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 "kseq.h"
  14 #include "khash.h"
  15
  16 KSTREAM_INIT(gzFile, gzread, 8192)
  17 KHASH_MAP_INIT_STR(ref, uint64_t)
  18
  19 void bam_init_header_hash(bam_header_t *header);
  20 void bam_destroy_header_hash(bam_header_t *header);
  21 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
  22
  23 unsigned char bam_nt16_table[256] = {
  24         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  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          1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
  28         15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
  29         15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
  30         15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
  31         15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 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         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 };
  41
  42 unsigned short bam_char2flag_table[256] = {
  43         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  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,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  47         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  48         BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
  49         0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
  50         BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
  51         0,0,0,0, 0,0,0,0, 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 };
  60
  61 char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
  62
  63 struct __tamFile_t {
  64         gzFile fp;
  65         kstream_t *ks;
  66         kstring_t *str;
  67         uint64_t n_lines;
  68         int is_first;
  69 };
  70
  71 char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
  72 {
  73         char **list = 0, *s;
  74         int n = 0, dret, m = 0;
  75         gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
  76         kstream_t *ks;
  77         kstring_t *str;
  78         str = (kstring_t*)calloc(1, sizeof(kstring_t));
  79         ks = ks_init(fp);
  80         while (ks_getuntil(ks, '\n', str, &dret) > 0) {
  81                 if (n == m) {
  82                         m = m? m << 1 : 16;
  83                         list = (char**)realloc(list, m * sizeof(char*));
  84                 }
  85                 if (str->s[str->l-1] == '\r')
  86                         str->s[--str->l] = '\0';
  87                 s = list[n++] = (char*)calloc(str->l + 1, 1);
  88                 strcpy(s, str->s);
  89         }
  90         ks_destroy(ks);
  91         gzclose(fp);
  92         free(str->s); free(str);
  93         *_n = n;
  94         return list;
  95 }
  96
  97 static bam_header_t *hash2header(const kh_ref_t *hash)
  98 {
  99         bam_header_t *header;
 100         khiter_t k;
 101         header = bam_header_init();
 102         header->n_targets = kh_size(hash);
 103         header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
 104         header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
 105         for (k = kh_begin(hash); k != kh_end(hash); ++k) {
 106                 if (kh_exist(hash, k)) {
 107                         int i = (int)kh_value(hash, k);
 108                         header->target_name[i] = (char*)kh_key(hash, k);
 109                         header->target_len[i] = kh_value(hash, k)>>32;
 110                 }
 111         }
 112         bam_init_header_hash(header);
 113         return header;
 114 }
 115 bam_header_t *sam_header_read2(const char *fn)
 116 {
 117         bam_header_t *header;
 118         int c, dret, ret;
 119         gzFile fp;
 120         kstream_t *ks;
 121         kstring_t *str;
 122         kh_ref_t *hash;
 123         khiter_t k;
 124         if (fn == 0) return 0;
 125         fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
 126         if (fp == 0) return 0;
 127         hash = kh_init(ref);
 128         ks = ks_init(fp);
 129         str = (kstring_t*)calloc(1, sizeof(kstring_t));
 130         while (ks_getuntil(ks, 0, str, &dret) > 0) {
 131                 char *s = strdup(str->s);
 132                 int len, i;
 133                 i = kh_size(hash);
 134                 ks_getuntil(ks, 0, str, &dret);
 135                 len = atoi(str->s);
 136                 k = kh_put(ref, hash, s, &ret);
 137                 kh_value(hash, k) = (uint64_t)len<<32 | i;
 138                 if (dret != '\n')
 139                         while ((c = ks_getc(ks)) != '\n' && c != -1);
 140         }
 141         ks_destroy(ks);
 142         gzclose(fp);
 143         free(str->s); free(str);
 144         fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
 145         header = hash2header(hash);
 146         kh_destroy(ref, hash);
 147         return header;
 148 }
 149 static inline uint8_t *alloc_data(bam1_t *b, int size)
 150 {
 151         if (b->m_data < size) {
 152                 b->m_data = size;
 153                 kroundup32(b->m_data);
 154                 b->data = (uint8_t*)realloc(b->data, b->m_data);
 155         }
 156         return b->data;
 157 }
 158 static inline void parse_error(int64_t n_lines, const char * __restrict msg)
 159 {
 160         fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
 161         abort();
 162 }
 163 static inline void append_text(bam_header_t *header, kstring_t *str)
 164 {
 165         int x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
 166         kroundup32(x); kroundup32(y);
 167         if (x < y) header->text = (char*)realloc(header->text, y);
 168         strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
 169         header->l_text += str->l + 1;
 170         header->text[header->l_text] = 0;
 171 }
 172
 173 int sam_header_parse_rg(bam_header_t *h)
 174 {
 175         kstring_t *rgid, *rglib;
 176         char *p, *q, *s, *r;
 177         int n = 0;
 178
 179         // free
 180         if (h == 0) return 0;
 181         bam_strmap_destroy(h->rg2lib); h->rg2lib = 0;
 182         if (h->l_text < 3) return 0;
 183         // parse @RG lines
 184         h->rg2lib = bam_strmap_init();
 185         rgid = calloc(1, sizeof(kstring_t));
 186         rglib = calloc(1, sizeof(kstring_t));
 187         s = h->text;
 188         while ((s = strstr(s, "@RG")) != 0) {
 189                 if (rgid->l && rglib->l) {
 190                         bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
 191                         ++n;
 192                 }
 193                 rgid->l = rglib->l = 0;
 194                 s += 3;
 195                 r = s;
 196                 if ((p = strstr(s, "ID:")) != 0) {
 197                         q = p + 3;
 198                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 199                         kputsn(q, p - q, rgid);
 200                 } else {
 201                         fprintf(stderr, "[bam_header_parse] missing ID tag in @RG lines.\n");
 202                         break;
 203                 }
 204                 if (r < p) r = p;
 205                 if ((p = strstr(s, "LB:")) != 0) {
 206                         q = p + 3;
 207                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 208                         kputsn(q, p - q, rglib);
 209                 } else {
 210                         fprintf(stderr, "[bam_header_parse] missing LB tag in @RG lines.\n");
 211                         break;
 212                 }
 213                 if (r < p) r = p;
 214                 s = r + 3;
 215         }
 216         if (rgid->l && rglib->l) {
 217                 bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
 218                 ++n;
 219         }
 220         free(rgid->s); free(rgid);
 221         free(rglib->s); free(rglib);
 222         if (n == 0) {
 223                 bam_strmap_destroy(h->rg2lib);
 224                 h->rg2lib = 0;
 225         }
 226         return n;
 227 }
 228
 229 int sam_header_parse(bam_header_t *h)
 230 {
 231         int i;
 232         char *s, *p, *q, *r;
 233
 234         // free
 235         free(h->target_len); free(h->target_name);
 236         h->n_targets = 0; h->target_len = 0; h->target_name = 0;
 237         if (h->l_text < 3) return 0;
 238         // count number of @SQ
 239         s = h->text;
 240         while ((s = strstr(s, "@SQ")) != 0) {
 241                 ++h->n_targets;
 242                 s += 3;
 243         }
 244         if (h->n_targets == 0) return 0;
 245         h->target_len = (uint32_t*)calloc(h->n_targets, 4);
 246         h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
 247         // parse @SQ lines
 248         i = 0;
 249         s = h->text;
 250         while ((s = strstr(s, "@SQ")) != 0) {
 251                 s += 3;
 252                 r = s;
 253                 if ((p = strstr(s, "SN:")) != 0) {
 254                         q = p + 3;
 255                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 256                         h->target_name[i] = (char*)calloc(p - q + 1, 1);
 257                         strncpy(h->target_name[i], q, p - q);
 258                 } else goto header_err_ret;
 259                 if (r < p) r = p;
 260                 if ((p = strstr(s, "LN:")) != 0) h->target_len[i] = strtol(p + 3, 0, 10);
 261                 else goto header_err_ret;
 262                 if (r < p) r = p;
 263                 s = r + 3;
 264                 ++i;
 265         }
 266         sam_header_parse_rg(h);
 267         return h->n_targets;
 268
 269 header_err_ret:
 270         fprintf(stderr, "[bam_header_parse] missing SN or LN tag in @SQ lines.\n");
 271         free(h->target_len); free(h->target_name);
 272         h->n_targets = 0; h->target_len = 0; h->target_name = 0;
 273         return 0;
 274 }
 275
 276 bam_header_t *sam_header_read(tamFile fp)
 277 {
 278         int ret, dret;
 279         bam_header_t *header = bam_header_init();
 280         kstring_t *str = fp->str;
 281         while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
 282                 str->s[str->l] = dret; // note that str->s is NOT null terminated!!
 283                 append_text(header, str);
 284                 if (dret != '\n') {
 285                         ret = ks_getuntil(fp->ks, '\n', str, &dret);
 286                         str->s[str->l] = '\n'; // NOT null terminated!!
 287                         append_text(header, str);
 288                 }
 289                 ++fp->n_lines;
 290         }
 291         sam_header_parse(header);
 292         bam_init_header_hash(header);
 293         fp->is_first = 1;
 294         return header;
 295 }
 296
 297 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 298 {
 299         int ret, doff, doff0, dret, z = 0;
 300         bam1_core_t *c = &b->core;
 301         kstring_t *str = fp->str;
 302         kstream_t *ks = fp->ks;
 303
 304         if (fp->is_first) {
 305                 fp->is_first = 0;
 306                 ret = str->l;
 307         } else {
 308                 do { // special consideration for empty lines
 309                         ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
 310                         if (ret >= 0) z += str->l + 1;
 311                 } while (ret == 0);
 312         }
 313         if (ret < 0) return -1;
 314         ++fp->n_lines;
 315         doff = 0;
 316
 317         { // name
 318                 c->l_qname = strlen(str->s) + 1;
 319                 memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
 320                 doff += c->l_qname;
 321         }
 322         { // flag
 323                 long flag;
 324                 char *s;
 325                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 326                 flag = strtol((char*)str->s, &s, 0);
 327                 if (*s) { // not the end of the string
 328                         flag = 0;
 329                         for (s = str->s; *s; ++s)
 330                                 flag |= bam_char2flag_table[(int)*s];
 331                 }
 332                 c->flag = flag;
 333         }
 334         { // tid, pos, qual
 335                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
 336                 if (c->tid < 0 && strcmp(str->s, "*")) {
 337                         if (header->n_targets == 0) {
 338                                 fprintf(stderr, "[sam_read1] missing header? Abort!\n");
 339                                 exit(1);
 340                         } else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
 341                 }
 342                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 343                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
 344                 if (ret < 0) return -2;
 345         }
 346         { // cigar
 347                 char *s, *t;
 348                 int i, op;
 349                 long x;
 350                 c->n_cigar = 0;
 351                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
 352                 z += str->l + 1;
 353                 if (str->s[0] != '*') {
 354                         for (s = str->s; *s; ++s) {
 355                                 if (isalpha(*s)) ++c->n_cigar;
 356                                 else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
 357                         }
 358                         b->data = alloc_data(b, doff + c->n_cigar * 4);
 359                         for (i = 0, s = str->s; i != c->n_cigar; ++i) {
 360                                 x = strtol(s, &t, 10);
 361                                 op = toupper(*t);
 362                                 if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
 363                                 else if (op == 'I') op = BAM_CINS;
 364                                 else if (op == 'D') op = BAM_CDEL;
 365                                 else if (op == 'N') op = BAM_CREF_SKIP;
 366                                 else if (op == 'S') op = BAM_CSOFT_CLIP;
 367                                 else if (op == 'H') op = BAM_CHARD_CLIP;
 368                                 else if (op == 'P') op = BAM_CPAD;
 369                                 else parse_error(fp->n_lines, "invalid CIGAR operation");
 370                                 s = t + 1;
 371                                 bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
 372                         }
 373                         if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
 374                         c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
 375                         doff += c->n_cigar * 4;
 376                 } else {
 377                         if (!(c->flag&BAM_FUNMAP)) {
 378                                 fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
 379                                 c->flag |= BAM_FUNMAP;
 380                         }
 381                         c->bin = bam_reg2bin(c->pos, c->pos + 1);
 382                 }
 383         }
 384         { // mtid, mpos, isize
 385                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 386                 c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
 387                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 388                 c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 389                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 390                 c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
 391                 if (ret < 0) return -4;
 392         }
 393         { // seq and qual
 394                 int i;
 395                 uint8_t *p = 0;
 396                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
 397                 z += str->l + 1;
 398                 if (strcmp(str->s, "*")) {
 399                         c->l_qseq = strlen(str->s);
 400                         if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
 401                                 parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
 402                         p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
 403                         memset(p, 0, (c->l_qseq+1)/2);
 404                         for (i = 0; i < c->l_qseq; ++i)
 405                                 p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
 406                 } else c->l_qseq = 0;
 407                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
 408                 z += str->l + 1;
 409                 if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
 410                         parse_error(fp->n_lines, "sequence and quality are inconsistent");
 411                 p += (c->l_qseq+1)/2;
 412                 if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
 413                 else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
 414                 doff += c->l_qseq + (c->l_qseq+1)/2;
 415         }
 416         doff0 = doff;
 417         if (dret != '\n' && dret != '\r') { // aux
 418                 while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
 419                         uint8_t *s, type, key[2];
 420                         z += str->l + 1;
 421                         if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
 422                                 parse_error(fp->n_lines, "missing colon in auxiliary data");
 423                         key[0] = str->s[0]; key[1] = str->s[1];
 424                         type = str->s[3];
 425                         s = alloc_data(b, doff + 3) + doff;
 426                         s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
 427                         if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
 428                                 s = alloc_data(b, doff + 2) + doff;
 429                                 *s++ = 'A'; *s = str->s[5];
 430                                 doff += 2;
 431                         } else if (type == 'I' || type == 'i') {
 432                                 long long x;
 433                                 s = alloc_data(b, doff + 5) + doff;
 434                                 x = (long long)atoll(str->s + 5);
 435                                 if (x < 0) {
 436                                         if (x >= -127) {
 437                                                 *s++ = 'c'; *(int8_t*)s = (int8_t)x;
 438                                                 s += 1; doff += 2;
 439                                         } else if (x >= -32767) {
 440                                                 *s++ = 's'; *(int16_t*)s = (int16_t)x;
 441                                                 s += 2; doff += 3;
 442                                         } else {
 443                                                 *s++ = 'i'; *(int32_t*)s = (int32_t)x;
 444                                                 s += 4; doff += 5;
 445                                                 if (x < -2147483648ll)
 446                                                         fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
 447                                                                         (long long)fp->n_lines, x);
 448                                         }
 449                                 } else {
 450                                         if (x <= 255) {
 451                                                 *s++ = 'C'; *s++ = (uint8_t)x;
 452                                                 doff += 2;
 453                                         } else if (x <= 65535) {
 454                                                 *s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
 455                                                 s += 2; doff += 3;
 456                                         } else {
 457                                                 *s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
 458                                                 s += 4; doff += 5;
 459                                                 if (x > 4294967295ll)
 460                                                         fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
 461                                                                         (long long)fp->n_lines, x);
 462                                         }
 463                                 }
 464                         } else if (type == 'f') {
 465                                 s = alloc_data(b, doff + 5) + doff;
 466                                 *s++ = 'f';
 467                                 *(float*)s = (float)atof(str->s + 5);
 468                                 s += 4; doff += 5;
 469                         } else if (type == 'd') {
 470                                 s = alloc_data(b, doff + 9) + doff;
 471                                 *s++ = 'd';
 472                                 *(float*)s = (float)atof(str->s + 9);
 473                                 s += 8; doff += 9;
 474                         } else if (type == 'Z' || type == 'H') {
 475                                 int size = 1 + (str->l - 5) + 1;
 476                                 if (type == 'H') { // check whether the hex string is valid
 477                                         int i;
 478                                         if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
 479                                         for (i = 0; i < str->l - 5; ++i) {
 480                                                 int c = toupper(str->s[5 + i]);
 481                                                 if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
 482                                                         parse_error(fp->n_lines, "invalid hex character");
 483                                         }
 484                                 }
 485                                 s = alloc_data(b, doff + size) + doff;
 486                                 *s++ = type;
 487                                 memcpy(s, str->s + 5, str->l - 5);
 488                                 s[str->l - 5] = 0;
 489                                 doff += size;
 490                         } else parse_error(fp->n_lines, "unrecognized type");
 491                         if (dret == '\n' || dret == '\r') break;
 492                 }
 493         }
 494         b->l_aux = doff - doff0;
 495         b->data_len = doff;
 496         return z;
 497 }
 498
 499 tamFile sam_open(const char *fn)
 500 {
 501         tamFile fp;
 502         gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
 503         if (gzfp == 0) return 0;
 504         fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
 505         fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
 506         fp->fp = gzfp;
 507         fp->ks = ks_init(fp->fp);
 508         return fp;
 509 }
 510
 511 void sam_close(tamFile fp)
 512 {
 513         if (fp) {
 514                 ks_destroy(fp->ks);
 515                 gzclose(fp->fp);
 516                 free(fp->str->s); free(fp->str);
 517                 free(fp);
 518         }
 519 }