
 339                         if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
 340                         c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
 341                         doff += c->n_cigar * 4;
 342                 } else c->bin = bam_reg2bin(c->pos, c->pos + 1);
 343         }
 344         { // mtid, mpos, isize
 345                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 346                 c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
 347                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 348                 c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 349                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 350                 c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
 351                 if (ret < 0) return -4;
 352         }
 353         { // seq and qual
 354                 int i;
 355                 uint8_t *p;
 356                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
 357                 z += str->l + 1;
 358                 c->l_qseq = strlen(str->s);
 359                 if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
 360                         parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
 361                 p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
 362                 bzero(p, (c->l_qseq+1)/2);
 363                 for (i = 0; i < c->l_qseq; ++i)
 364                         p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
 365                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
 366                 z += str->l + 1;
 367                 if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
 368                         parse_error(fp->n_lines, "sequence and quality are inconsistent");
 369                 p += (c->l_qseq+1)/2;
 370                 if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
 371                 else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
 372                 doff += c->l_qseq + (c->l_qseq+1)/2;
 373         }
 374         doff0 = doff;
 375         if (dret != '\n' && dret != '\r') { // aux
 376                 while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
 377                         uint8_t *s, type, key[2];
 378                         z += str->l + 1;
 379                         if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
 380                                 parse_error(fp->n_lines, "missing colon in auxiliary data");
 381                         key[0] = str->s[0]; key[1] = str->s[1];
 382                         type = str->s[3];
 383                         s = alloc_data(b, doff + 3) + doff;
 384                         s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
 385                         if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
 386                                 s = alloc_data(b, doff + 2) + doff;
 387                                 *s++ = 'A'; *s = str->s[5];
 388                                 doff += 2;
 389                         } else if (type == 'I' || type == 'i') {
 390                                 long long x;
 391                                 s = alloc_data(b, doff + 5) + doff;
 392                                 x = (long long)atoll(str->s + 5);
 393                                 if (x < 0) {
 394                                         if (x >= -127) {
 395                                                 *s++ = 'c'; *(int8_t*)s = (int8_t)x;
 396                                                 s += 1; doff += 2;
 397                                         } else if (x >= -32767) {
 398                                                 *s++ = 's'; *(int16_t*)s = (int16_t)x;
 399                                                 s += 2; doff += 3;
 400                                         } else {
 401                                                 *s++ = 'i'; *(int32_t*)s = (int32_t)x;
 402                                                 s += 4; doff += 5;
 403                                                 if (x < -2147483648ll)
 404                                                         fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
 405                                                                         (long long)fp->n_lines, x);
 406                                         }
 407                                 } else {
 408                                         if (x <= 255) {
 409                                                 *s++ = 'C'; *s++ = (uint8_t)x;
 410                                                 doff += 2;
 411                                         } else if (x <= 65535) {
 412                                                 *s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
 413                                                 s += 2; doff += 3;
 414                                         } else {
 415                                                 *s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
 416                                                 s += 4; doff += 5;
 417                                                 if (x > 4294967295ll)
 418                                                         fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
 419                                                                         (long long)fp->n_lines, x);
 420                                         }
 421                                 }
 422                         } else if (type == 'f') {
 423                                 s = alloc_data(b, doff + 5) + doff;
 424                                 *s++ = 'f';
 425                                 *(float*)s = (float)atof(str->s + 5);
 426                                 s += 4; doff += 5;
 427                         } else if (type == 'd') {
 428                                 s = alloc_data(b, doff + 9) + doff;
 429                                 *s++ = 'd';
 430                                 *(float*)s = (float)atof(str->s + 9);
 431                                 s += 8; doff += 9;
 432                         } else if (type == 'Z' || type == 'H') {
 433                                 int size = 1 + (str->l - 5) + 1;
 434                                 if (type == 'H') { // check whether the hex string is valid
 435                                         int i;
 436                                         if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
 437                                         for (i = 0; i < str->l - 5; ++i) {
 438                                                 int c = toupper(str->s[5 + i]);
 439                                                 if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
 440                                                         parse_error(fp->n_lines, "invalid hex character");
 441                                         }
 442                                 }
 443                                 s = alloc_data(b, doff + size) + doff;
 444                                 *s++ = type;
 445                                 memcpy(s, str->s + 5, str->l - 5);
 446                                 s[str->l - 5] = 0;
 447                                 doff += size;
 448                         } else parse_error(fp->n_lines, "unrecognized type");
 449                         if (dret == '\n' || dret == '\r') break;
 450                 }
 451         }
 452         b->l_aux = doff - doff0;
 453         b->data_len = doff;
 454         return z;
 455 }
 456
 457 tamFile sam_open(const char *fn)
 458 {
 459         tamFile fp;
 460         fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
 461         fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
 462         fp->fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
 463         fp->ks = ks_init(fp->fp);
 464         return fp;
 465 }
 466
 467 void sam_close(tamFile fp)
 468 {
 469         if (fp) {
 470                 ks_destroy(fp->ks);
 471                 gzclose(fp->fp);
 472                 free(fp->str->s); free(fp->str);
 473                 free(fp);
 474         }
 475 }