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