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 #ifdef _WIN32
   9 #include <fcntl.h>
  10 #endif
  11 #include "kstring.h"
  12 #include "bam.h"
  13 #include "sam_header.h"
  14 #include "kseq.h"
  15 #include "khash.h"
  16
  17 KSTREAM_INIT(gzFile, gzread, 8192)
  18 KHASH_MAP_INIT_STR(ref, uint64_t)
  19
  20 void bam_init_header_hash(bam_header_t *header);
  21 void bam_destroy_header_hash(bam_header_t *header);
  22 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
  23
  24 unsigned char bam_nt16_table[256] = {
  25         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  26         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  27         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  28          1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
  29         15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
  30         15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
  31         15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
  32         15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 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         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  38         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  39         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  40         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
  41 };
  42
  43 unsigned short bam_char2flag_table[256] = {
  44         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  45         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  46         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  47         0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  48         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  49         BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
  50         0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
  51         BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
  52         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  53         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  54         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  55         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  56         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  57         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  58         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  59         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
  60 };
  61
  62 char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
  63
  64 struct __tamFile_t {
  65         gzFile fp;
  66         kstream_t *ks;
  67         kstring_t *str;
  68         uint64_t n_lines;
  69         int is_first;
  70 };
  71
  72 char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
  73 {
  74         char **list = 0, *s;
  75         int n = 0, dret, m = 0;
  76         gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
  77         kstream_t *ks;
  78         kstring_t *str;
  79         str = (kstring_t*)calloc(1, sizeof(kstring_t));
  80         ks = ks_init(fp);
  81         while (ks_getuntil(ks, '\n', str, &dret) > 0) {
  82                 if (n == m) {
  83                         m = m? m << 1 : 16;
  84                         list = (char**)realloc(list, m * sizeof(char*));
  85                 }
  86                 if (str->s[str->l-1] == '\r')
  87                         str->s[--str->l] = '\0';
  88                 s = list[n++] = (char*)calloc(str->l + 1, 1);
  89                 strcpy(s, str->s);
  90         }
  91         ks_destroy(ks);
  92         gzclose(fp);
  93         free(str->s); free(str);
  94         *_n = n;
  95         return list;
  96 }
  97
  98 static bam_header_t *hash2header(const kh_ref_t *hash)
  99 {
 100         bam_header_t *header;
 101         khiter_t k;
 102         header = bam_header_init();
 103         header->n_targets = kh_size(hash);
 104         header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
 105         header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
 106         for (k = kh_begin(hash); k != kh_end(hash); ++k) {
 107                 if (kh_exist(hash, k)) {
 108                         int i = (int)kh_value(hash, k);
 109                         header->target_name[i] = (char*)kh_key(hash, k);
 110                         header->target_len[i] = kh_value(hash, k)>>32;
 111                 }
 112         }
 113         bam_init_header_hash(header);
 114         return header;
 115 }
 116 bam_header_t *sam_header_read2(const char *fn)
 117 {
 118         bam_header_t *header;
 119         int c, dret, ret, error = 0;
 120         gzFile fp;
 121         kstream_t *ks;
 122         kstring_t *str;
 123         kh_ref_t *hash;
 124         khiter_t k;
 125         if (fn == 0) return 0;
 126         fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
 127         if (fp == 0) return 0;
 128         hash = kh_init(ref);
 129         ks = ks_init(fp);
 130         str = (kstring_t*)calloc(1, sizeof(kstring_t));
 131         while (ks_getuntil(ks, 0, str, &dret) > 0) {
 132                 char *s = strdup(str->s);
 133                 int len, i;
 134                 i = kh_size(hash);
 135                 ks_getuntil(ks, 0, str, &dret);
 136                 len = atoi(str->s);
 137                 k = kh_put(ref, hash, s, &ret);
 138                 if (ret == 0) {
 139                         fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
 140                         error = 1;
 141                 }
 142                 kh_value(hash, k) = (uint64_t)len<<32 | i;
 143                 if (dret != '\n')
 144                         while ((c = ks_getc(ks)) != '\n' && c != -1);
 145         }
 146         ks_destroy(ks);
 147         gzclose(fp);
 148         free(str->s); free(str);
 149         fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
 150         if (error) return 0;
 151         header = hash2header(hash);
 152         kh_destroy(ref, hash);
 153         return header;
 154 }
 155 static inline uint8_t *alloc_data(bam1_t *b, int size)
 156 {
 157         if (b->m_data < size) {
 158                 b->m_data = size;
 159                 kroundup32(b->m_data);
 160                 b->data = (uint8_t*)realloc(b->data, b->m_data);
 161         }
 162         return b->data;
 163 }
 164 static inline void parse_error(int64_t n_lines, const char * __restrict msg)
 165 {
 166         fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
 167         abort();
 168 }
 169 static inline void append_text(bam_header_t *header, kstring_t *str)
 170 {
 171         int x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
 172         kroundup32(x); kroundup32(y);
 173         if (x < y) header->text = (char*)realloc(header->text, y);
 174         strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
 175         header->l_text += str->l + 1;
 176         header->text[header->l_text] = 0;
 177 }
 178
 179 int sam_header_parse(bam_header_t *h)
 180 {
 181         char **tmp;
 182         int i;
 183         free(h->target_len); free(h->target_name);
 184         h->n_targets = 0; h->target_len = 0; h->target_name = 0;
 185         if (h->l_text < 3) return 0;
 186         if (h->dict == 0) h->dict = sam_header_parse2(h->text);
 187         tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
 188         if (h->n_targets == 0) return 0;
 189         h->target_name = calloc(h->n_targets, sizeof(void*));
 190         for (i = 0; i < h->n_targets; ++i)
 191                 h->target_name[i] = strdup(tmp[i]);
 192         free(tmp);
 193         tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
 194         h->target_len = calloc(h->n_targets, 4);
 195         for (i = 0; i < h->n_targets; ++i)
 196                 h->target_len[i] = atoi(tmp[i]);
 197         free(tmp);
 198         return h->n_targets;
 199 }
 200
 201 bam_header_t *sam_header_read(tamFile fp)
 202 {
 203         int ret, dret;
 204         bam_header_t *header = bam_header_init();
 205         kstring_t *str = fp->str;
 206         while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
 207                 str->s[str->l] = dret; // note that str->s is NOT null terminated!!
 208                 append_text(header, str);
 209                 if (dret != '\n') {
 210                         ret = ks_getuntil(fp->ks, '\n', str, &dret);
 211                         str->s[str->l] = '\n'; // NOT null terminated!!
 212                         append_text(header, str);
 213                 }
 214                 ++fp->n_lines;
 215         }
 216         sam_header_parse(header);
 217         bam_init_header_hash(header);
 218         fp->is_first = 1;
 219         return header;
 220 }
 221
 222 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 223 {
 224         int ret, doff, doff0, dret, z = 0;
 225         bam1_core_t *c = &b->core;
 226         kstring_t *str = fp->str;
 227         kstream_t *ks = fp->ks;
 228
 229         if (fp->is_first) {
 230                 fp->is_first = 0;
 231                 ret = str->l;
 232         } else {
 233                 do { // special consideration for empty lines
 234                         ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
 235                         if (ret >= 0) z += str->l + 1;
 236                 } while (ret == 0);
 237         }
 238         if (ret < 0) return -1;
 239         ++fp->n_lines;
 240         doff = 0;
 241
 242         { // name
 243                 c->l_qname = strlen(str->s) + 1;
 244                 memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
 245                 doff += c->l_qname;
 246         }
 247         { // flag
 248                 long flag;
 249                 char *s;
 250                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 251                 flag = strtol((char*)str->s, &s, 0);
 252                 if (*s) { // not the end of the string
 253                         flag = 0;
 254                         for (s = str->s; *s; ++s)
 255                                 flag |= bam_char2flag_table[(int)*s];
 256                 }
 257                 c->flag = flag;
 258         }
 259         { // tid, pos, qual
 260                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
 261                 if (c->tid < 0 && strcmp(str->s, "*")) {
 262                         if (header->n_targets == 0) {
 263                                 fprintf(stderr, "[sam_read1] missing header? Abort!\n");
 264                                 exit(1);
 265                         } else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
 266                 }
 267                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 268                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
 269                 if (ret < 0) return -2;
 270         }
 271         { // cigar
 272                 char *s, *t;
 273                 int i, op;
 274                 long x;
 275                 c->n_cigar = 0;
 276                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
 277                 z += str->l + 1;
 278                 if (str->s[0] != '*') {
 279                         for (s = str->s; *s; ++s) {
 280                                 if (isalpha(*s)) ++c->n_cigar;
 281                                 else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
 282                         }
 283                         b->data = alloc_data(b, doff + c->n_cigar * 4);
 284                         for (i = 0, s = str->s; i != c->n_cigar; ++i) {
 285                                 x = strtol(s, &t, 10);
 286                                 op = toupper(*t);
 287                                 if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
 288                                 else if (op == 'I') op = BAM_CINS;
 289                                 else if (op == 'D') op = BAM_CDEL;
 290                                 else if (op == 'N') op = BAM_CREF_SKIP;
 291                                 else if (op == 'S') op = BAM_CSOFT_CLIP;
 292                                 else if (op == 'H') op = BAM_CHARD_CLIP;
 293                                 else if (op == 'P') op = BAM_CPAD;
 294                                 else parse_error(fp->n_lines, "invalid CIGAR operation");
 295                                 s = t + 1;
 296                                 bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
 297                         }
 298                         if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
 299                         c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
 300                         doff += c->n_cigar * 4;
 301                 } else {
 302                         if (!(c->flag&BAM_FUNMAP)) {
 303                                 fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
 304                                 c->flag |= BAM_FUNMAP;
 305                         }
 306                         c->bin = bam_reg2bin(c->pos, c->pos + 1);
 307                 }
 308         }
 309         { // mtid, mpos, isize
 310                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 311                 c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
 312                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 313                 c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 314                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 315                 c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
 316                 if (ret < 0) return -4;
 317         }
 318         { // seq and qual
 319                 int i;
 320                 uint8_t *p = 0;
 321                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
 322                 z += str->l + 1;
 323                 if (strcmp(str->s, "*")) {
 324                         c->l_qseq = strlen(str->s);
 325                         if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
 326                                 parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
 327                         p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
 328                         memset(p, 0, (c->l_qseq+1)/2);
 329                         for (i = 0; i < c->l_qseq; ++i)
 330                                 p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
 331                 } else c->l_qseq = 0;
 332                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
 333                 z += str->l + 1;
 334                 if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
 335                         parse_error(fp->n_lines, "sequence and quality are inconsistent");
 336                 p += (c->l_qseq+1)/2;
 337                 if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
 338                 else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
 339                 doff += c->l_qseq + (c->l_qseq+1)/2;
 340         }
 341         doff0 = doff;
 342         if (dret != '\n' && dret != '\r') { // aux
 343                 while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
 344                         uint8_t *s, type, key[2];
 345                         z += str->l + 1;
 346                         if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
 347                                 parse_error(fp->n_lines, "missing colon in auxiliary data");
 348                         key[0] = str->s[0]; key[1] = str->s[1];
 349                         type = str->s[3];
 350                         s = alloc_data(b, doff + 3) + doff;
 351                         s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
 352                         if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
 353                                 s = alloc_data(b, doff + 2) + doff;
 354                                 *s++ = 'A'; *s = str->s[5];
 355                                 doff += 2;
 356                         } else if (type == 'I' || type == 'i') {
 357                                 long long x;
 358                                 s = alloc_data(b, doff + 5) + doff;
 359                                 x = (long long)atoll(str->s + 5);
 360                                 if (x < 0) {
 361                                         if (x >= -127) {
 362                                                 *s++ = 'c'; *(int8_t*)s = (int8_t)x;
 363                                                 s += 1; doff += 2;
 364                                         } else if (x >= -32767) {
 365                                                 *s++ = 's'; *(int16_t*)s = (int16_t)x;
 366                                                 s += 2; doff += 3;
 367                                         } else {
 368                                                 *s++ = 'i'; *(int32_t*)s = (int32_t)x;
 369                                                 s += 4; doff += 5;
 370                                                 if (x < -2147483648ll)
 371                                                         fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
 372                                                                         (long long)fp->n_lines, x);
 373                                         }
 374                                 } else {
 375                                         if (x <= 255) {
 376                                                 *s++ = 'C'; *s++ = (uint8_t)x;
 377                                                 doff += 2;
 378                                         } else if (x <= 65535) {
 379                                                 *s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
 380                                                 s += 2; doff += 3;
 381                                         } else {
 382                                                 *s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
 383                                                 s += 4; doff += 5;
 384                                                 if (x > 4294967295ll)
 385                                                         fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
 386                                                                         (long long)fp->n_lines, x);
 387                                         }
 388                                 }
 389                         } else if (type == 'f') {
 390                                 s = alloc_data(b, doff + 5) + doff;
 391                                 *s++ = 'f';
 392                                 *(float*)s = (float)atof(str->s + 5);
 393                                 s += 4; doff += 5;
 394                         } else if (type == 'd') {
 395                                 s = alloc_data(b, doff + 9) + doff;
 396                                 *s++ = 'd';
 397                                 *(float*)s = (float)atof(str->s + 9);
 398                                 s += 8; doff += 9;
 399                         } else if (type == 'Z' || type == 'H') {
 400                                 int size = 1 + (str->l - 5) + 1;
 401                                 if (type == 'H') { // check whether the hex string is valid
 402                                         int i;
 403                                         if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
 404                                         for (i = 0; i < str->l - 5; ++i) {
 405                                                 int c = toupper(str->s[5 + i]);
 406                                                 if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
 407                                                         parse_error(fp->n_lines, "invalid hex character");
 408                                         }
 409                                 }
 410                                 s = alloc_data(b, doff + size) + doff;
 411                                 *s++ = type;
 412                                 memcpy(s, str->s + 5, str->l - 5);
 413                                 s[str->l - 5] = 0;
 414                                 doff += size;
 415                         } else parse_error(fp->n_lines, "unrecognized type");
 416                         if (dret == '\n' || dret == '\r') break;
 417                 }
 418         }
 419         b->l_aux = doff - doff0;
 420         b->data_len = doff;
 421         return z;
 422 }
 423
 424 tamFile sam_open(const char *fn)
 425 {
 426         tamFile fp;
 427         gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
 428         if (gzfp == 0) return 0;
 429         fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
 430         fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
 431         fp->fp = gzfp;
 432         fp->ks = ks_init(fp->fp);
 433         return fp;
 434 }
 435
 436 void sam_close(tamFile fp)
 437 {
 438         if (fp) {
 439                 ks_destroy(fp->ks);
 440                 gzclose(fp->fp);
 441                 free(fp->str->s); free(fp->str);
 442                 free(fp);
 443         }
 444 }