htslib/bgzip.c at develop · SelfHacked/htslib · GitHub

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/* bgzip.c -- Block compression/decompression utility.

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 notices 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 <config.h>

#include <stdlib.h>

#include <string.h>

#include <strings.h>

#include <stdio.h>

#include <fcntl.h>

#include <unistd.h>

#include <errno.h>

#include <stdarg.h>

#include <getopt.h>

#include <inttypes.h>

#include "htslib/bgzf.h"

#include "htslib/hts.h"

#ifdef _WIN32

# define WIN32_LEAN_AND_MEAN

# include <windows.h>

#endif

static const int WINDOW_SIZE = 64 * 1024;

static void error(const char *format, ...)

{

va_list ap;

va_start(ap, format);

vfprintf(stderr, format, ap);

va_end(ap);

exit(EXIT_FAILURE);

}

static int ask_yn()

{

char line[1024];

if (fgets(line, sizeof line, stdin) == NULL)

return 0;

return line[0] == 'Y' || line[0] == 'y';

}

static int confirm_overwrite(const char *fn)

{

int save_errno = errno;

int ret = 0;

if (isatty(STDIN_FILENO)) {

fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn);

if (ask_yn()) ret = 1;

}

errno = save_errno;

return ret;

}

static int known_extension(const char *ext)

{

static const char *known[] = {

"gz", "bgz", "bgzf",

NULL

};

const char **p;

for (p = known; *p; p++)

if (strcasecmp(ext, *p) == 0) return 1;

return 0;

}

static int confirm_filename(int *is_forced, const char *name, const char *ext)

{

if (*is_forced) {

(*is_forced)--;

return 1;

}

if (!isatty(STDIN_FILENO))

return 0;

fprintf(stderr, "[bgzip] .%s is not a known extension; do you wish to decompress to %s (y or n)? ", ext, name);

return ask_yn();

}

static int bgzip_main_usage(FILE *fp, int status)

{

fprintf(fp, "\n");

fprintf(fp, "Version: %s\n", hts_version());

fprintf(fp, "Usage: bgzip [OPTIONS] [FILE] ...\n");

fprintf(fp, "Options:\n");

fprintf(fp, " -b, --offset INT decompress at virtual file pointer (0-based uncompressed offset)\n");

fprintf(fp, " -c, --stdout write on standard output, keep original files unchanged\n");

fprintf(fp, " -d, --decompress decompress\n");

fprintf(fp, " -f, --force overwrite files without asking\n");

fprintf(fp, " -h, --help give this help\n");

fprintf(fp, " -i, --index compress and create BGZF index\n");

fprintf(fp, " -I, --index-name FILE name of BGZF index file [file.gz.gzi]\n");

fprintf(fp, " -l, --compress-level INT Compression level to use when compressing; 0 to 9, or -1 for default [-1]\n");

fprintf(fp, " -r, --reindex (re)index compressed file\n");

fprintf(fp, " -g, --rebgzip use an index file to bgzip a file\n");

fprintf(fp, " -s, --size INT decompress INT bytes (uncompressed size)\n");

fprintf(fp, " -@, --threads INT number of compression threads to use [1]\n");

fprintf(fp, " -t, --test test integrity of compressed file");

fprintf(fp, "\n");

return status;

}

int main(int argc, char **argv)

{

int c, compress, compress_level = -1, pstdout, is_forced, test, index = 0, rebgzip = 0, reindex = 0;

BGZF *fp;

void *buffer;

long start, end, size;

char *index_fname = NULL;

int threads = 1;

static const struct option loptions[] =

{

{"help", no_argument, NULL, 'h'},

{"offset", required_argument, NULL, 'b'},

{"stdout", no_argument, NULL, 'c'},

{"decompress", no_argument, NULL, 'd'},

{"force", no_argument, NULL, 'f'},

{"index", no_argument, NULL, 'i'},

{"index-name", required_argument, NULL, 'I'},

{"compress-level", required_argument, NULL, 'l'},

{"reindex", no_argument, NULL, 'r'},

{"rebgzip",no_argument,NULL,'g'},

{"size", required_argument, NULL, 's'},

{"threads", required_argument, NULL, '@'},

{"test", no_argument, NULL, 't'},

{"version", no_argument, NULL, 1},

{NULL, 0, NULL, 0}

};

compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0; test = 0;

while((c = getopt_long(argc, argv, "cdh?fb:@:s:iI:l:grt",loptions,NULL)) >= 0){

switch(c){

case 'd': compress = 0; break;

case 'c': pstdout = 1; break;

case 'b': start = atol(optarg); compress = 0; pstdout = 1; break;

case 's': size = atol(optarg); pstdout = 1; break;

case 'f': is_forced++; break;

case 'i': index = 1; break;

case 'I': index_fname = optarg; break;

case 'l': compress_level = atol(optarg); break;

case 'g': rebgzip = 1; break;

case 'r': reindex = 1; compress = 0; break;

case '@': threads = atoi(optarg); break;

case 't': test = 1; compress = 0; reindex = 0; break;

case 1:

printf(

"bgzip (htslib) %s\n"

return EXIT_SUCCESS;

case 'h': return bgzip_main_usage(stdout, EXIT_SUCCESS);

case '?': return bgzip_main_usage(stderr, EXIT_FAILURE);

}

if (size >= 0) end = start + size;

if (end >= 0 && end < start) {

fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end);

return 1;

}

if (compress == 1) {

int f_src = fileno(stdin);

char out_mode[3] = "w\0";

char out_mode_exclusive[4] = "wx\0";

if (compress_level < -1 || compress_level > 9) {

fprintf(stderr, "[bgzip] Invalid compress-level: %d\n", compress_level);

return 1;

}

if (compress_level >= 0) {

out_mode[1] = compress_level + '0';

out_mode_exclusive[2] = compress_level + '0';

}

if ( argc>optind )

{

if ((f_src = open(argv[optind], O_RDONLY)) < 0) {

fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);

return 1;

}

if (pstdout)

fp = bgzf_open("-", out_mode);

else

{

char *name = malloc(strlen(argv[optind]) + 5);

strcpy(name, argv[optind]);

strcat(name, ".gz");

fp = bgzf_open(name, is_forced? out_mode : out_mode_exclusive);

if (fp == NULL && errno == EEXIST && confirm_overwrite(name))

fp = bgzf_open(name, out_mode);

if (fp == NULL) {

fprintf(stderr, "[bgzip] can't create %s: %s\n", name, strerror(errno));

free(name);

return 1;

}

free(name);

}

else if (!pstdout && isatty(fileno((FILE *)stdout)) )

return bgzip_main_usage(stderr, EXIT_FAILURE);

else if ( index && !index_fname )

{

fprintf(stderr, "[bgzip] Index file name expected when writing to stdout\n");

return 1;

}

else

fp = bgzf_open("-", out_mode);

if ( index && rebgzip )

{

fprintf(stderr, "[bgzip] Can't produce a index and rebgzip simultaneously\n");

return 1;

}

if ( rebgzip && !index_fname )

{

fprintf(stderr, "[bgzip] Index file name expected when writing to stdout\n");

return 1;

}

if ( index ) bgzf_index_build_init(fp);

if (threads > 1)

bgzf_mt(fp, threads, 256);

buffer = malloc(WINDOW_SIZE);

#ifdef _WIN32

_setmode(f_src, O_BINARY);

#endif

if (rebgzip){

if ( bgzf_index_load(fp, index_fname, NULL) < 0 ) error("Could not load index: %s.gzi\n", argv[optind]);

while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)

if (bgzf_block_write(fp, buffer, c) < 0) error("Could not write %d bytes: Error %d\n", c, fp->errcode);

}

else {

while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)

if (bgzf_write(fp, buffer, c) < 0) error("Could not write %d bytes: Error %d\n", c, fp->errcode);

}

if ( index )

{

if (index_fname) {

if (bgzf_index_dump(fp, index_fname, NULL) < 0)

error("Could not write index to '%s'\n", index_fname);

} else {

if (bgzf_index_dump(fp, argv[optind], ".gz.gzi") < 0)

error("Could not write index to '%s.gz.gzi'", argv[optind]);

}

if (bgzf_close(fp) < 0) error("Close failed: Error %d", fp->errcode);

if (argc > optind && !pstdout) unlink(argv[optind]);

free(buffer);

close(f_src);

return 0;

}

else if ( reindex )

{

if ( argc>optind )

{

fp = bgzf_open(argv[optind], "r");

if ( !fp ) error("[bgzip] Could not open file: %s\n", argv[optind]);

}

else

{

if ( !index_fname ) error("[bgzip] Index file name expected when reading from stdin\n");

fp = bgzf_open("-", "r");

if ( !fp ) error("[bgzip] Could not read from stdin: %s\n", strerror(errno));

}

buffer = malloc(BGZF_BLOCK_SIZE);

bgzf_index_build_init(fp);

int ret;

while ( (ret=bgzf_read(fp, buffer, BGZF_BLOCK_SIZE))>0 ) ;

free(buffer);

if ( ret<0 ) error("Is the file gzipped or bgzipped? The latter is required for indexing.\n");

if ( index_fname ) {

if (bgzf_index_dump(fp, index_fname, NULL) < 0)

error("Could not write index to '%s'\n", index_fname);

} else {

if (bgzf_index_dump(fp, argv[optind], ".gzi") < 0)

error("Could not write index to '%s.gzi'\n", argv[optind]);

}

if ( bgzf_close(fp)<0 ) error("Close failed: Error %d\n",fp->errcode);

return 0;

}

else

{

int f_dst;

if ( argc>optind )

{

fp = bgzf_open(argv[optind], "r");

if (fp == NULL) {

fprintf(stderr, "[bgzip] Could not open %s: %s\n", argv[optind], strerror(errno));

return 1;

}

if (bgzf_compression(fp) == no_compression) {

fprintf(stderr, "[bgzip] %s: not a compressed file -- ignored\n", argv[optind]);

bgzf_close(fp);

return 1;

}

if (pstdout || test) {

f_dst = fileno(stdout);

}

else {

const int wrflags = O_WRONLY | O_CREAT | O_TRUNC;

char *name = argv[optind], *ext;

size_t pos;

for (pos = strlen(name); pos > 0; --pos)

if (name[pos] == '.' || name[pos] == '/') break;

if (pos == 0 || name[pos] != '.') {

fprintf(stderr, "[bgzip] can't remove an extension from %s -- please rename\n", argv[optind]);

bgzf_close(fp);

return 1;

}

name = strdup(argv[optind]);

name[pos] = '\0';

ext = &name[pos+1];

if (! (known_extension(ext) || confirm_filename(&is_forced, name, ext))) {

fprintf(stderr, "[bgzip] unknown extension .%s -- declining to decompress to %s\n", ext, name);

bgzf_close(fp);

free(name);

return 1;

}

f_dst = open(name, is_forced? wrflags : wrflags|O_EXCL, 0666);

if (f_dst < 0 && errno == EEXIST && confirm_overwrite(name))

f_dst = open(name, wrflags, 0666);

if (f_dst < 0) {

fprintf(stderr, "[bgzip] can't create %s: %s\n", name, strerror(errno));

free(name);

return 1;

}

free(name);

}

else if (!pstdout && isatty(fileno((FILE *)stdin)) )

return bgzip_main_usage(stderr, EXIT_FAILURE);

else

{

f_dst = fileno(stdout);

fp = bgzf_open("-", "r");

if (fp == NULL) {

fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));

return 1;

}

if (bgzf_compression(fp) == no_compression) {

fprintf(stderr, "[bgzip] stdin is not compressed -- ignored\n");

bgzf_close(fp);

return 1;

}

buffer = malloc(WINDOW_SIZE);

if ( start>0 )

{

if (index_fname) {

if ( bgzf_index_load(fp, index_fname, NULL) < 0 )

error("Could not load index: %s\n", index_fname);

} else {

if (optind >= argc) {

error("The -b option requires -I when reading from stdin "

"(and stdin must be seekable)\n");

}

if ( bgzf_index_load(fp, argv[optind], ".gzi") < 0 )

error("Could not load index: %s.gzi\n", argv[optind]);

}

if ( bgzf_useek(fp, start, SEEK_SET) < 0 ) error("Could not seek to %d-th (uncompressd) byte\n", start);

}

if (threads > 1)

bgzf_mt(fp, threads, 256);

#ifdef _WIN32

_setmode(f_dst, O_BINARY);

#endif

while (1) {

if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE);

else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));

if (c == 0) break;

if (c < 0) error("Error %d in block starting at offset %" PRId64 "(%" PRIX64 ")\n", fp->errcode, fp->block_address, fp->block_address);

start += c;

if ( !test && write(f_dst, buffer, c) != c ) {

#ifdef _WIN32

if (GetLastError() != ERROR_NO_DATA)

#endif

error("Could not write %d bytes\n", c);

}

if (end >= 0 && start >= end) break;

}

free(buffer);

if (bgzf_close(fp) < 0) error("Close failed: Error %d\n",fp->errcode);

if (argc > optind && !pstdout && !test) unlink(argv[optind]);

return 0;

}

htslib/bgzip.c at develop · SelfHacked/htslib · GitHub

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