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 unsigned short bam_char2flag_table[256] = {
  40         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  41         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  42         0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
  43         0,BAM_FREAD1,BAM_FREAD2,0, 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         BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
  46         0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
  47         BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,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         0,0,0,0, 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         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 };
  57
  58 char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
  59
  60 struct __tamFile_t {
  61         gzFile fp;
  62         kstream_t *ks;
  63         kstring_t *str;
  64         uint64_t n_lines;
  65         int is_first;
  66 };
  67
  68 char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
  69 {
  70         char **list = 0, *s;
  71         int n = 0, dret, m = 0;
  72         gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
  73         kstream_t *ks;
  74         kstring_t *str;
  75         str = (kstring_t*)calloc(1, sizeof(kstring_t));
  76         ks = ks_init(fp);
  77         while (ks_getuntil(ks, '\n', str, &dret) > 0) {
  78                 if (n == m) {
  79                         m = m? m << 1 : 16;
  80                         list = (char**)realloc(list, m * sizeof(char*));
  81                 }
  82                 if (str->s[str->l-1] == '\r')
  83                         str->s[--str->l] = '\0';
  84                 s = list[n++] = (char*)calloc(str->l + 1, 1);
  85                 strcpy(s, str->s);
  86         }
  87         ks_destroy(ks);
  88         gzclose(fp);
  89         free(str->s); free(str);
  90         *_n = n;
  91         return list;
  92 }
  93
  94 static bam_header_t *hash2header(const kh_ref_t *hash)
  95 {
  96         bam_header_t *header;
  97         khiter_t k;
  98         header = bam_header_init();
  99         header->n_targets = kh_size(hash);
 100         header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
 101         header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
 102         for (k = kh_begin(hash); k != kh_end(hash); ++k) {
 103                 if (kh_exist(hash, k)) {
 104                         int i = (int)kh_value(hash, k);
 105                         header->target_name[i] = (char*)kh_key(hash, k);
 106                         header->target_len[i] = kh_value(hash, k)>>32;
 107                 }
 108         }
 109         bam_init_header_hash(header);
 110         return header;
 111 }
 112 bam_header_t *sam_header_read2(const char *fn)
 113 {
 114         bam_header_t *header;
 115         int c, dret, ret;
 116         gzFile fp;
 117         kstream_t *ks;
 118         kstring_t *str;
 119         kh_ref_t *hash;
 120         khiter_t k;
 121         if (fn == 0) return 0;
 122         fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
 123         if (fp == 0) return 0;
 124         hash = kh_init(ref);
 125         ks = ks_init(fp);
 126         str = (kstring_t*)calloc(1, sizeof(kstring_t));
 127         while (ks_getuntil(ks, 0, str, &dret) > 0) {
 128                 char *s = strdup(str->s);
 129                 int len, i;
 130                 i = kh_size(hash);
 131                 ks_getuntil(ks, 0, str, &dret);
 132                 len = atoi(str->s);
 133                 k = kh_put(ref, hash, s, &ret);
 134                 kh_value(hash, k) = (uint64_t)len<<32 | i;
 135                 if (dret != '\n')
 136                         while ((c = ks_getc(ks)) != '\n' && c != -1);
 137         }
 138         ks_destroy(ks);
 139         gzclose(fp);
 140         free(str->s); free(str);
 141         fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
 142         header = hash2header(hash);
 143         kh_destroy(ref, hash);
 144         return header;
 145 }
 146 static inline uint8_t *alloc_data(bam1_t *b, int size)
 147 {
 148         if (b->m_data < size) {
 149                 b->m_data = size;
 150                 kroundup32(b->m_data);
 151                 b->data = (uint8_t*)realloc(b->data, b->m_data);
 152         }
 153         return b->data;
 154 }
 155 static inline void parse_error(int64_t n_lines, const char * __restrict msg)
 156 {
 157         fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
 158         abort();
 159 }
 160 static inline void append_text(bam_header_t *header, kstring_t *str)
 161 {
 162         int x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
 163         kroundup32(x); kroundup32(y);
 164         if (x < y) header->text = (char*)realloc(header->text, y);
 165         strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
 166         header->l_text += str->l + 1;
 167         header->text[header->l_text] = 0;
 168 }
 169
 170 int sam_header_parse_rg(bam_header_t *h)
 171 {
 172         kstring_t *rgid, *rglib;
 173         char *p, *q, *s, *r;
 174         int n = 0;
 175
 176         // free
 177         if (h == 0) return 0;
 178         bam_strmap_destroy(h->rg2lib); h->rg2lib = 0;
 179         if (h->l_text < 3) return 0;
 180         // parse @RG lines
 181         h->rg2lib = bam_strmap_init();
 182         rgid = calloc(1, sizeof(kstring_t));
 183         rglib = calloc(1, sizeof(kstring_t));
 184         s = h->text;
 185         while ((s = strstr(s, "@RG")) != 0) {
 186                 if (rgid->l && rglib->l) {
 187                         bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
 188                         ++n;
 189                 }
 190                 rgid->l = rglib->l = 0;
 191                 s += 3;
 192                 r = s;
 193                 if ((p = strstr(s, "ID:")) != 0) {
 194                         q = p + 3;
 195                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 196                         kputsn(q, p - q, rgid);
 197                 } else {
 198                         fprintf(stderr, "[bam_header_parse] missing ID tag in @RG lines.\n");
 199                         break;
 200                 }
 201                 if (r < p) r = p;
 202                 if ((p = strstr(s, "LB:")) != 0) {
 203                         q = p + 3;
 204                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 205                         kputsn(q, p - q, rglib);
 206                 } else {
 207                         fprintf(stderr, "[bam_header_parse] missing LB tag in @RG lines.\n");
 208                         break;
 209                 }
 210                 if (r < p) r = p;
 211                 s = r + 3;
 212         }
 213         if (rgid->l && rglib->l) {
 214                 bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
 215                 ++n;
 216         }
 217         free(rgid->s); free(rgid);
 218         free(rglib->s); free(rglib);
 219         if (n == 0) {
 220                 bam_strmap_destroy(h->rg2lib);
 221                 h->rg2lib = 0;
 222         }
 223         return n;
 224 }
 225
 226 int sam_header_parse(bam_header_t *h)
 227 {
 228         int i;
 229         char *s, *p, *q, *r;
 230
 231         // free
 232         free(h->target_len); free(h->target_name);
 233         h->n_targets = 0; h->target_len = 0; h->target_name = 0;
 234         if (h->l_text < 3) return 0;
 235         // count number of @SQ
 236         s = h->text;
 237         while ((s = strstr(s, "@SQ")) != 0) {
 238                 ++h->n_targets;
 239                 s += 3;
 240         }
 241         if (h->n_targets == 0) return 0;
 242         h->target_len = (uint32_t*)calloc(h->n_targets, 4);
 243         h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
 244         // parse @SQ lines
 245         i = 0;
 246         s = h->text;
 247         while ((s = strstr(s, "@SQ")) != 0) {
 248                 s += 3;
 249                 r = s;
 250                 if ((p = strstr(s, "SN:")) != 0) {
 251                         q = p + 3;
 252                         for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
 253                         h->target_name[i] = (char*)calloc(p - q + 1, 1);
 254                         strncpy(h->target_name[i], q, p - q);
 255                 } else goto header_err_ret;
 256                 if (r < p) r = p;
 257                 if ((p = strstr(s, "LN:")) != 0) h->target_len[i] = strtol(p + 3, 0, 10);
 258                 else goto header_err_ret;
 259                 if (r < p) r = p;
 260                 s = r + 3;
 261                 ++i;
 262         }
 263         sam_header_parse_rg(h);
 264         return h->n_targets;
 265
 266 header_err_ret:
 267         fprintf(stderr, "[bam_header_parse] missing SN or LN tag in @SQ lines.\n");
 268         free(h->target_len); free(h->target_name);
 269         h->n_targets = 0; h->target_len = 0; h->target_name = 0;
 270         return 0;
 271 }
 272
 273 bam_header_t *sam_header_read(tamFile fp)
 274 {
 275         int ret, dret;
 276         bam_header_t *header = bam_header_init();
 277         kstring_t *str = fp->str;
 278         while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
 279                 str->s[str->l] = dret; // note that str->s is NOT null terminated!!
 280                 append_text(header, str);
 281                 if (dret != '\n') {
 282                         ret = ks_getuntil(fp->ks, '\n', str, &dret);
 283                         str->s[str->l] = '\n'; // NOT null terminated!!
 284                         append_text(header, str);
 285                 }
 286                 ++fp->n_lines;
 287         }
 288         sam_header_parse(header);
 289         bam_init_header_hash(header);
 290         fp->is_first = 1;
 291         return header;
 292 }
 293
 294 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 295 {
 296         int ret, doff, doff0, dret, z = 0;
 297         bam1_core_t *c = &b->core;
 298         kstring_t *str = fp->str;
 299         kstream_t *ks = fp->ks;
 300
 301         if (fp->is_first) {
 302                 fp->is_first = 0;
 303                 ret = str->l;
 304         } else {
 305                 do { // special consideration for empty lines
 306                         ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
 307                         if (ret >= 0) z += str->l + 1;
 308                 } while (ret == 0);
 309         }
 310         if (ret < 0) return -1;
 311         ++fp->n_lines;
 312         doff = 0;
 313
 314         { // name
 315                 c->l_qname = strlen(str->s) + 1;
 316                 memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
 317                 doff += c->l_qname;
 318         }
 319         { // flag
 320                 long flag;
 321                 char *s;
 322                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 323                 flag = strtol((char*)str->s, &s, 0);
 324                 if (*s) { // not the end of the string
 325                         flag = 0;
 326                         for (s = str->s; *s; ++s)
 327                                 flag |= bam_char2flag_table[(int)*s];
 328                 }
 329                 c->flag = flag;
 330         }
 331         { // tid, pos, qual
 332                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
 333                 if (c->tid < 0 && strcmp(str->s, "*")) {
 334                         if (header->n_targets == 0) {
 335                                 fprintf(stderr, "[sam_read1] missing header? Abort!\n");
 336                                 exit(1);
 337                         } else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
 338                 }
 339                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 340                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
 341                 if (ret < 0) return -2;
 342         }
 343         { // cigar
 344                 char *s, *t;
 345                 int i, op;
 346                 long x;
 347                 c->n_cigar = 0;
 348                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
 349                 z += str->l + 1;
 350                 if (str->s[0] != '*') {
 351                         for (s = str->s; *s; ++s) {
 352                                 if (isalpha(*s)) ++c->n_cigar;
 353                                 else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
 354                         }
 355                         b->data = alloc_data(b, doff + c->n_cigar * 4);
 356                         for (i = 0, s = str->s; i != c->n_cigar; ++i) {
 357                                 x = strtol(s, &t, 10);
 358                                 op = toupper(*t);
 359                                 if (op == 'M') op = BAM_CMATCH;
 360                                 else if (op == 'I') op = BAM_CINS;
 361                                 else if (op == 'D') op = BAM_CDEL;
 362                                 else if (op == 'N') op = BAM_CREF_SKIP;
 363                                 else if (op == 'S') op = BAM_CSOFT_CLIP;
 364                                 else if (op == 'H') op = BAM_CHARD_CLIP;
 365                                 else if (op == 'P') op = BAM_CPAD;
 366                                 else parse_error(fp->n_lines, "invalid CIGAR operation");
 367                                 s = t + 1;
 368                                 bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
 369                         }
 370                         if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
 371                         c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
 372                         doff += c->n_cigar * 4;
 373                 } else c->bin = bam_reg2bin(c->pos, c->pos + 1);
 374         }
 375         { // mtid, mpos, isize
 376                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 377                 c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
 378                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 379                 c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
 380                 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
 381                 c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
 382                 if (ret < 0) return -4;
 383         }
 384         { // seq and qual
 385                 int i;
 386                 uint8_t *p;
 387                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
 388                 z += str->l + 1;
 389                 c->l_qseq = strlen(str->s);
 390                 if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
 391                         parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
 392                 p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
 393                 memset(p, 0, (c->l_qseq+1)/2);
 394                 for (i = 0; i < c->l_qseq; ++i)
 395                         p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
 396                 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
 397                 z += str->l + 1;
 398                 if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
 399                         parse_error(fp->n_lines, "sequence and quality are inconsistent");
 400                 p += (c->l_qseq+1)/2;
 401                 if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
 402                 else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
 403                 doff += c->l_qseq + (c->l_qseq+1)/2;
 404         }
 405         doff0 = doff;
 406         if (dret != '\n' && dret != '\r') { // aux
 407                 while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
 408                         uint8_t *s, type, key[2];
 409                         z += str->l + 1;
 410                         if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
 411                                 parse_error(fp->n_lines, "missing colon in auxiliary data");
 412                         key[0] = str->s[0]; key[1] = str->s[1];
 413                         type = str->s[3];
 414                         s = alloc_data(b, doff + 3) + doff;
 415                         s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
 416                         if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
 417                                 s = alloc_data(b, doff + 2) + doff;
 418                                 *s++ = 'A'; *s = str->s[5];
 419                                 doff += 2;
 420                         } else if (type == 'I' || type == 'i') {
 421                                 long long x;
 422                                 s = alloc_data(b, doff + 5) + doff;
 423                                 x = (long long)atoll(str->s + 5);
 424                                 if (x < 0) {
 425                                         if (x >= -127) {
 426                                                 *s++ = 'c'; *(int8_t*)s = (int8_t)x;
 427                                                 s += 1; doff += 2;
 428                                         } else if (x >= -32767) {
 429                                                 *s++ = 's'; *(int16_t*)s = (int16_t)x;
 430                                                 s += 2; doff += 3;
 431                                         } else {
 432                                                 *s++ = 'i'; *(int32_t*)s = (int32_t)x;
 433                                                 s += 4; doff += 5;
 434                                                 if (x < -2147483648ll)
 435                                                         fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
 436                                                                         (long long)fp->n_lines, x);
 437                                         }
 438                                 } else {
 439                                         if (x <= 255) {
 440                                                 *s++ = 'C'; *s++ = (uint8_t)x;
 441                                                 doff += 2;
 442                                         } else if (x <= 65535) {
 443                                                 *s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
 444                                                 s += 2; doff += 3;
 445                                         } else {
 446                                                 *s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
 447                                                 s += 4; doff += 5;
 448                                                 if (x > 4294967295ll)
 449                                                         fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
 450                                                                         (long long)fp->n_lines, x);
 451                                         }
 452                                 }
 453                         } else if (type == 'f') {
 454                                 s = alloc_data(b, doff + 5) + doff;
 455                                 *s++ = 'f';
 456                                 *(float*)s = (float)atof(str->s + 5);
 457                                 s += 4; doff += 5;
 458                         } else if (type == 'd') {
 459                                 s = alloc_data(b, doff + 9) + doff;
 460                                 *s++ = 'd';
 461                                 *(float*)s = (float)atof(str->s + 9);
 462                                 s += 8; doff += 9;
 463                         } else if (type == 'Z' || type == 'H') {
 464                                 int size = 1 + (str->l - 5) + 1;
 465                                 if (type == 'H') { // check whether the hex string is valid
 466                                         int i;
 467                                         if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
 468                                         for (i = 0; i < str->l - 5; ++i) {
 469                                                 int c = toupper(str->s[5 + i]);
 470                                                 if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
 471                                                         parse_error(fp->n_lines, "invalid hex character");
 472                                         }
 473                                 }
 474                                 s = alloc_data(b, doff + size) + doff;
 475                                 *s++ = type;
 476                                 memcpy(s, str->s + 5, str->l - 5);
 477                                 s[str->l - 5] = 0;
 478                                 doff += size;
 479                         } else parse_error(fp->n_lines, "unrecognized type");
 480                         if (dret == '\n' || dret == '\r') break;
 481                 }
 482         }
 483         b->l_aux = doff - doff0;
 484         b->data_len = doff;
 485         return z;
 486 }
 487
 488 tamFile sam_open(const char *fn)
 489 {
 490         tamFile fp;
 491         gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
 492         if (gzfp == 0) return 0;
 493         fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
 494         fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
 495         fp->fp = gzfp;
 496         fp->ks = ks_init(fp->fp);
 497         return fp;
 498 }
 499
 500 void sam_close(tamFile fp)
 501 {
 502         if (fp) {
 503                 ks_destroy(fp->ks);
 504                 gzclose(fp->fp);
 505                 free(fp->str->s); free(fp->str);
 506                 free(fp);
 507         }
 508 }