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