| 1 |
#include "GCdbYank.h" |
| 2 |
#include "GBase.h" |
| 3 |
#include <ctype.h> |
| 4 |
|
| 5 |
#define ERR_READ "GCdbYank: error reading from file.\n" |
| 6 |
#define ERR_READFMT "GCdbYank read error: incorrect file format.\n" |
| 7 |
#define ERR_RANGEFMT "Sequence range parsing error for key '%s'\n" |
| 8 |
#define ERR_RANGE_INVALID "Invalid range (%d-%d) specified for sequence '%s' of length %d\n" |
| 9 |
// 1MB memory buffer: |
| 10 |
#define MAX_MEM_RECSIZE 1048576 |
| 11 |
#ifndef O_BINARY |
| 12 |
#define O_BINARY 0x0000 |
| 13 |
#endif |
| 14 |
|
| 15 |
|
| 16 |
#ifdef ENABLE_COMPRESSION |
| 17 |
|
| 18 |
GCdbZFasta::GCdbZFasta(FILE* azf, int zrsize, char* r_delim) { |
| 19 |
zrecsize=-1; |
| 20 |
zpos=0; |
| 21 |
recdelim=Gstrdup(r_delim); |
| 22 |
zf=azf; |
| 23 |
decomp_start(zrsize); |
| 24 |
chrhandler=new GFastaCharHandler(recdelim); |
| 25 |
} |
| 26 |
|
| 27 |
GCdbZFasta::~GCdbZFasta() { |
| 28 |
//if (zf!=NULL && zf!=stdout && zf!=stdin) fclose(zf); |
| 29 |
// FULL_FLUSH method instead of finish |
| 30 |
delete chrhandler; |
| 31 |
GFREE(recdelim); |
| 32 |
decomp_end(); |
| 33 |
} |
| 34 |
|
| 35 |
void GCdbZFasta::decomp_start(int zrsize) { |
| 36 |
zstream.zalloc = (alloc_func)0; |
| 37 |
zstream.zfree = (free_func)0; |
| 38 |
zstream.opaque = (voidpf)0; |
| 39 |
zstream.next_in = (Bytef*)sbuf; |
| 40 |
zstream.avail_in = 0; |
| 41 |
zstream.next_out = (Bytef*)lbuf; |
| 42 |
int err = inflateInit(&zstream); |
| 43 |
if (err!=Z_OK) |
| 44 |
GMessage("Error at inflateInit()\n"); |
| 45 |
//-- now read and discard the first record, so we can use random access later |
| 46 |
// (needed by zlib) |
| 47 |
int bytes_read=fread(sbuf, 1, zrsize, zf); |
| 48 |
if (bytes_read<zrsize) |
| 49 |
GError("Error reading 1st record from zrec file\n"); |
| 50 |
zstream.next_in = (Bytef*)sbuf; |
| 51 |
zstream.avail_in = bytes_read; |
| 52 |
//decompress first chunk |
| 53 |
zstream.next_out = (Bytef*)lbuf; |
| 54 |
zstream.avail_out = GCDBZ_LBUF_LEN; |
| 55 |
err = inflate(&zstream, Z_SYNC_FLUSH); |
| 56 |
if (err !=Z_OK && err!=Z_STREAM_END) |
| 57 |
GError("GCdbZFasta error: 1st record inflate failed! (err=%d)\n",err); |
| 58 |
} |
| 59 |
|
| 60 |
void GCdbZFasta::decomp_end() { |
| 61 |
int err = inflateEnd(&zstream); |
| 62 |
if (err!=Z_OK) |
| 63 |
GError("Error at inflateEnd() (err=%d)\n", err); |
| 64 |
} |
| 65 |
|
| 66 |
|
| 67 |
//fasta record decompress |
| 68 |
//returns: the number of bytes decompressed |
| 69 |
int GCdbZFasta::decompress(FastaSeq& rec, int csize, int zfofs, charFunc* seqCallBack) { |
| 70 |
if (zfofs>=0) { |
| 71 |
if (fseek(zf, zfofs, 0)) |
| 72 |
GError("GCdbZFasta::decompress: error fseek() to %d\n", zfofs); |
| 73 |
} |
| 74 |
else |
| 75 |
if (feof(zf)) return 0; |
| 76 |
bool in_rec=true; |
| 77 |
int err=0; |
| 78 |
int total_read=0; |
| 79 |
int total_written=0; |
| 80 |
chrhandler->init(&rec, seqCallBack); |
| 81 |
while (in_rec) { // read loop |
| 82 |
int to_read=0; |
| 83 |
int bytes_read=0; |
| 84 |
if (csize<=0) { //read one byte at a time |
| 85 |
to_read=1; |
| 86 |
int c; |
| 87 |
if ((c =fgetc(zf))!=EOF) { |
| 88 |
bytes_read = 1; |
| 89 |
sbuf[0]=c; |
| 90 |
} |
| 91 |
else { |
| 92 |
//bytes_read=0; |
| 93 |
return 0; //eof |
| 94 |
} |
| 95 |
total_read+=bytes_read; |
| 96 |
} |
| 97 |
else { |
| 98 |
to_read = csize-total_read>GCDBZ_SBUF_LEN ? |
| 99 |
GCDBZ_SBUF_LEN : csize-total_read; |
| 100 |
// check for csize vs bytes_read match: |
| 101 |
if (to_read==0) return 0; |
| 102 |
bytes_read=fread(sbuf, 1, to_read, zf); |
| 103 |
if (bytes_read!=to_read) |
| 104 |
GError("Error reading from zrec file\n"); |
| 105 |
total_read+=bytes_read; |
| 106 |
in_rec=(total_read<csize); |
| 107 |
} |
| 108 |
if (bytes_read==0) { |
| 109 |
//GMessage("bytes_read = 0\n"); |
| 110 |
return 0; |
| 111 |
} |
| 112 |
if (in_rec && bytes_read<to_read) in_rec=false; |
| 113 |
zstream.next_in = (Bytef*)sbuf; |
| 114 |
zstream.avail_in = bytes_read; |
| 115 |
|
| 116 |
do { //decompression loop |
| 117 |
zstream.next_out = (Bytef*)lbuf; |
| 118 |
zstream.avail_out = GCDBZ_LBUF_LEN; |
| 119 |
uLong t_out=zstream.total_out; |
| 120 |
err = inflate(&zstream, Z_SYNC_FLUSH); |
| 121 |
uLong toWrite=zstream.total_out-t_out; |
| 122 |
if (toWrite>0) { |
| 123 |
/* if (fwrite(lbuf, 1, toWrite, outf)<toWrite) { |
| 124 |
GError("Error writing inflated chunk!\n"); |
| 125 |
} */ |
| 126 |
for (unsigned int i=0;i<toWrite;i++) |
| 127 |
chrhandler->processChar(lbuf[i]); |
| 128 |
|
| 129 |
total_written+=toWrite; |
| 130 |
} |
| 131 |
if (err==Z_STREAM_END) { |
| 132 |
in_rec=false; |
| 133 |
if (total_written==0) { |
| 134 |
GMessage("Z_STREAM_END found but total_written=0!\n"); |
| 135 |
} |
| 136 |
break; |
| 137 |
} |
| 138 |
else if (err !=Z_OK) |
| 139 |
GError("GCdbZFasta error: inflate failed! (err=%d)\n",err); |
| 140 |
} while (zstream.avail_in!=0); //decompression loop |
| 141 |
} //read loop |
| 142 |
chrhandler->done(); |
| 143 |
/*if (err!=Z_STREAM_END) { |
| 144 |
GError("decompress: Z_STREAM_END not found!\n"); |
| 145 |
}*/ |
| 146 |
return total_written; |
| 147 |
} |
| 148 |
|
| 149 |
GCdbZFasta* GCdbYank::openCdbz(char* p) { |
| 150 |
//in case this was not done before: |
| 151 |
gcvt_uint=(endian_test())? &uint32_sun : &uint32_x86; |
| 152 |
FILE* zf=fopen(p, "rb"); |
| 153 |
if (zf==NULL) { |
| 154 |
GMessage("Error: cannot open compressed file '%s'!\n",p); |
| 155 |
return NULL; |
| 156 |
} |
| 157 |
//check if the file is valid and read the length of the first record |
| 158 |
// |
| 159 |
char ztag[5]; |
| 160 |
ztag[4]='\0'; |
| 161 |
if (fread(ztag, 1, 4, zf)<4) { |
| 162 |
GMessage("Error reading header of compressed file '%s'\n",p); |
| 163 |
return NULL; |
| 164 |
} |
| 165 |
if (strcmp(ztag, "CDBZ")!=0) { |
| 166 |
GMessage("Error: file '%s' doesn't appear to be a zlib compressed cdb?\n",p); |
| 167 |
return NULL; |
| 168 |
} |
| 169 |
unsigned int zrecsize; |
| 170 |
if (fread((void*) &zrecsize,1,4,zf)<4) { |
| 171 |
GMessage("Error reading 1st compressed record size for file '%s'!\n",p); |
| 172 |
return NULL; |
| 173 |
} |
| 174 |
zrecsize=gcvt_uint(&zrecsize); |
| 175 |
return new GCdbZFasta(zf, zrecsize, recdelim); |
| 176 |
} |
| 177 |
#else |
| 178 |
static const char err_COMPRESSED[]="Error: compression detected but not compiled in!\n"; |
| 179 |
#endif |
| 180 |
//decompression stuff |
| 181 |
|
| 182 |
|
| 183 |
void inplace_Lower(char* c) { |
| 184 |
char *p=c; |
| 185 |
while (*p!='\0') { *p=tolower(*p);p++; } |
| 186 |
} |
| 187 |
|
| 188 |
void buf_get(GCDBuffer* b, uint32& pos, char *buf, unsigned int len) { |
| 189 |
int r; |
| 190 |
while (len > 0) { |
| 191 |
r = b->get(buf,len); |
| 192 |
if (r == -1) GError(ERR_READ); |
| 193 |
if (r == 0) |
| 194 |
GError(ERR_READFMT); |
| 195 |
pos += r; |
| 196 |
buf += r; |
| 197 |
len -= r; |
| 198 |
} |
| 199 |
} |
| 200 |
|
| 201 |
void buf_getnum(GCDBuffer* b, uint32& pos, uint32 *num) { |
| 202 |
char buf[4]; |
| 203 |
buf_get(b, pos, buf, 4); |
| 204 |
uint32_unpack(buf,num); |
| 205 |
} |
| 206 |
|
| 207 |
|
| 208 |
int read_dbinfo(int fd, char** fnameptr, cdbInfo& dbstat) { |
| 209 |
//this is messy due to the need of compatibility with the |
| 210 |
//old 32bit file-length |
| 211 |
char* dbname=*fnameptr; |
| 212 |
//read just the tag first: 4 bytes ID |
| 213 |
lseek(fd, -cdbInfoSIZE, SEEK_END); |
| 214 |
int r=read(fd, &dbstat, cdbInfoSIZE ); |
| 215 |
if (r!=cdbInfoSIZE) return 2; |
| 216 |
//GMessage("Size of dbstat=%d\n", cdbInfoSIZE); |
| 217 |
if (strncmp(dbstat.oldtag, "CIDX", 4)==0) { |
| 218 |
//old dbstat structure -- convert it |
| 219 |
dbstat.num_keys=gcvt_uint(&dbstat.oldnum[0]); |
| 220 |
dbstat.num_records=gcvt_uint(&dbstat.oldnum[1]); |
| 221 |
dbstat.dbsize=gcvt_uint(&dbstat.old_dbsize); |
| 222 |
dbstat.idxflags = gcvt_uint(&dbstat.old_idxflags); |
| 223 |
//position on the dbnamelen entry |
| 224 |
dbstat.dbnamelen = gcvt_uint(&dbstat.old_dbnamelen); |
| 225 |
//GMessage("dbnamelen=%d\n", dbstat.dbnamelen); |
| 226 |
lseek(fd, -(off_t)(cdbInfoSIZE-4+dbstat.dbnamelen), SEEK_END); |
| 227 |
} |
| 228 |
else if (strncmp(dbstat.tag, "CDBX", 4)!=0) { |
| 229 |
GMessage("Error: this doesn't appear to be a cdbfasta created file!\n"); |
| 230 |
return 1; |
| 231 |
} |
| 232 |
else { // new CDBX type: |
| 233 |
dbstat.dbsize = gcvt_offt(&dbstat.dbsize); |
| 234 |
dbstat.num_keys=gcvt_uint(&dbstat.num_keys); |
| 235 |
dbstat.num_records=gcvt_uint(&dbstat.num_records); |
| 236 |
dbstat.idxflags = gcvt_uint(&dbstat.idxflags); |
| 237 |
//position on the dbnamelen entry |
| 238 |
dbstat.dbnamelen = gcvt_uint(&dbstat.dbnamelen); |
| 239 |
//GMessage("dbnamelen=%d\n", dbstat.dbnamelen); |
| 240 |
lseek(fd, -(off_t)(cdbInfoSIZE+dbstat.dbnamelen), SEEK_END); |
| 241 |
} |
| 242 |
|
| 243 |
GMALLOC(dbname, dbstat.dbnamelen+1); |
| 244 |
dbname[dbstat.dbnamelen]='\0'; |
| 245 |
r=read(fd, dbname, dbstat.dbnamelen); |
| 246 |
*fnameptr=dbname; |
| 247 |
if (r!=dbstat.dbnamelen) |
| 248 |
return 2; |
| 249 |
return 0; |
| 250 |
} |
| 251 |
|
| 252 |
int parse_int(FILE* f, char* buf, const char* key, int& e) { |
| 253 |
char* p, *q; |
| 254 |
while (e!=EOF && isspace(e)) { //skip any spaces |
| 255 |
if (e=='\n') GError(ERR_RANGEFMT, key); |
| 256 |
e=fgetc(stdin); |
| 257 |
} |
| 258 |
if (e==EOF) GError(ERR_RANGEFMT, key); |
| 259 |
//now e is the first non-space |
| 260 |
p=buf; |
| 261 |
q=p; |
| 262 |
while (e!=EOF && !isspace(e)) { |
| 263 |
*q=e; |
| 264 |
q++; |
| 265 |
e=fgetc(stdin); |
| 266 |
} |
| 267 |
*q='\0'; //now p is the starting coordinate string |
| 268 |
return atoi(p); |
| 269 |
//now the file pointer should be on the first space after the parsed value |
| 270 |
} |
| 271 |
|
| 272 |
int parse_int(char*& f, const char* key, int& e) { |
| 273 |
char* p, *q; |
| 274 |
char buf[16]; |
| 275 |
while (e!='\0' && isspace(e)) { //skip any spaces |
| 276 |
if (e=='\n') GError(ERR_RANGEFMT, key); |
| 277 |
f++; |
| 278 |
e=*f; |
| 279 |
} |
| 280 |
if (e=='\0') GError(ERR_RANGEFMT, key); |
| 281 |
//now e is the first non-space char |
| 282 |
p=buf; |
| 283 |
q=p; |
| 284 |
while (e!='\0' && !isspace(e)) { |
| 285 |
*q=e; |
| 286 |
q++; |
| 287 |
f++; |
| 288 |
e=*f; |
| 289 |
} |
| 290 |
*q='\0'; |
| 291 |
return atoi(p); |
| 292 |
//now f and e should be on the first space after the parsed value (or '\0') |
| 293 |
} |
| 294 |
|
| 295 |
GCdbYank::GCdbYank(const char* fidx, const char* recsep) { |
| 296 |
is_compressed=false; |
| 297 |
fd=-1; |
| 298 |
cdb=NULL; |
| 299 |
#ifdef ENABLE_COMPRESSION |
| 300 |
cdbz=NULL; |
| 301 |
#endif |
| 302 |
fdb=-1; |
| 303 |
fz=NULL; |
| 304 |
dbname=NULL; |
| 305 |
recdelim=Gstrdup(recsep); |
| 306 |
if (fidx==NULL) GError("GCdbYank Error: NULL index file name!"); |
| 307 |
idxfile=Gstrdup(fidx); |
| 308 |
cdb=new GCdbRead(idxfile); |
| 309 |
fd=cdb->getfd(); |
| 310 |
db_size=0; |
| 311 |
dbstat.dbsize=0; |
| 312 |
info_dbname=NULL; |
| 313 |
int r=read_dbinfo(fd, &info_dbname, dbstat); |
| 314 |
lseek(fd, 0, SEEK_SET); |
| 315 |
if (r==1) GError("This file does not seem to be a cdbfasta generated file.\n"); |
| 316 |
else if (r==2) |
| 317 |
GError("Error reading info chunk!\n"); |
| 318 |
/*try to find the database file |
| 319 |
rules: if given, only the -d given filename is used |
| 320 |
otherwise: |
| 321 |
1) the same directory with the given index file(stripping the suffix) |
| 322 |
2) the dbstat filepath/name stored by cdbfasta |
| 323 |
*/ |
| 324 |
if (dbname==NULL) { |
| 325 |
char* p = rstrchr(idxfile, '.'); |
| 326 |
if (p!=NULL) { |
| 327 |
/*GError("%s\ncdbyank error: cannot use %s as an index file. When no -d is\n\ |
| 328 |
given, so the database file can be located in the same directory \n\ |
| 329 |
by removing the index file suffix (.cidx)\n", USAGE, idxfile);*/ |
| 330 |
int nlen=p-idxfile; |
| 331 |
char* namebuf=NULL; |
| 332 |
GMALLOC(namebuf, nlen+1); |
| 333 |
strncpy(namebuf, idxfile, nlen); |
| 334 |
namebuf[nlen]='\0'; |
| 335 |
if (fileExists(namebuf)) |
| 336 |
dbname=namebuf; |
| 337 |
|
| 338 |
} // strip the index file extenstion |
| 339 |
// 2) try the stored dbstat name |
| 340 |
if (dbname==NULL) { |
| 341 |
if (fileExists(info_dbname)) dbname=info_dbname; |
| 342 |
else GError("Cannot locate the database file for this index\n"); |
| 343 |
} |
| 344 |
}// database name not given |
| 345 |
is_compressed=(dbstat.idxflags & CDBMSK_OPT_COMPRESS); |
| 346 |
if (is_compressed) |
| 347 |
//try to open the dbname as a compressed file |
| 348 |
fz=fopen(dbname, "rb"); |
| 349 |
else fdb=open(dbname, O_RDONLY|O_BINARY); |
| 350 |
if (fdb==-1 && fz==NULL) |
| 351 |
GError("Error: cannot open database file %s\n",dbname); |
| 352 |
if (is_compressed) { |
| 353 |
#ifndef ENABLE_COMPRESSION |
| 354 |
GError(err_COMPRESSED); |
| 355 |
#else |
| 356 |
fclose(fz);//just to start fresh here |
| 357 |
//determine size: |
| 358 |
int ftmp = open(dbname, O_RDONLY|O_BINARY); |
| 359 |
if (ftmp == -1) GError("Error reopening db '%s'?\n",dbname); |
| 360 |
struct stat fdbstat; |
| 361 |
fstat(ftmp, &fdbstat); |
| 362 |
db_size=fdbstat.st_size; |
| 363 |
close(ftmp); |
| 364 |
//-------- reopen here |
| 365 |
cdbz=openCdbz(dbname); |
| 366 |
if (cdbz==NULL) |
| 367 |
GError("Error opening the cdbz file '%s'\n"); |
| 368 |
fz=cdbz->getZFile(); |
| 369 |
#endif |
| 370 |
} |
| 371 |
else { |
| 372 |
struct stat fdbstat; |
| 373 |
if (stat(dbname, &fdbstat)!=0) { |
| 374 |
perror("stat()"); |
| 375 |
exit(1); |
| 376 |
} |
| 377 |
db_size=fdbstat.st_size; |
| 378 |
} |
| 379 |
//abort if the database size was read and it doesn't match the cdbfasta stored size |
| 380 |
if (dbstat.dbsize>0 && dbstat.dbsize!=db_size) |
| 381 |
GError("Error: invalid %d database size - (%lld vs %lld) please rerun cdbfasta for '%s'\n", |
| 382 |
fdb, dbstat.dbsize, db_size, dbname); |
| 383 |
fastahandler=new GFastaCharHandler(recdelim); |
| 384 |
} //* GCdbYank constructor *// |
| 385 |
|
| 386 |
GCdbYank::~GCdbYank() { |
| 387 |
if (is_compressed) { |
| 388 |
fclose(fz); |
| 389 |
#ifdef ENABLE_COMPRESSION |
| 390 |
delete cdbz; |
| 391 |
#endif |
| 392 |
} |
| 393 |
else close(fdb); |
| 394 |
GFREE(info_dbname); |
| 395 |
delete fastahandler; |
| 396 |
GFREE(recdelim); |
| 397 |
GFREE(dbname); |
| 398 |
GFREE(idxfile); |
| 399 |
delete cdb; |
| 400 |
close(fd); |
| 401 |
} |
| 402 |
|
| 403 |
|
| 404 |
int GCdbYank::getRecord(const char* key, FastaSeq& rec, charFunc* seqCallBack) { |
| 405 |
//assumes fdb is open, cdb was created on the index file |
| 406 |
int r=cdb->find(key); |
| 407 |
if (r==0) return 0; |
| 408 |
if (r==-1) |
| 409 |
GError("cdbyank: error searching for key %s in %s\n", key, idxfile); |
| 410 |
/* while (r>0) { */ |
| 411 |
off_t pos = cdb->datapos(); //position of this key's record in the index file |
| 412 |
unsigned int len=cdb->datalen(); // length of this key's record |
| 413 |
char bytes[32]; // data buffer -- should just accomodate fastarec_pos, fastarec_length |
| 414 |
if (cdb->read(bytes,len,pos) == -1) |
| 415 |
GError("cdbyank: error at GCbd::read (%s)!\n", idxfile); |
| 416 |
|
| 417 |
off_t fpos; //this will be the fastadb offset |
| 418 |
uint32 reclen; //this will be the fasta record offset |
| 419 |
if (len>8) { //64 bit file offset was used |
| 420 |
fpos=gcvt_offt(bytes); |
| 421 |
reclen=gcvt_uint(&bytes[sizeof(uint32)<<1]); |
| 422 |
} |
| 423 |
else { //32bit offset used |
| 424 |
fpos=gcvt_uint(bytes); |
| 425 |
reclen=gcvt_uint(&bytes[sizeof(uint32)]); |
| 426 |
} |
| 427 |
//GMessage("reclen=%d\n", reclen); |
| 428 |
|
| 429 |
/* if (showQuery) |
| 430 |
fprintf(fout, "%c%s%c\t", delimQuery, key, delimQuery);*/ |
| 431 |
/*========= FETCHING RECORD CONTENT ======= */ |
| 432 |
if (is_compressed) { |
| 433 |
//for now: ignore special retrievals, just print the whole record |
| 434 |
#ifdef ENABLE_COMPRESSION |
| 435 |
return cdbz->decompress(rec, reclen, fpos, seqCallBack); |
| 436 |
#else |
| 437 |
GError(err_COMPRESSED); |
| 438 |
#endif |
| 439 |
} |
| 440 |
else { // not compressed -- position into the file and build an ad hoc GFastaFile |
| 441 |
lseek(fdb, fpos, SEEK_SET); |
| 442 |
// read it char by char and return it as output |
| 443 |
char c='\0'; |
| 444 |
int charsread=0; |
| 445 |
fastahandler->init(&rec, seqCallBack); |
| 446 |
while (reclen-- && read(fdb, &c, 1)==1) { |
| 447 |
fastahandler->processChar(c); |
| 448 |
charsread++; |
| 449 |
} |
| 450 |
fastahandler->done(); |
| 451 |
return charsread; |
| 452 |
} // not compressed |
| 453 |
/* if (many) r=cdb->findnext(key, strlen(key)); |
| 454 |
else r=0; |
| 455 |
} */ |
| 456 |
return 0; |
| 457 |
} |
| 458 |
|
| 459 |
off_t GCdbYank::getRecordPos(const char* key) { |
| 460 |
//assumes fdb is open, cdb was created on the index file |
| 461 |
int r=cdb->find(key); |
| 462 |
if (r==0 && warnings) { |
| 463 |
GMessage("cdbyank: key \"%s\" not found in %s\n", key, idxfile); |
| 464 |
return -1; |
| 465 |
} |
| 466 |
if (r==-1) |
| 467 |
GError("cdbyank: error searching for key %s in %s\n", key, idxfile); |
| 468 |
off_t pos = cdb->datapos(); //position of this key's record in the index file |
| 469 |
unsigned int len=cdb->datalen(); // length of this key's record |
| 470 |
char bytes[32]; // data buffer -- should just accomodate fastarec_pos, fastarec_length |
| 471 |
if (cdb->read(bytes,len,pos) == -1) |
| 472 |
GError("cdbyank: error at GCbd::read (%s)!\n", idxfile); |
| 473 |
|
| 474 |
off_t fpos; //this will be the fastadb offset |
| 475 |
//uint32 reclen; this will be the fasta record length |
| 476 |
if (len>8) //64 bit file offset was used |
| 477 |
fpos=gcvt_offt(bytes); |
| 478 |
else //32bit offset used |
| 479 |
fpos=gcvt_uint(bytes); |
| 480 |
return fpos; |
| 481 |
} |
