Skip to content
This repository

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
tree: fbdde774ad
Fetching contributors…

Cannot retrieve contributors at this time

file 714 lines (658 sloc) 19.942 kb
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714
/* The MIT License

Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
*/

/*
2009-06-29 by lh3: cache recent uncompressed blocks.
2009-06-25 by lh3: optionally use my knetfile library to access file on a FTP.
2009-06-12 by lh3: support a mode string like "wu" where 'u' for uncompressed output */

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <fcntl.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "bgzf.h"

#include "khash.h"
typedef struct {
int size;
uint8_t *block;
int64_t end_offset;
} cache_t;
KHASH_MAP_INIT_INT64(cache, cache_t)

#if defined(_WIN32) || defined(_MSC_VER)
#define ftello(fp) ftell(fp)
#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
#else
extern off_t ftello(FILE *stream);
extern int fseeko(FILE *stream, off_t offset, int whence);
#endif

typedef int8_t bgzf_byte_t;

static const int DEFAULT_BLOCK_SIZE = 64 * 1024;
static const int MAX_BLOCK_SIZE = 64 * 1024;

static const int BLOCK_HEADER_LENGTH = 18;
static const int BLOCK_FOOTER_LENGTH = 8;

static const int GZIP_ID1 = 31;
static const int GZIP_ID2 = 139;
static const int CM_DEFLATE = 8;
static const int FLG_FEXTRA = 4;
static const int OS_UNKNOWN = 255;
static const int BGZF_ID1 = 66; // 'B'
static const int BGZF_ID2 = 67; // 'C'
static const int BGZF_LEN = 2;
static const int BGZF_XLEN = 6; // BGZF_LEN+4

static const int GZIP_WINDOW_BITS = -15; // no zlib header
static const int Z_DEFAULT_MEM_LEVEL = 8;


inline
void
packInt16(uint8_t* buffer, uint16_t value)
{
    buffer[0] = value;
    buffer[1] = value >> 8;
}

inline
int
unpackInt16(const uint8_t* buffer)
{
    return (buffer[0] | (buffer[1] << 8));
}

inline
void
packInt32(uint8_t* buffer, uint32_t value)
{
    buffer[0] = value;
    buffer[1] = value >> 8;
    buffer[2] = value >> 16;
    buffer[3] = value >> 24;
}

static inline
int
bgzf_min(int x, int y)
{
    return (x < y) ? x : y;
}

static
void
report_error(BGZF* fp, const char* message) {
    fp->error = message;
}

int bgzf_check_bgzf(const char *fn)
{
    BGZF *fp;
    uint8_t buf[10],magic[10]="\037\213\010\4\0\0\0\0\0\377";
    int n;

    if ((fp = bgzf_open(fn, "r")) == 0)
    {
        fprintf(stderr, "[bgzf_check_bgzf] failed to open the file: %s\n",fn);
        return -1;
    }

#ifdef _USE_KNETFILE
    n = knet_read(fp->x.fpr, buf, 10);
#else
    n = fread(buf, 1, 10, fp->file);
#endif
    bgzf_close(fp);

    if ( n!=10 )
        return -1;

    if ( !memcmp(magic, buf, 10) ) return 1;
    return 0;
}

static BGZF *bgzf_read_init()
{
BGZF *fp;
fp = calloc(1, sizeof(BGZF));
    fp->uncompressed_block_size = MAX_BLOCK_SIZE;
    fp->uncompressed_block = malloc(MAX_BLOCK_SIZE);
    fp->compressed_block_size = MAX_BLOCK_SIZE;
    fp->compressed_block = malloc(MAX_BLOCK_SIZE);
fp->cache_size = 0;
fp->cache = kh_init(cache);
return fp;
}

static
BGZF*
open_read(int fd)
{
#ifdef _USE_KNETFILE
    knetFile *file = knet_dopen(fd, "r");
#else
    FILE* file = fdopen(fd, "r");
#endif
    BGZF* fp;
if (file == 0) return 0;
fp = bgzf_read_init();
    fp->file_descriptor = fd;
    fp->open_mode = 'r';
#ifdef _USE_KNETFILE
    fp->x.fpr = file;
#else
    fp->file = file;
#endif
    return fp;
}

static
BGZF*
open_write(int fd, int compress_level) // compress_level==-1 for the default level
{
    FILE* file = fdopen(fd, "w");
    BGZF* fp;
if (file == 0) return 0;
fp = malloc(sizeof(BGZF));
    fp->file_descriptor = fd;
    fp->open_mode = 'w';
    fp->owned_file = 0;
fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
#ifdef _USE_KNETFILE
    fp->x.fpw = file;
#else
    fp->file = file;
#endif
    fp->uncompressed_block_size = DEFAULT_BLOCK_SIZE;
    fp->uncompressed_block = NULL;
    fp->compressed_block_size = MAX_BLOCK_SIZE;
    fp->compressed_block = malloc(MAX_BLOCK_SIZE);
    fp->block_address = 0;
    fp->block_offset = 0;
    fp->block_length = 0;
    fp->error = NULL;
    return fp;
}

BGZF*
bgzf_open(const char* __restrict path, const char* __restrict mode)
{
    BGZF* fp = NULL;
    if (strchr(mode, 'r') || strchr(mode, 'R')) { /* The reading mode is preferred. */
#ifdef _USE_KNETFILE
knetFile *file = knet_open(path, mode);
if (file == 0) return 0;
fp = bgzf_read_init();
fp->file_descriptor = -1;
fp->open_mode = 'r';
fp->x.fpr = file;
#else
int fd, oflag = O_RDONLY;
#ifdef _WIN32
oflag |= O_BINARY;
#endif
fd = open(path, oflag);
if (fd == -1) return 0;
        fp = open_read(fd);
#endif
    } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
int fd, compress_level = -1, oflag = O_WRONLY | O_CREAT | O_TRUNC;
#ifdef _WIN32
oflag |= O_BINARY;
#endif
fd = open(path, oflag, 0666);
if (fd == -1) return 0;
{ // set compress_level
int i;
for (i = 0; mode[i]; ++i)
if (mode[i] >= '0' && mode[i] <= '9') break;
if (mode[i]) compress_level = (int)mode[i] - '0';
if (strchr(mode, 'u')) compress_level = 0;
}
        fp = open_write(fd, compress_level);
    }
    if (fp != NULL) fp->owned_file = 1;
    return fp;
}

BGZF*
bgzf_fdopen(int fd, const char * __restrict mode)
{
if (fd == -1) return 0;
    if (mode[0] == 'r' || mode[0] == 'R') {
        return open_read(fd);
    } else if (mode[0] == 'w' || mode[0] == 'W') {
int i, compress_level = -1;
for (i = 0; mode[i]; ++i)
if (mode[i] >= '0' && mode[i] <= '9') break;
if (mode[i]) compress_level = (int)mode[i] - '0';
if (strchr(mode, 'u')) compress_level = 0;
        return open_write(fd, compress_level);
    } else {
        return NULL;
    }
}

static
int
deflate_block(BGZF* fp, int block_length)
{
    // Deflate the block in fp->uncompressed_block into fp->compressed_block.
    // Also adds an extra field that stores the compressed block length.

    bgzf_byte_t* buffer = fp->compressed_block;
    int buffer_size = fp->compressed_block_size;

    // Init gzip header
    buffer[0] = GZIP_ID1;
    buffer[1] = GZIP_ID2;
    buffer[2] = CM_DEFLATE;
    buffer[3] = FLG_FEXTRA;
    buffer[4] = 0; // mtime
    buffer[5] = 0;
    buffer[6] = 0;
    buffer[7] = 0;
    buffer[8] = 0;
    buffer[9] = OS_UNKNOWN;
    buffer[10] = BGZF_XLEN;
    buffer[11] = 0;
    buffer[12] = BGZF_ID1;
    buffer[13] = BGZF_ID2;
    buffer[14] = BGZF_LEN;
    buffer[15] = 0;
    buffer[16] = 0; // placeholder for block length
    buffer[17] = 0;

    // loop to retry for blocks that do not compress enough
    int input_length = block_length;
    int compressed_length = 0;
    while (1) {
        z_stream zs;
        zs.zalloc = NULL;
        zs.zfree = NULL;
        zs.next_in = fp->uncompressed_block;
        zs.avail_in = input_length;
        zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
        zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;

        int status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED,
                                  GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
        if (status != Z_OK) {
            report_error(fp, "deflate init failed");
            return -1;
        }
        status = deflate(&zs, Z_FINISH);
        if (status != Z_STREAM_END) {
            deflateEnd(&zs);
            if (status == Z_OK) {
                // Not enough space in buffer.
                // Can happen in the rare case the input doesn't compress enough.
                // Reduce the amount of input until it fits.
                input_length -= 1024;
                if (input_length <= 0) {
                    // should never happen
                    report_error(fp, "input reduction failed");
                    return -1;
                }
                continue;
            }
            report_error(fp, "deflate failed");
            return -1;
        }
        status = deflateEnd(&zs);
        if (status != Z_OK) {
            report_error(fp, "deflate end failed");
            return -1;
        }
        compressed_length = zs.total_out;
        compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
        if (compressed_length > MAX_BLOCK_SIZE) {
            // should never happen
            report_error(fp, "deflate overflow");
            return -1;
        }
        break;
    }

    packInt16((uint8_t*)&buffer[16], compressed_length-1);
    uint32_t crc = crc32(0L, NULL, 0L);
    crc = crc32(crc, fp->uncompressed_block, input_length);
    packInt32((uint8_t*)&buffer[compressed_length-8], crc);
    packInt32((uint8_t*)&buffer[compressed_length-4], input_length);

    int remaining = block_length - input_length;
    if (remaining > 0) {
        if (remaining > input_length) {
            // should never happen (check so we can use memcpy)
            report_error(fp, "remainder too large");
            return -1;
        }
        memcpy(fp->uncompressed_block,
               fp->uncompressed_block + input_length,
               remaining);
    }
    fp->block_offset = remaining;
    return compressed_length;
}

static
int
inflate_block(BGZF* fp, int block_length)
{
    // Inflate the block in fp->compressed_block into fp->uncompressed_block

    z_stream zs;
int status;
    zs.zalloc = NULL;
    zs.zfree = NULL;
    zs.next_in = fp->compressed_block + 18;
    zs.avail_in = block_length - 16;
    zs.next_out = fp->uncompressed_block;
    zs.avail_out = fp->uncompressed_block_size;

    status = inflateInit2(&zs, GZIP_WINDOW_BITS);
    if (status != Z_OK) {
        report_error(fp, "inflate init failed");
        return -1;
    }
    status = inflate(&zs, Z_FINISH);
    if (status != Z_STREAM_END) {
        inflateEnd(&zs);
        report_error(fp, "inflate failed");
        return -1;
    }
    status = inflateEnd(&zs);
    if (status != Z_OK) {
        report_error(fp, "inflate failed");
        return -1;
    }
    return zs.total_out;
}

static
int
check_header(const bgzf_byte_t* header)
{
    return (header[0] == GZIP_ID1 &&
            header[1] == (bgzf_byte_t) GZIP_ID2 &&
            header[2] == Z_DEFLATED &&
            (header[3] & FLG_FEXTRA) != 0 &&
            unpackInt16((uint8_t*)&header[10]) == BGZF_XLEN &&
            header[12] == BGZF_ID1 &&
            header[13] == BGZF_ID2 &&
            unpackInt16((uint8_t*)&header[14]) == BGZF_LEN);
}

static void free_cache(BGZF *fp)
{
khint_t k;
khash_t(cache) *h = (khash_t(cache)*)fp->cache;
if (fp->open_mode != 'r') return;
for (k = kh_begin(h); k < kh_end(h); ++k)
if (kh_exist(h, k)) free(kh_val(h, k).block);
kh_destroy(cache, h);
}

static int load_block_from_cache(BGZF *fp, int64_t block_address)
{
khint_t k;
cache_t *p;
khash_t(cache) *h = (khash_t(cache)*)fp->cache;
k = kh_get(cache, h, block_address);
if (k == kh_end(h)) return 0;
p = &kh_val(h, k);
if (fp->block_length != 0) fp->block_offset = 0;
fp->block_address = block_address;
fp->block_length = p->size;
memcpy(fp->uncompressed_block, p->block, MAX_BLOCK_SIZE);
#ifdef _USE_KNETFILE
knet_seek(fp->x.fpr, p->end_offset, SEEK_SET);
#else
fseeko(fp->file, p->end_offset, SEEK_SET);
#endif
return p->size;
}

static void cache_block(BGZF *fp, int size)
{
int ret;
khint_t k;
cache_t *p;
khash_t(cache) *h = (khash_t(cache)*)fp->cache;
if (MAX_BLOCK_SIZE >= fp->cache_size) return;
if ((kh_size(h) + 1) * MAX_BLOCK_SIZE > fp->cache_size) {
/* A better way would be to remove the oldest block in the
* cache, but here we remove a random one for simplicity. This
* should not have a big impact on performance. */
for (k = kh_begin(h); k < kh_end(h); ++k)
if (kh_exist(h, k)) break;
if (k < kh_end(h)) {
free(kh_val(h, k).block);
kh_del(cache, h, k);
}
}
k = kh_put(cache, h, fp->block_address, &ret);
if (ret == 0) return; // if this happens, a bug!
p = &kh_val(h, k);
p->size = fp->block_length;
p->end_offset = fp->block_address + size;
p->block = malloc(MAX_BLOCK_SIZE);
memcpy(kh_val(h, k).block, fp->uncompressed_block, MAX_BLOCK_SIZE);
}

int
bgzf_read_block(BGZF* fp)
{
    bgzf_byte_t header[BLOCK_HEADER_LENGTH];
int count, size = 0, block_length, remaining;
#ifdef _USE_KNETFILE
    int64_t block_address = knet_tell(fp->x.fpr);
if (load_block_from_cache(fp, block_address)) return 0;
    count = knet_read(fp->x.fpr, header, sizeof(header));
#else
    int64_t block_address = ftello(fp->file);
if (load_block_from_cache(fp, block_address)) return 0;
    count = fread(header, 1, sizeof(header), fp->file);
#endif
    if (count == 0) {
        fp->block_length = 0;
        return 0;
    }
size = count;
    if (count != sizeof(header)) {
        report_error(fp, "read failed");
        return -1;
    }
    if (!check_header(header)) {
        report_error(fp, "invalid block header");
        return -1;
    }
    block_length = unpackInt16((uint8_t*)&header[16]) + 1;
    bgzf_byte_t* compressed_block = (bgzf_byte_t*) fp->compressed_block;
    memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
    remaining = block_length - BLOCK_HEADER_LENGTH;
#ifdef _USE_KNETFILE
    count = knet_read(fp->x.fpr, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
#else
    count = fread(&compressed_block[BLOCK_HEADER_LENGTH], 1, remaining, fp->file);
#endif
    if (count != remaining) {
        report_error(fp, "read failed");
        return -1;
    }
size += count;
    count = inflate_block(fp, block_length);
    if (count < 0) return -1;
    if (fp->block_length != 0) {
        // Do not reset offset if this read follows a seek.
        fp->block_offset = 0;
    }
    fp->block_address = block_address;
    fp->block_length = count;
cache_block(fp, size);
    return 0;
}

int
bgzf_read(BGZF* fp, void* data, int length)
{
    if (length <= 0) {
        return 0;
    }
    if (fp->open_mode != 'r') {
        report_error(fp, "file not open for reading");
        return -1;
    }

    int bytes_read = 0;
    bgzf_byte_t* output = data;
    while (bytes_read < length) {
        int copy_length, available = fp->block_length - fp->block_offset;
bgzf_byte_t *buffer;
        if (available <= 0) {
            if (bgzf_read_block(fp) != 0) {
                return -1;
            }
            available = fp->block_length - fp->block_offset;
            if (available <= 0) {
                break;
            }
        }
        copy_length = bgzf_min(length-bytes_read, available);
        buffer = fp->uncompressed_block;
        memcpy(output, buffer + fp->block_offset, copy_length);
        fp->block_offset += copy_length;
        output += copy_length;
        bytes_read += copy_length;
    }
    if (fp->block_offset == fp->block_length) {
#ifdef _USE_KNETFILE
        fp->block_address = knet_tell(fp->x.fpr);
#else
        fp->block_address = ftello(fp->file);
#endif
        fp->block_offset = 0;
        fp->block_length = 0;
    }
    return bytes_read;
}

int bgzf_flush(BGZF* fp)
{
    while (fp->block_offset > 0) {
        int count, block_length;
block_length = deflate_block(fp, fp->block_offset);
        if (block_length < 0) return -1;
#ifdef _USE_KNETFILE
        count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
#else
        count = fwrite(fp->compressed_block, 1, block_length, fp->file);
#endif
        if (count != block_length) {
            report_error(fp, "write failed");
            return -1;
        }
        fp->block_address += block_length;
    }
    return 0;
}

int bgzf_flush_try(BGZF *fp, int size)
{
if (fp->block_offset + size > fp->uncompressed_block_size)
return bgzf_flush(fp);
return -1;
}

int bgzf_write(BGZF* fp, const void* data, int length)
{
const bgzf_byte_t *input = data;
int block_length, bytes_written;
    if (fp->open_mode != 'w') {
        report_error(fp, "file not open for writing");
        return -1;
    }

    if (fp->uncompressed_block == NULL)
        fp->uncompressed_block = malloc(fp->uncompressed_block_size);

    input = data;
    block_length = fp->uncompressed_block_size;
    bytes_written = 0;
    while (bytes_written < length) {
        int copy_length = bgzf_min(block_length - fp->block_offset, length - bytes_written);
        bgzf_byte_t* buffer = fp->uncompressed_block;
        memcpy(buffer + fp->block_offset, input, copy_length);
        fp->block_offset += copy_length;
        input += copy_length;
        bytes_written += copy_length;
        if (fp->block_offset == block_length) {
            if (bgzf_flush(fp) != 0) {
                break;
            }
        }
    }
    return bytes_written;
}

int bgzf_close(BGZF* fp)
{
    if (fp->open_mode == 'w') {
        if (bgzf_flush(fp) != 0) return -1;
{ // add an empty block
int count, block_length = deflate_block(fp, 0);
#ifdef _USE_KNETFILE
count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
#else
count = fwrite(fp->compressed_block, 1, block_length, fp->file);
#endif
}
#ifdef _USE_KNETFILE
        if (fflush(fp->x.fpw) != 0) {
#else
        if (fflush(fp->file) != 0) {
#endif
            report_error(fp, "flush failed");
            return -1;
        }
    }
    if (fp->owned_file) {
#ifdef _USE_KNETFILE
int ret;
if (fp->open_mode == 'w') ret = fclose(fp->x.fpw);
else ret = knet_close(fp->x.fpr);
        if (ret != 0) return -1;
#else
        if (fclose(fp->file) != 0) return -1;
#endif
    }
    free(fp->uncompressed_block);
    free(fp->compressed_block);
free_cache(fp);
    free(fp);
    return 0;
}

void bgzf_set_cache_size(BGZF *fp, int cache_size)
{
if (fp) fp->cache_size = cache_size;
}

int bgzf_check_EOF(BGZF *fp)
{
static uint8_t magic[28] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0";
uint8_t buf[28];
off_t offset;
#ifdef _USE_KNETFILE
offset = knet_tell(fp->x.fpr);
if (knet_seek(fp->x.fpr, -28, SEEK_END) != 0) return -1;
knet_read(fp->x.fpr, buf, 28);
knet_seek(fp->x.fpr, offset, SEEK_SET);
#else
offset = ftello(fp->file);
if (fseeko(fp->file, -28, SEEK_END) != 0) return -1;
fread(buf, 1, 28, fp->file);
fseeko(fp->file, offset, SEEK_SET);
#endif
return (memcmp(magic, buf, 28) == 0)? 1 : 0;
}

int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
{
int block_offset;
int64_t block_address;

    if (fp->open_mode != 'r') {
        report_error(fp, "file not open for read");
        return -1;
    }
    if (where != SEEK_SET) {
        report_error(fp, "unimplemented seek option");
        return -1;
    }
    block_offset = pos & 0xFFFF;
    block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
#ifdef _USE_KNETFILE
    if (knet_seek(fp->x.fpr, block_address, SEEK_SET) != 0) {
#else
    if (fseeko(fp->file, block_address, SEEK_SET) != 0) {
#endif
        report_error(fp, "seek failed");
        return -1;
    }
    fp->block_length = 0; // indicates current block is not loaded
    fp->block_address = block_address;
    fp->block_offset = block_offset;
    return 0;
}
Something went wrong with that request. Please try again.