int fai_build(const char *fn)
{
char *str;
BGZF *bgzf;
FILE *fp;
faidx_t *fai;
str = (char*)calloc(strlen(fn) + 5, 1);
sprintf(str, "%s.fai", fn);
bgzf = bgzf_open(fn, "r");
if ( !bgzf ) {
fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn);
free(str);
return -1;
}
if ( bgzf->is_compressed ) bgzf_index_build_init(bgzf);
fai = fai_build_core(bgzf);
if ( bgzf->is_compressed ) bgzf_index_dump(bgzf, fn, ".gzi");
bgzf_close(bgzf);
fp = fopen(str, "wb");
if ( !fp ) {
fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str);
fai_destroy(fai); free(str);
return -1;
}
fai_save(fai, fp);
fclose(fp);
free(str);
fai_destroy(fai);
return 0;
}
bcf_sweep_t *bcf_sweep_init(const char *fname)
{
bcf_sweep_t *sw = (bcf_sweep_t*) calloc(1,sizeof(bcf_sweep_t));
sw->file = hts_open(fname, "r");
sw->fp = hts_get_bgzfp(sw->file);
bgzf_index_build_init(sw->fp);
sw->hdr = bcf_hdr_read(sw->file);
sw->mrec = 1;
sw->rec = (bcf1_t*) calloc(sw->mrec,(sizeof(bcf1_t)));
sw->block_size = 1024*1024*3;
sw->direction = SW_FWD;
return sw;
}
int main(int argc, char **argv)
{
int c, compress, pstdout, is_forced, 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'},
{"reindex", no_argument, NULL, 'r'},
{"rebgzip",no_argument,NULL,'g'},
{"size", required_argument, NULL, 's'},
{"threads", required_argument, NULL, '@'},
{"version", no_argument, NULL, 1},
{NULL, 0, NULL, 0}
};
compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
while((c = getopt_long(argc, argv, "cdh?fb:@:s:iI:gr",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 = 1; break;
case 'i': index = 1; break;
case 'I': index_fname = optarg; break;
case 'g': rebgzip = 1; break;
case 'r': reindex = 1; compress = 0; break;
case '@': threads = atoi(optarg); break;
case 1:
printf(
"bgzip (htslib) %s\n"
"Copyright (C) 2017 Genome Research Ltd.\n", hts_version());
return EXIT_SUCCESS;
case 'h':
case '?': return bgzip_main_usage();
}
}
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) {
struct stat sbuf;
int f_src = fileno(stdin);
if ( argc>optind )
{
if ( stat(argv[optind],&sbuf)<0 )
{
fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
return 1;
}
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("-", "w");
else
{
char *name = malloc(strlen(argv[optind]) + 5);
strcpy(name, argv[optind]);
strcat(name, ".gz");
fp = bgzf_open(name, is_forced? "w" : "wx");
if (fp == NULL && errno == EEXIST && confirm_overwrite(name))
fp = bgzf_open(name, "w");
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();
else if ( index && !index_fname )
{
fprintf(stderr, "[bgzip] Index file name expected when writing to stdout\n");
return 1;
}
else
fp = bgzf_open("-", "w");
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 (threads > 1)
bgzf_mt(fp, threads, 256);
if ( index ) bgzf_index_build_init(fp);
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
{
struct stat sbuf;
int f_dst;
if ( argc>optind )
{
if ( stat(argv[optind],&sbuf)<0 )
{
fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
return 1;
}
char *name;
int len = strlen(argv[optind]);
if ( strcmp(argv[optind]+len-3,".gz") )
{
fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]);
return 1;
}
fp = bgzf_open(argv[optind], "r");
if (fp == NULL) {
fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]);
return 1;
}
if (pstdout) {
f_dst = fileno(stdout);
}
else {
const int wrflags = O_WRONLY | O_CREAT | O_TRUNC;
name = strdup(argv[optind]);
name[strlen(name) - 3] = '\0';
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();
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 (threads > 1)
bgzf_mt(fp, threads, 256);
buffer = malloc(WINDOW_SIZE);
if ( start>0 )
{
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);
}
#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("Could not read %d bytes: Error %d\n", (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start), fp->errcode);
start += c;
if ( 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 (!pstdout) unlink(argv[optind]);
return 0;
}
}
int main(int argc, char **argv)
{
int c, compress, pstdout, is_forced, index = 0, reindex = 0;
BGZF *fp;
void *buffer;
long start, end, size;
char *index_fname = NULL;
static struct option loptions[] =
{
{"help",0,0,'h'},
{"offset",1,0,'b'},
{"stdout",0,0,'c'},
{"decompress",0,0,'d'},
{"force",0,0,'f'},
{"index",0,0,'i'},
{"index-name",1,0,'I'},
{"reindex",0,0,'r'},
{"size",1,0,'s'},
{0,0,0,0}
};
compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
while((c = getopt_long(argc, argv, "cdh?fb:s:iI:r",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 = 1; break;
case 'i': index = 1; break;
case 'I': index_fname = optarg; break;
case 'r': reindex = 1; compress = 0; break;
case 'h':
case '?': return bgzip_main_usage();
}
}
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) {
struct stat sbuf;
int f_src = fileno(stdin);
int f_dst = fileno(stdout);
if ( argc>optind )
{
if ( stat(argv[optind],&sbuf)<0 )
{
fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
return 1;
}
if ((f_src = open(argv[optind], O_RDONLY)) < 0) {
fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
return 1;
}
if (pstdout)
f_dst = fileno(stdout);
else
{
char *name = malloc(strlen(argv[optind]) + 5);
strcpy(name, argv[optind]);
strcat(name, ".gz");
f_dst = write_open(name, is_forced);
if (f_dst < 0) return 1;
free(name);
}
}
else if (!pstdout && isatty(fileno((FILE *)stdout)) )
return bgzip_main_usage();
else if ( index && !index_fname )
{
fprintf(stderr, "[bgzip] Index file name expected when writing to stdout\n");
return 1;
}
fp = bgzf_fdopen(f_dst, "w");
if ( index ) bgzf_index_build_init(fp);
buffer = malloc(WINDOW_SIZE);
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);
// f_dst will be closed here
if ( index )
{
if ( index_fname ) bgzf_index_dump(fp, index_fname, NULL);
else bgzf_index_dump(fp, argv[optind], ".gz.gzi");
}
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_fdopen(fileno(stdin), "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 )
bgzf_index_dump(fp, index_fname, NULL);
else
bgzf_index_dump(fp, argv[optind], ".gzi");
if ( bgzf_close(fp)<0 ) error("Close failed: Error %d\n",fp->errcode);
return 0;
}
else
{
struct stat sbuf;
int f_dst;
if ( argc>optind )
{
if ( stat(argv[optind],&sbuf)<0 )
{
fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
return 1;
}
char *name;
int len = strlen(argv[optind]);
if ( strcmp(argv[optind]+len-3,".gz") )
{
fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]);
return 1;
}
fp = bgzf_open(argv[optind], "r");
if (fp == NULL) {
fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]);
return 1;
}
if (pstdout) {
f_dst = fileno(stdout);
}
else {
name = strdup(argv[optind]);
name[strlen(name) - 3] = '\0';
f_dst = write_open(name, is_forced);
free(name);
}
}
else if (!pstdout && isatty(fileno((FILE *)stdin)) )
return bgzip_main_usage();
else
{
f_dst = fileno(stdout);
fp = bgzf_fdopen(fileno(stdin), "r");
if (fp == NULL) {
fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
return 1;
}
}
buffer = malloc(WINDOW_SIZE);
if ( start>0 )
{
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);
}
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("Could not read %d bytes: Error %d\n", (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start), fp->errcode);
start += c;
if ( write(f_dst, buffer, c) != c ) 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 (!pstdout) unlink(argv[optind]);
return 0;
}
return 0;
}