/* The MIT License Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology 2011 Attractive Chaos 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. */ #include #include #include #include #include #include #include #include "bgzf.h" #ifdef _USE_KNETFILE #include "knetfile.h" typedef knetFile *_bgzf_file_t; #define _bgzf_open(fn, mode) knet_open(fn, mode) #define _bgzf_dopen(fp, mode) knet_dopen(fp, mode) #define _bgzf_close(fp) knet_close(fp) #define _bgzf_fileno(fp) ((fp)->fd) #define _bgzf_tell(fp) knet_tell(fp) #define _bgzf_seek(fp, offset, whence) knet_seek(fp, offset, whence) #define _bgzf_read(fp, buf, len) knet_read(fp, buf, len) #define _bgzf_write(fp, buf, len) knet_write(fp, buf, len) #else // ~defined(_USE_KNETFILE) #if defined(_WIN32) || defined(_MSC_VER) #define ftello(fp) ftell(fp) #define fseeko(fp, offset, whence) fseek(fp, offset, whence) #else // ~defined(_WIN32) extern off_t ftello(FILE *stream); extern int fseeko(FILE *stream, off_t offset, int whence); #endif // ~defined(_WIN32) typedef FILE *_bgzf_file_t; #define _bgzf_open(fn, mode) fopen(fn, mode) #define _bgzf_dopen(fp, mode) fdopen(fp, mode) #define _bgzf_close(fp) fclose(fp) #define _bgzf_fileno(fp) fileno(fp) #define _bgzf_tell(fp) ftello(fp) #define _bgzf_seek(fp, offset, whence) fseeko(fp, offset, whence) #define _bgzf_read(fp, buf, len) fread(buf, 1, len, fp) #define _bgzf_write(fp, buf, len) fwrite(buf, 1, len, fp) #endif // ~define(_USE_KNETFILE) #define BLOCK_HEADER_LENGTH 18 #define BLOCK_FOOTER_LENGTH 8 /* BGZF/GZIP header (speciallized from RFC 1952; little endian): +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ | 31|139| 8| 4| 0| 0|255| 6| 66| 67| 2|BLK_LEN| +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ */ static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0"; #ifdef BGZF_CACHE typedef struct { int size; uint8_t *block; int64_t end_offset; } cache_t; #include "khash.h" KHASH_MAP_INIT_INT64(cache, cache_t) #endif static inline void packInt16(uint8_t *buffer, uint16_t value) { buffer[0] = value; buffer[1] = value >> 8; } static inline int unpackInt16(const uint8_t *buffer) { return buffer[0] | buffer[1] << 8; } static 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 BGZF *bgzf_read_init() { BGZF *fp; fp = calloc(1, sizeof(BGZF)); fp->is_write = 0; fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE); fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE); #ifdef BGZF_CACHE fp->cache = kh_init(cache); #endif return fp; } static BGZF *bgzf_write_init(int compress_level) // compress_level==-1 for the default level { BGZF *fp; fp = calloc(1, sizeof(BGZF)); fp->is_write = 1; fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE); fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE); 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; return fp; } // get the compress level from the mode string static int mode2level(const char *__restrict mode) { 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 compress_level; } BGZF *bgzf_open(const char *path, const char *mode) { BGZF *fp = 0; assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE); if (strchr(mode, 'r') || strchr(mode, 'R')) { _bgzf_file_t fpr; if ((fpr = _bgzf_open(path, "r")) == 0) return 0; fp = bgzf_read_init(); fp->fp = fpr; } else if (strchr(mode, 'w') || strchr(mode, 'W')) { FILE *fpw; if ((fpw = fopen(path, "w")) == 0) return 0; fp = bgzf_write_init(mode2level(mode)); fp->fp = fpw; } return fp; } BGZF *bgzf_dopen(int fd, const char *mode) { BGZF *fp = 0; assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE); if (strchr(mode, 'r') || strchr(mode, 'R')) { _bgzf_file_t fpr; if ((fpr = _bgzf_dopen(fd, "r")) == 0) return 0; fp = bgzf_read_init(); fp->fp = fpr; } else if (strchr(mode, 'w') || strchr(mode, 'W')) { FILE *fpw; if ((fpw = fdopen(fd, "w")) == 0) return 0; fp = bgzf_write_init(mode2level(mode)); fp->fp = fpw; } return fp; } static int bgzf_compress(void *_dst, int *dlen, void *src, int slen, int level) { uint32_t crc; z_stream zs; uint8_t *dst = (uint8_t*)_dst; // compress the body zs.zalloc = NULL; zs.zfree = NULL; zs.next_in = src; zs.avail_in = slen; zs.next_out = dst + BLOCK_HEADER_LENGTH; zs.avail_out = *dlen - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH; if (deflateInit2(&zs, level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY) != Z_OK) return -1; // -15 to disable zlib header/footer if (deflate(&zs, Z_FINISH) != Z_STREAM_END) return -1; if (deflateEnd(&zs) != Z_OK) return -1; *dlen = zs.total_out + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; // write the header memcpy(dst, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block packInt16(&dst[16], *dlen - 1); // write the compressed length; -1 to fit 2 bytes // write the footer crc = crc32(crc32(0L, NULL, 0L), src, slen); packInt32((uint8_t*)&dst[*dlen - 8], crc); packInt32((uint8_t*)&dst[*dlen - 4], slen); return 0; } // Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length. static int deflate_block(BGZF *fp, int block_length) { int comp_size = BGZF_MAX_BLOCK_SIZE; if (bgzf_compress(fp->compressed_block, &comp_size, fp->uncompressed_block, block_length, fp->compress_level) != 0) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } fp->block_offset = 0; return comp_size; } // Inflate the block in fp->compressed_block into fp->uncompressed_block static int inflate_block(BGZF* fp, int block_length) { z_stream zs; 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 = BGZF_MAX_BLOCK_SIZE; if (inflateInit2(&zs, -15) != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } if (inflate(&zs, Z_FINISH) != Z_STREAM_END) { inflateEnd(&zs); fp->errcode |= BGZF_ERR_ZLIB; return -1; } if (inflateEnd(&zs) != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } return zs.total_out; } static int check_header(const uint8_t *header) { return (header[0] == 31 && header[1] == 139 && header[2] == 8 && (header[3] & 4) != 0 && unpackInt16((uint8_t*)&header[10]) == 6 && header[12] == 'B' && header[13] == 'C' && unpackInt16((uint8_t*)&header[14]) == 2); } #ifdef BGZF_CACHE static void free_cache(BGZF *fp) { khint_t k; khash_t(cache) *h = (khash_t(cache)*)fp->cache; if (fp->is_write) 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, BGZF_MAX_BLOCK_SIZE); _bgzf_seek((_bgzf_file_t)fp->fp, p->end_offset, SEEK_SET); 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 (BGZF_MAX_BLOCK_SIZE >= fp->cache_size) return; if ((kh_size(h) + 1) * BGZF_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(BGZF_MAX_BLOCK_SIZE); memcpy(kh_val(h, k).block, fp->uncompressed_block, BGZF_MAX_BLOCK_SIZE); } #else static void free_cache(BGZF *fp) {} static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;} static void cache_block(BGZF *fp, int size) {} #endif int bgzf_read_block(BGZF *fp) { uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block; int count, size = 0, block_length, remaining; int64_t block_address; block_address = _bgzf_tell((_bgzf_file_t)fp->fp); if (fp->cache_size && load_block_from_cache(fp, block_address)) return 0; count = _bgzf_read(fp->fp, header, sizeof(header)); if (count == 0) { // no data read fp->block_length = 0; return 0; } if (count != sizeof(header) || !check_header(header)) { fp->errcode |= BGZF_ERR_HEADER; return -1; } size = count; block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1" compressed_block = (uint8_t*)fp->compressed_block; memcpy(compressed_block, header, BLOCK_HEADER_LENGTH); remaining = block_length - BLOCK_HEADER_LENGTH; count = _bgzf_read(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining); if (count != remaining) { fp->errcode |= BGZF_ERR_IO; return -1; } size += count; if ((count = inflate_block(fp, block_length)) < 0) return -1; if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek. fp->block_address = block_address; fp->block_length = count; cache_block(fp, size); return 0; } ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length) { ssize_t bytes_read = 0; uint8_t *output = data; if (length <= 0) return 0; assert(fp->is_write == 0); while (bytes_read < length) { int copy_length, available = fp->block_length - fp->block_offset; uint8_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 = length - bytes_read < available? 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) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = fp->block_length = 0; } return bytes_read; } /***** BEGIN: multi-threading *****/ typedef struct { BGZF *fp; struct mtaux_t *mt; void *buf; int i, errcode, toproc; } worker_t; typedef struct mtaux_t { int n_threads, n_blks, curr, done; volatile int proc_cnt; void **blk; int *len; worker_t *w; pthread_t *tid; pthread_mutex_t lock; pthread_cond_t cv; } mtaux_t; static int worker_aux(worker_t *w) { int i, tmp, stop = 0; // wait for condition: to process or all done pthread_mutex_lock(&w->mt->lock); while (!w->toproc && !w->mt->done) pthread_cond_wait(&w->mt->cv, &w->mt->lock); if (w->mt->done) stop = 1; w->toproc = 0; pthread_mutex_unlock(&w->mt->lock); if (stop) return 1; // to quit the thread w->errcode = 0; for (i = w->i; i < w->mt->curr; i += w->mt->n_threads) { int clen = BGZF_MAX_BLOCK_SIZE; if (bgzf_compress(w->buf, &clen, w->mt->blk[i], w->mt->len[i], w->fp->compress_level) != 0) w->errcode |= BGZF_ERR_ZLIB; memcpy(w->mt->blk[i], w->buf, clen); w->mt->len[i] = clen; } tmp = __sync_fetch_and_add(&w->mt->proc_cnt, 1); return 0; } static void *mt_worker(void *data) { while (worker_aux(data) == 0); return 0; } int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks) { int i; mtaux_t *mt; pthread_attr_t attr; if (!fp->is_write || fp->mt || n_threads <= 1) return -1; mt = calloc(1, sizeof(mtaux_t)); mt->n_threads = n_threads; mt->n_blks = n_threads * n_sub_blks; mt->len = calloc(mt->n_blks, sizeof(int)); mt->blk = calloc(mt->n_blks, sizeof(void*)); for (i = 0; i < mt->n_blks; ++i) mt->blk[i] = malloc(BGZF_MAX_BLOCK_SIZE); mt->tid = calloc(mt->n_threads, sizeof(pthread_t)); // tid[0] is not used, as the worker 0 is launched by the master mt->w = calloc(mt->n_threads, sizeof(worker_t)); for (i = 0; i < mt->n_threads; ++i) { mt->w[i].i = i; mt->w[i].mt = mt; mt->w[i].fp = fp; mt->w[i].buf = malloc(BGZF_MAX_BLOCK_SIZE); } pthread_attr_init(&attr); pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE); pthread_mutex_init(&mt->lock, 0); pthread_cond_init(&mt->cv, 0); for (i = 1; i < mt->n_threads; ++i) // worker 0 is effectively launched by the master thread pthread_create(&mt->tid[i], &attr, mt_worker, &mt->w[i]); fp->mt = mt; return 0; } static void mt_destroy(mtaux_t *mt) { int i; // signal all workers to quit pthread_mutex_lock(&mt->lock); mt->done = 1; mt->proc_cnt = 0; pthread_cond_broadcast(&mt->cv); pthread_mutex_unlock(&mt->lock); for (i = 1; i < mt->n_threads; ++i) pthread_join(mt->tid[i], 0); // worker 0 is effectively launched by the master thread // free other data allocated on heap for (i = 0; i < mt->n_blks; ++i) free(mt->blk[i]); for (i = 0; i < mt->n_threads; ++i) free(mt->w[i].buf); free(mt->blk); free(mt->len); free(mt->w); free(mt->tid); pthread_cond_destroy(&mt->cv); pthread_mutex_destroy(&mt->lock); free(mt); } static void mt_queue(BGZF *fp) { mtaux_t *mt = (mtaux_t*)fp->mt; assert(mt->curr < mt->n_blks); // guaranteed by the caller memcpy(mt->blk[mt->curr], fp->uncompressed_block, fp->block_offset); mt->len[mt->curr] = fp->block_offset; fp->block_offset = 0; ++mt->curr; } static int mt_flush(BGZF *fp) { int i; mtaux_t *mt = (mtaux_t*)fp->mt; if (fp->block_offset) mt_queue(fp); // guaranteed that assertion does not fail // signal all the workers to compress pthread_mutex_lock(&mt->lock); for (i = 0; i < mt->n_threads; ++i) mt->w[i].toproc = 1; mt->proc_cnt = 0; pthread_cond_broadcast(&mt->cv); pthread_mutex_unlock(&mt->lock); // worker 0 is doing things here worker_aux(&mt->w[0]); // wait for all the threads to complete while (mt->proc_cnt < mt->n_threads); // dump data to disk for (i = 0; i < mt->n_threads; ++i) fp->errcode |= mt->w[i].errcode; for (i = 0; i < mt->curr; ++i) if (fwrite(mt->blk[i], 1, mt->len[i], fp->fp) != mt->len[i]) fp->errcode |= BGZF_ERR_IO; mt->curr = 0; return 0; } static int mt_lazy_flush(BGZF *fp) { mtaux_t *mt = (mtaux_t*)fp->mt; if (fp->block_offset) mt_queue(fp); if (mt->curr == mt->n_blks) return mt_flush(fp); return -1; } static ssize_t mt_write(BGZF *fp, const void *data, ssize_t length) { const uint8_t *input = data; ssize_t rest = length; while (rest) { int copy_length = BGZF_BLOCK_SIZE - fp->block_offset < rest? BGZF_BLOCK_SIZE - fp->block_offset : rest; memcpy(fp->uncompressed_block + fp->block_offset, input, copy_length); fp->block_offset += copy_length; input += copy_length; rest -= copy_length; if (fp->block_offset == BGZF_BLOCK_SIZE) mt_lazy_flush(fp); } return length - rest; } /***** END: multi-threading *****/ int bgzf_flush(BGZF *fp) { if (!fp->is_write) return 0; if (fp->mt) return mt_flush(fp); while (fp->block_offset > 0) { int block_length; block_length = deflate_block(fp, fp->block_offset); if (block_length < 0) return -1; if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) { fp->errcode |= BGZF_ERR_IO; // possibly truncated file return -1; } fp->block_address += block_length; } return 0; } int bgzf_flush_try(BGZF *fp, ssize_t size) { if (fp->block_offset + size > BGZF_BLOCK_SIZE) { if (fp->mt) return mt_lazy_flush(fp); else return bgzf_flush(fp); } return -1; } ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length) { const uint8_t *input = data; int block_length = BGZF_BLOCK_SIZE, bytes_written = 0; assert(fp->is_write); if (fp->mt) return mt_write(fp, data, length); while (bytes_written < length) { uint8_t* buffer = fp->uncompressed_block; int copy_length = block_length - fp->block_offset < length - bytes_written? block_length - fp->block_offset : length - bytes_written; 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 && bgzf_flush(fp)) break; } return bytes_written; } int bgzf_close(BGZF* fp) { int ret, count, block_length; if (fp == 0) return -1; if (fp->is_write) { if (bgzf_flush(fp) != 0) return -1; fp->compress_level = -1; block_length = deflate_block(fp, 0); // write an empty block count = fwrite(fp->compressed_block, 1, block_length, fp->fp); if (fflush(fp->fp) != 0) { fp->errcode |= BGZF_ERR_IO; return -1; } if (fp->mt) mt_destroy(fp->mt); } ret = fp->is_write? fclose(fp->fp) : _bgzf_close(fp->fp); if (ret != 0) return -1; 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; offset = _bgzf_tell((_bgzf_file_t)fp->fp); if (_bgzf_seek(fp->fp, -28, SEEK_END) < 0) return 0; _bgzf_read(fp->fp, buf, 28); _bgzf_seek(fp->fp, offset, SEEK_SET); 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->is_write || where != SEEK_SET) { fp->errcode |= BGZF_ERR_MISUSE; return -1; } block_offset = pos & 0xFFFF; block_address = pos >> 16; if (_bgzf_seek(fp->fp, block_address, SEEK_SET) < 0) { fp->errcode |= BGZF_ERR_IO; return -1; } fp->block_length = 0; // indicates current block has not been loaded fp->block_address = block_address; fp->block_offset = block_offset; return 0; } int bgzf_is_bgzf(const char *fn) { uint8_t buf[16]; int n; _bgzf_file_t fp; if ((fp = _bgzf_open(fn, "r")) == 0) return 0; n = _bgzf_read(fp, buf, 16); _bgzf_close(fp); if (n != 16) return 0; return memcmp(g_magic, buf, 16) == 0? 1 : 0; } int bgzf_getc(BGZF *fp) { int c; if (fp->block_offset >= fp->block_length) { if (bgzf_read_block(fp) != 0) return -2; /* error */ if (fp->block_length == 0) return -1; /* end-of-file */ } c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++]; if (fp->block_offset == fp->block_length) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = 0; fp->block_length = 0; } return c; } #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif int bgzf_getline(BGZF *fp, int delim, kstring_t *str) { int l, state = 0; unsigned char *buf = (unsigned char*)fp->uncompressed_block; str->l = 0; do { if (fp->block_offset >= fp->block_length) { if (bgzf_read_block(fp) != 0) { state = -2; break; } if (fp->block_length == 0) { state = -1; break; } } for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l); if (l < fp->block_length) state = 1; l -= fp->block_offset; if (str->l + l + 1 >= str->m) { str->m = str->l + l + 2; kroundup32(str->m); str->s = (char*)realloc(str->s, str->m); } memcpy(str->s + str->l, buf + fp->block_offset, l); str->l += l; fp->block_offset += l + 1; if (fp->block_offset >= fp->block_length) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = 0; fp->block_length = 0; } } while (state == 0); if (str->l == 0 && state < 0) return state; str->s[str->l] = 0; return str->l; }