samtools/bam_import.c.pysam.c

   1 #include "pysam.h"
   2
   3 #include <zlib.h>
   4 #include <stdio.h>
   5 #include <ctype.h>
   6 #include <string.h>
   7 #include <stdlib.h>
   8 #include <unistd.h>
   9 #include <assert.h>
  10 #ifdef _WIN32
  11 #include <fcntl.h>
  12 #endif
  13 #include "kstring.h"
  14 #include "bam.h"
  15 #include "sam_header.h"
  16 #include "kseq.h"
  17 #include "khash.h"
  18
  19 KSTREAM_INIT(gzFile, gzread, 8192)
  20 KHASH_MAP_INIT_STR(ref, uint64_t)
  21
  22 void bam_init_header_hash(bam_header_t *header);
  23 void bam_destroy_header_hash(bam_header_t *header);
  24 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
  25
  26 unsigned char bam_nt16_table[256] = {
  27         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  28         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  29         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  30          1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,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, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
  34         15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 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         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
  42         15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
  43 };
  44
  45 unsigned short bam_char2flag_table[256] = {
  46         0,0,0,0, 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         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  49         0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  50         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  51         BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
  52         0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
  53         BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,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         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  61         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
  62 };
  63
  64 char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
  65
  66 struct __tamFile_t {
  67         gzFile fp;
  68         kstream_t *ks;
  69         kstring_t *str;
  70         uint64_t n_lines;
  71         int is_first;
  72 };
  73
  74 char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
  75 {
  76         char **list = 0, *s;
  77         int n = 0, dret, m = 0;
  78         gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
  79         kstream_t *ks;
  80         kstring_t *str;
  81         str = (kstring_t*)calloc(1, sizeof(kstring_t));
  82         ks = ks_init(fp);
  83         while (ks_getuntil(ks, '\n', str, &dret) > 0) {
  84                 if (n == m) {
  85                         m = m? m << 1 : 16;
  86                         list = (char**)realloc(list, m * sizeof(char*));
  87                 }
  88                 if (str->s[str->l-1] == '\r')
  89                         str->s[--str->l] = '\0';
  90                 s = list[n++] = (char*)calloc(str->l + 1, 1);
  91                 strcpy(s, str->s);
  92         }
  93         ks_destroy(ks);
  94         gzclose(fp);
  95         free(str->s); free(str);
  96         *_n = n;
  97         return list;
  98 }
  99
 100 static bam_header_t *hash2header(const kh_ref_t *hash)
 101 {
 102         bam_header_t *header;
 103         khiter_t k;
 104         header = bam_header_init();
 105         header->n_targets = kh_size(hash);
 106         header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
 107         header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
 108         for (k = kh_begin(hash); k != kh_end(hash); ++k) {
 109                 if (kh_exist(hash, k)) {
 110                         int i = (int)kh_value(hash, k);
 111                         header->target_name[i] = (char*)kh_key(hash, k);
 112                         header->target_len[i] = kh_value(hash, k)>>32;
 113                 }
 114         }
 115         bam_init_header_hash(header);
 116         return header;
 117 }
 118 bam_header_t *sam_header_read2(const char *fn)
 119 {
 120         bam_header_t *header;
 121         int c, dret, ret, error = 0;
 122         gzFile fp;
 123         kstream_t *ks;
 124         kstring_t *str;
 125         kh_ref_t *hash;
 126         khiter_t k;
 127         if (fn == 0) return 0;
 128         fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
 129         if (fp == 0) return 0;
 130         hash = kh_init(ref);
 131         ks = ks_init(fp);
 132         str = (kstring_t*)calloc(1, sizeof(kstring_t));
 133         while (ks_getuntil(ks, 0, str, &dret) > 0) {
 134                 char *s = strdup(str->s);
 135                 int len, i;
 136                 i = kh_size(hash);
 137                 ks_getuntil(ks, 0, str, &dret);
 138                 len = atoi(str->s);
 139                 k = kh_put(ref, hash, s, &ret);
 140                 if (ret == 0) {
 141                         fprintf(pysamerr, "[sam_header_read2] duplicated sequence name: %s\n", s);
 142                         error = 1;
 143                 }
 144                 kh_value(hash, k) = (uint64_t)len<<32 | i;
 145                 if (dret != '\n')
 146                         while ((c = ks_getc(ks)) != '\n' && c != -1);
 147         }
 148         ks_destroy(ks);
 149         gzclose(fp);
 150         free(str->s); free(str);
 151         fprintf(pysamerr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
 152         if (error) return 0;
 153         header = hash2header(hash);
 154         kh_destroy(ref, hash);
 155         return header;
 156 }
 157 static inline uint8_t *alloc_data(bam1_t *b, int size)
 158 {
 159         if (b->m_data < size) {
 160                 b->m_data = size;
 161                 kroundup32(b->m_data);
 162                 b->data = (uint8_t*)realloc(b->data, b->m_data);
 163         }
 164         return b->data;
 165 }
 166 static inline void parse_error(int64_t n_lines, const char * __restrict msg)
 167 {
 168         fprintf(pysamerr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
 169         abort();
 170 }
 171 static inline void append_text(bam_header_t *header, kstring_t *str)
 172 {
 173         size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
 174         kroundup32(x); kroundup32(y);
 175         if (x < y)
 176     {
 177         header->n_text = y;
 178         header->text = (char*)realloc(header->text, y);
 179         if ( !header->text )
 180         {
 181             fprintf(pysamerr,"realloc failed to alloc %ld bytes\n", y);
 182             abort();
 183         }
 184     }
 185     // Sanity check
 186     if ( header->l_text+str->l+1 >= header->n_text )
 187     {
 188         fprintf(pysamerr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,header->n_text,x,y);
 189         abort();
 190     }
 191         strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
 192         header->l_text += str->l + 1;
 193         header->text[header->l_text] = 0;
 194 }
 195
 196 int sam_header_parse(bam_header_t *h)
 197 {
 198         char **tmp;
 199         int i;
 200         free(h->target_len); free(h->target_name);
 201         h->n_targets = 0; h->target_len = 0; h->target_name = 0;
 202         if (h->l_text < 3) return 0;
 203         if (h->dict == 0) h->dict = sam_header_parse2(h->text);
 204         tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
 205         if (h->n_targets == 0) return 0;
 206         h->target_name = calloc(h->n_targets, sizeof(void*));
 207         for (i = 0; i < h->n_targets; ++i)
 208                 h->target_name[i] = strdup(tmp[i]);
 209         free(tmp);
 210         tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
 211         h->target_len = calloc(h->n_targets, 4);
 212         for (i = 0; i < h->n_targets; ++i)
 213                 h->target_len[i] = atoi(tmp[i]);
 214         free(tmp);
 215         return h->n_targets;
 216 }
 217
 218 bam_header_t *sam_header_read(tamFile fp)
 219 {
 220         int ret, dret;
 221         bam_header_t *header = bam_header_init();
 222         kstring_t *str = fp->str;
 223         while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
 224                 str->s[str->l] = dret; // note that str->s is NOT null terminated!!
 225                 append_text(header, str);
 226                 if (dret != '\n') {
 227                         ret = ks_getuntil(fp->ks, '\n', str, &dret);
 228                         str->s[str->l] = '\n'; // NOT null terminated!!
 229                         append_text(header, str);
 230                 }
 231                 ++fp->n_lines;
 232         }
 233         sam_header_parse(header);
 234         bam_init_header_hash(header);
 235         fp->is_first = 1;
 236         return header;
 237 }
 238
 239 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 240 {
 241         int ret, doff, doff0, dret, z = 0;
 242         bam1_core_t *c = &b->core;
 243         kstring_t *str = fp->str;
 244         kstream_t *ks = fp->ks;
 245
 246         if (fp->is_first) {
 247                 fp->is_first = 0;
 248                 ret = str->l;
 249         } else {
 250                 do { // special consideration for empty lines
 251                         ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
 252                         if (ret >= 0) z += str->l + 1;
 253                 } while (ret == 0);
 254         }
 255         if (ret < 0) return -1;
 256         ++fp->n_lines;
 257         doff = 0;
 258
 259         { // name
 260                 c->l_qname = strlen(str->s) + 1;
 261                 memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
 262                 doff += c->l_qname;
 263         }
 264         { // flag
 265                 long flag;
 266                 char *s;
 267                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 268                 flag = strtol((char*)str->s, &s, 0);
 269                 if (*s) { // not the end of the string
 270                         flag = 0;
 271                         for (s = str->s; *s; ++s)
 272                                 flag |= bam_char2flag_table[(int)*s];
 273                 }
 274                 c->flag = flag;
 275         }
 276         { // tid, pos, qual
 277                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
 278                 if (c->tid < 0 && strcmp(str->s, "*")) {
 279                         if (header->n_targets == 0) {
 280                                 fprintf(pysamerr, "[sam_read1] missing header? Abort!\n");
 281                                 exit(1);
 282                         } else fprintf(pysamerr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
 283                 }
 284                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 285                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
 286                 if (ret < 0) return -2;
 287         }
 288         { // cigar
 289                 char *s, *t;
 290                 int i, op;
 291                 long x;
 292                 c->n_cigar = 0;
 293                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
 294                 z += str->l + 1;
 295                 if (str->s[0] != '*') {
 296                         for (s = str->s; *s; ++s) {
 297                                 if (isalpha(*s)) ++c->n_cigar;
 298                                 else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
 299                         }
 300                         b->data = alloc_data(b, doff + c->n_cigar * 4);
 301                         for (i = 0, s = str->s; i != c->n_cigar; ++i) {
 302                                 x = strtol(s, &t, 10);
 303                                 op = toupper(*t);
 304                                 if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
 305                                 else if (op == 'I') op = BAM_CINS;
 306                                 else if (op == 'D') op = BAM_CDEL;
 307                                 else if (op == 'N') op = BAM_CREF_SKIP;
 308                                 else if (op == 'S') op = BAM_CSOFT_CLIP;
 309                                 else if (op == 'H') op = BAM_CHARD_CLIP;
 310                                 else if (op == 'P') op = BAM_CPAD;
 311                                 else parse_error(fp->n_lines, "invalid CIGAR operation");
 312                                 s = t + 1;
 313                                 bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
 314                         }
 315                         if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
 316                         c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
 317                         doff += c->n_cigar * 4;
 318                 } else {
 319                         if (!(c->flag&BAM_FUNMAP)) {
 320                                 fprintf(pysamerr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
 321                                 c->flag |= BAM_FUNMAP;
 322                         }
 323                         c->bin = bam_reg2bin(c->pos, c->pos + 1);
 324                 }
 325         }
 326         { // mtid, mpos, isize
 327                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 328                 c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
 329                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 330                 c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 331                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 332                 c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
 333                 if (ret < 0) return -4;
 334         }
 335         { // seq and qual
 336                 int i;
 337                 uint8_t *p = 0;
 338                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
 339                 z += str->l + 1;
 340                 if (strcmp(str->s, "*")) {
 341                         c->l_qseq = strlen(str->s);
 342                         if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
 343                                 parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
 344                         p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
 345                         memset(p, 0, (c->l_qseq+1)/2);
 346                         for (i = 0; i < c->l_qseq; ++i)
 347                                 p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
 348                 } else c->l_qseq = 0;
 349                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
 350                 z += str->l + 1;
 351                 if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
 352                         parse_error(fp->n_lines, "sequence and quality are inconsistent");
 353                 p += (c->l_qseq+1)/2;
 354                 if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
 355                 else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
 356                 doff += c->l_qseq + (c->l_qseq+1)/2;
 357         }
 358         doff0 = doff;
 359         if (dret != '\n' && dret != '\r') { // aux
 360                 while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
 361                         uint8_t *s, type, key[2];
 362                         z += str->l + 1;
 363                         if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
 364                                 parse_error(fp->n_lines, "missing colon in auxiliary data");
 365                         key[0] = str->s[0]; key[1] = str->s[1];
 366                         type = str->s[3];
 367                         s = alloc_data(b, doff + 3) + doff;
 368                         s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
 369                         if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
 370                                 s = alloc_data(b, doff + 2) + doff;
 371                                 *s++ = 'A'; *s = str->s[5];
 372                                 doff += 2;
 373                         } else if (type == 'I' || type == 'i') {
 374                                 long long x;
 375                                 s = alloc_data(b, doff + 5) + doff;
 376                                 x = (long long)atoll(str->s + 5);
 377                                 if (x < 0) {
 378                                         if (x >= -127) {
 379                                                 *s++ = 'c'; *(int8_t*)s = (int8_t)x;
 380                                                 s += 1; doff += 2;
 381                                         } else if (x >= -32767) {
 382                                                 *s++ = 's'; *(int16_t*)s = (int16_t)x;
 383                                                 s += 2; doff += 3;
 384                                         } else {
 385                                                 *s++ = 'i'; *(int32_t*)s = (int32_t)x;
 386                                                 s += 4; doff += 5;
 387                                                 if (x < -2147483648ll)
 388                                                         fprintf(pysamerr, "Parse warning at line %lld: integer %lld is out of range.",
 389                                                                         (long long)fp->n_lines, x);
 390                                         }
 391                                 } else {
 392                                         if (x <= 255) {
 393                                                 *s++ = 'C'; *s++ = (uint8_t)x;
 394                                                 doff += 2;
 395                                         } else if (x <= 65535) {
 396                                                 *s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
 397                                                 s += 2; doff += 3;
 398                                         } else {
 399                                                 *s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
 400                                                 s += 4; doff += 5;
 401                                                 if (x > 4294967295ll)
 402                                                         fprintf(pysamerr, "Parse warning at line %lld: integer %lld is out of range.",
 403                                                                         (long long)fp->n_lines, x);
 404                                         }
 405                                 }
 406                         } else if (type == 'f') {
 407                                 s = alloc_data(b, doff + 5) + doff;
 408                                 *s++ = 'f';
 409                                 *(float*)s = (float)atof(str->s + 5);
 410                                 s += 4; doff += 5;
 411                         } else if (type == 'd') {
 412                                 s = alloc_data(b, doff + 9) + doff;
 413                                 *s++ = 'd';
 414                                 *(float*)s = (float)atof(str->s + 9);
 415                                 s += 8; doff += 9;
 416                         } else if (type == 'Z' || type == 'H') {
 417                                 int size = 1 + (str->l - 5) + 1;
 418                                 if (type == 'H') { // check whether the hex string is valid
 419                                         int i;
 420                                         if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
 421                                         for (i = 0; i < str->l - 5; ++i) {
 422                                                 int c = toupper(str->s[5 + i]);
 423                                                 if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
 424                                                         parse_error(fp->n_lines, "invalid hex character");
 425                                         }
 426                                 }
 427                                 s = alloc_data(b, doff + size) + doff;
 428                                 *s++ = type;
 429                                 memcpy(s, str->s + 5, str->l - 5);
 430                                 s[str->l - 5] = 0;
 431                                 doff += size;
 432                         } else if (type == 'B') {
 433                                 int32_t n = 0, Bsize, k = 0, size;
 434                                 char *p;
 435                                 if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
 436                                 Bsize = bam_aux_type2size(str->s[5]); // the size of each element
 437                                 for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array
 438                                         if (*p == ',') ++n;
 439                                 p = str->s + 7; // now p points to the first number in the array
 440                                 size = 6 + Bsize * n; // total number of bytes allocated to this tag
 441                                 s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
 442                                 *s++ = 'B'; *s++ = str->s[5];
 443                                 memcpy(s, &n, 4); s += 4; // write the number of elements
 444                                 if (str->s[5] == 'c')      while (p < str->s + str->l) ((int8_t*)s)[k++]   = (int8_t)strtol(p, &p, 0),   ++p;
 445                                 else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++]  = (uint8_t)strtol(p, &p, 0),  ++p;
 446                                 else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++]  = (int16_t)strtol(p, &p, 0),  ++p; // FIXME: avoid unaligned memory
 447                                 else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
 448                                 else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++]  = (int32_t)strtol(p, &p, 0),  ++p;
 449                                 else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
 450                                 else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++]    = (float)strtof(p, &p),       ++p;
 451                                 else parse_error(fp->n_lines, "unrecognized array type");
 452                                 s += Bsize * n; doff += size;
 453                         } else parse_error(fp->n_lines, "unrecognized type");
 454                         if (dret == '\n' || dret == '\r') break;
 455                 }
 456         }
 457         b->l_aux = doff - doff0;
 458         b->data_len = doff;
 459         return z;
 460 }
 461
 462 tamFile sam_open(const char *fn)
 463 {
 464         tamFile fp;
 465         gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
 466         if (gzfp == 0) return 0;
 467         fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
 468         fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
 469         fp->fp = gzfp;
 470         fp->ks = ks_init(fp->fp);
 471         return fp;
 472 }
 473
 474 void sam_close(tamFile fp)
 475 {
 476         if (fp) {
 477                 ks_destroy(fp->ks);
 478                 gzclose(fp->fp);
 479                 free(fp->str->s); free(fp->str);
 480                 free(fp);
 481         }
 482 }