3 * SOFTWARE COPYRIGHT NOTICE AGREEMENT
4 * This software and its documentation are copyright 2008 by the
5 * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
7 * This software is supplied without any warranty or guaranteed support whatsoever.
8 * Neither the Broad Institute nor MIT can be responsible for its use, misuse,
17 #include <sys/types.h>
21 extern off_t ftello(FILE *stream);
22 extern int fseeko(FILE *stream, off_t offset, int whence);
26 static const int DEFAULT_BLOCK_SIZE = 64 * 1024;
27 static const int MAX_BLOCK_SIZE = 64 * 1024;
29 static const int BLOCK_HEADER_LENGTH = 18;
30 static const int BLOCK_FOOTER_LENGTH = 8;
32 static const int GZIP_ID1 = 31;
33 static const int GZIP_ID2 = 139;
34 static const int CM_DEFLATE = 8;
35 static const int FLG_FEXTRA = 4;
36 static const int OS_UNKNOWN = 255;
37 static const int BGZF_ID1 = 66; // 'B'
38 static const int BGZF_ID2 = 67; // 'C'
39 static const int BGZF_LEN = 2;
40 static const int BGZF_XLEN = 6; // BGZF_LEN+4
42 static const int GZIP_WINDOW_BITS = -15; // no zlib header
43 static const int Z_DEFAULT_MEM_LEVEL = 8;
48 packInt16(uint8_t* buffer, uint16_t value)
51 buffer[1] = value >> 8;
56 unpackInt16(const uint8_t* buffer)
58 return (buffer[0] | (buffer[1] << 8));
63 packInt32(uint8_t* buffer, uint32_t value)
66 buffer[1] = value >> 8;
67 buffer[2] = value >> 16;
68 buffer[3] = value >> 24;
75 return (x < y) ? x : y;
80 report_error(BGZF* fp, const char* message) {
88 FILE* file = fdopen(fd, "r");
90 if (file == 0) return 0;
91 fp = malloc(sizeof(BGZF));
92 fp->file_descriptor = fd;
96 fp->uncompressed_block_size = MAX_BLOCK_SIZE;
97 fp->uncompressed_block = malloc(MAX_BLOCK_SIZE);
98 fp->compressed_block_size = MAX_BLOCK_SIZE;
99 fp->compressed_block = malloc(MAX_BLOCK_SIZE);
100 fp->block_address = 0;
101 fp->block_offset = 0;
102 fp->block_length = 0;
111 FILE* file = fdopen(fd, "w");
113 if (file == 0) return 0;
114 fp = malloc(sizeof(BGZF));
115 fp->file_descriptor = fd;
119 fp->uncompressed_block_size = DEFAULT_BLOCK_SIZE;
120 fp->uncompressed_block = NULL;
121 fp->compressed_block_size = MAX_BLOCK_SIZE;
122 fp->compressed_block = malloc(MAX_BLOCK_SIZE);
123 fp->block_address = 0;
124 fp->block_offset = 0;
125 fp->block_length = 0;
131 bgzf_open(const char* __restrict path, const char* __restrict mode)
134 if (strcasecmp(mode, "r") == 0) {
135 int oflag = O_RDONLY;
136 int fd = open(path, oflag);
138 } else if (strcasecmp(mode, "w") == 0) {
139 int oflag = O_WRONLY | O_CREAT | O_TRUNC;
140 int fd = open(path, oflag, 0644);
150 bgzf_fdopen(int fd, const char * __restrict mode)
152 if (strcasecmp(mode, "r") == 0) {
153 return open_read(fd);
154 } else if (strcasecmp(mode, "w") == 0) {
155 return open_write(fd);
163 deflate_block(BGZF* fp, int block_length)
165 // Deflate the block in fp->uncompressed_block into fp->compressed_block.
166 // Also adds an extra field that stores the compressed block length.
168 byte* buffer = fp->compressed_block;
169 int buffer_size = fp->compressed_block_size;
172 buffer[0] = GZIP_ID1;
173 buffer[1] = GZIP_ID2;
174 buffer[2] = CM_DEFLATE;
175 buffer[3] = FLG_FEXTRA;
176 buffer[4] = 0; // mtime
181 buffer[9] = OS_UNKNOWN;
182 buffer[10] = BGZF_XLEN;
184 buffer[12] = BGZF_ID1;
185 buffer[13] = BGZF_ID2;
186 buffer[14] = BGZF_LEN;
188 buffer[16] = 0; // placeholder for block length
191 // loop to retry for blocks that do not compress enough
192 int input_length = block_length;
193 int compressed_length = 0;
199 zs.next_in = fp->uncompressed_block;
200 zs.avail_in = input_length;
201 zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
202 zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
204 int status = deflateInit2(&zs, Z_DEFAULT_COMPRESSION, Z_DEFLATED,
205 GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
206 if (status != Z_OK) {
207 report_error(fp, "deflate init failed");
210 status = deflate(&zs, Z_FINISH);
211 if (status != Z_STREAM_END) {
213 if (status == Z_OK) {
214 // Not enough space in buffer.
215 // Can happen in the rare case the input doesn't compress enough.
216 // Reduce the amount of input until it fits.
217 input_length -= 1024;
218 if (input_length <= 0) {
219 // should never happen
220 report_error(fp, "input reduction failed");
225 report_error(fp, "deflate failed");
228 status = deflateEnd(&zs);
229 if (status != Z_OK) {
230 report_error(fp, "deflate end failed");
233 compressed_length = zs.total_out;
234 compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
235 if (compressed_length > MAX_BLOCK_SIZE) {
236 // should never happen
237 report_error(fp, "deflate overflow");
243 packInt16((uint8_t*)&buffer[16], compressed_length-1);
244 uint32_t crc = crc32(0L, NULL, 0L);
245 crc = crc32(crc, fp->uncompressed_block, input_length);
246 packInt32((uint8_t*)&buffer[compressed_length-8], crc);
247 packInt32((uint8_t*)&buffer[compressed_length-4], input_length);
249 int remaining = block_length - input_length;
251 if (remaining > input_length) {
252 // should never happen (check so we can use memcpy)
253 report_error(fp, "remainder too large");
256 memcpy(fp->uncompressed_block,
257 fp->uncompressed_block + input_length,
260 fp->block_offset = remaining;
261 return compressed_length;
266 inflate_block(BGZF* fp, int block_length)
268 // Inflate the block in fp->compressed_block into fp->uncompressed_block
273 zs.next_in = fp->compressed_block + 18;
274 zs.avail_in = block_length - 16;
275 zs.next_out = fp->uncompressed_block;
276 zs.avail_out = fp->uncompressed_block_size;
278 int status = inflateInit2(&zs, GZIP_WINDOW_BITS);
279 if (status != Z_OK) {
280 report_error(fp, "inflate init failed");
283 status = inflate(&zs, Z_FINISH);
284 if (status != Z_STREAM_END) {
286 report_error(fp, "inflate failed");
289 status = inflateEnd(&zs);
290 if (status != Z_OK) {
291 report_error(fp, "inflate failed");
299 check_header(const byte* header)
301 return (header[0] == GZIP_ID1 &&
302 header[1] == (byte) GZIP_ID2 &&
303 header[2] == Z_DEFLATED &&
304 (header[3] & FLG_FEXTRA) != 0 &&
305 unpackInt16((uint8_t*)&header[10]) == BGZF_XLEN &&
306 header[12] == BGZF_ID1 &&
307 header[13] == BGZF_ID2 &&
308 unpackInt16((uint8_t*)&header[14]) == BGZF_LEN);
315 byte header[BLOCK_HEADER_LENGTH];
316 int64_t block_address = ftello(fp->file);
317 int count = fread(header, 1, sizeof(header), fp->file);
319 fp->block_length = 0;
322 if (count != sizeof(header)) {
323 report_error(fp, "read failed");
326 if (!check_header(header)) {
327 report_error(fp, "invalid block header");
330 int block_length = unpackInt16((uint8_t*)&header[16]) + 1;
331 byte* compressed_block = (byte*) fp->compressed_block;
332 memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
333 int remaining = block_length - BLOCK_HEADER_LENGTH;
334 count = fread(&compressed_block[BLOCK_HEADER_LENGTH], 1, remaining, fp->file);
335 if (count != remaining) {
336 report_error(fp, "read failed");
339 count = inflate_block(fp, block_length);
343 if (fp->block_length != 0) {
344 // Do not reset offset if this read follows a seek.
345 fp->block_offset = 0;
347 fp->block_address = block_address;
348 fp->block_length = count;
353 bgzf_read(BGZF* fp, void* data, int length)
358 if (fp->open_mode != 'r') {
359 report_error(fp, "file not open for reading");
365 while (bytes_read < length) {
366 int available = fp->block_length - fp->block_offset;
367 if (available <= 0) {
368 if (read_block(fp) != 0) {
371 available = fp->block_length - fp->block_offset;
372 if (available <= 0) {
376 int copy_length = min(length-bytes_read, available);
377 byte* buffer = fp->uncompressed_block;
378 memcpy(output, buffer + fp->block_offset, copy_length);
379 fp->block_offset += copy_length;
380 output += copy_length;
381 bytes_read += copy_length;
383 if (fp->block_offset == fp->block_length) {
384 fp->block_address = ftello(fp->file);
385 fp->block_offset = 0;
386 fp->block_length = 0;
393 flush_block(BGZF* fp)
395 while (fp->block_offset > 0) {
396 int block_length = deflate_block(fp, fp->block_offset);
397 if (block_length < 0) {
400 int count = fwrite(fp->compressed_block, 1, block_length, fp->file);
401 if (count != block_length) {
402 report_error(fp, "write failed");
405 fp->block_address += block_length;
411 bgzf_write(BGZF* fp, const void* data, int length)
413 if (fp->open_mode != 'w') {
414 report_error(fp, "file not open for writing");
418 if (fp->uncompressed_block == NULL) {
419 fp->uncompressed_block = malloc(fp->uncompressed_block_size);
422 const byte* input = data;
423 int block_length = fp->uncompressed_block_size;
424 int bytes_written = 0;
425 while (bytes_written < length) {
426 int copy_length = min(block_length - fp->block_offset, length - bytes_written);
427 byte* buffer = fp->uncompressed_block;
428 memcpy(buffer + fp->block_offset, input, copy_length);
429 fp->block_offset += copy_length;
430 input += copy_length;
431 bytes_written += copy_length;
432 if (fp->block_offset == block_length) {
433 if (flush_block(fp) != 0) {
438 return bytes_written;
444 if (fp->open_mode == 'w') {
445 if (flush_block(fp) != 0) {
448 if (fflush(fp->file) != 0) {
449 report_error(fp, "flush failed");
453 if (fp->owned_file) {
454 if (fclose(fp->file) != 0) {
458 free(fp->uncompressed_block);
459 free(fp->compressed_block);
467 return ((fp->block_address << 16) | (fp->block_offset & 0xFFFF));
471 bgzf_seek(BGZF* fp, int64_t pos, int where)
473 if (fp->open_mode != 'r') {
474 report_error(fp, "file not open for read");
477 if (where != SEEK_SET) {
478 report_error(fp, "unimplemented seek option");
481 int block_offset = pos & 0xFFFF;
482 int64_t block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
483 if (fseeko(fp->file, block_address, SEEK_SET) != 0) {
484 report_error(fp, "seek failed");
487 fp->block_length = 0; // indicates current block is not loaded
488 fp->block_address = block_address;
489 fp->block_offset = block_offset;