// write a widget and all it's children:
void Fl_Type::write() {
int level = 0;
for (Fl_Type* p = parent; p; p = p->parent) level++;
write_indent(level);
write_word(type_name());
write_word(name());
write_open(level);
write_properties();
write_close(level);
if (!is_parent()) return;
// now do children:
write_open(level);
Fl_Type *child;
for (child = first_child; child; child = child->next_brother) child->write();
write_close(level);
}
int main(int argc, char **argv)
{
int c, compress, pstdout, is_forced;
_mpu_bgzf *fp;
void *buffer;
long start, end, size;
compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
while((c = getopt(argc, argv, "cdhfb:s:")) >= 0){
switch(c){
case 'h': return bgzip_main_usage();
case 'd': compress = 0; break;
case 'c': pstdout = 1; break;
case 'b': start = atol(optarg); break;
case 's': size = atol(optarg); break;
case 'f': is_forced = 1; break;
}
}
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();
fp = _mpu_bgzf_fdopen(f_dst, "w");
buffer = malloc(WINDOW_SIZE);
while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)
if (_mpu_bgzf_write(fp, buffer, c) < 0) fail(fp);
// f_dst will be closed here
if (_mpu_bgzf_close(fp) < 0) fail(fp);
if (argc > optind && !pstdout) unlink(argv[optind]);
free(buffer);
close(f_src);
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 = _mpu_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 = _mpu_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 (_mpu_bgzf_seek(fp, start, SEEK_SET) < 0) fail(fp);
while (1) {
if (end < 0) c = _mpu_bgzf_read(fp, buffer, WINDOW_SIZE);
else c = _mpu_bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
if (c == 0) break;
if (c < 0) fail(fp);
start += c;
write(f_dst, buffer, c);
if (end >= 0 && start >= end) break;
}
free(buffer);
if (_mpu_bgzf_close(fp) < 0) fail(fp);
if (!pstdout) unlink(argv[optind]);
return 0;
}
}
static void write_open_space(Context* ctx, const char* name) {
write_open(ctx, name, NEXT_CHAR_SPACE);
}
static void write_open_newline(Context* ctx, const char* name) {
write_open(ctx, name, NEXT_CHAR_NEWLINE);
}
int main(int argc, char **argv)
{
int c, compress, pstdout, is_forced;
RAZF *rz;
void *buffer;
long start, end, size;
compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
while((c = getopt(argc, argv, "cdlhfb:s:")) >= 0){
switch(c){
case 'h': return razf_main_usage();
case 'd': compress = 0; break;
case 'c': pstdout = 1; break;
case 'l': compress = 2; break;
case 'b': start = atol(optarg); break;
case 's': size = atol(optarg); break;
case 'f': is_forced = 1; break;
}
}
if (size >= 0) end = start + size;
if(end >= 0 && end < start){
fprintf(stderr, " -- Illegal region: [%ld, %ld] --\n", start, end);
return 1;
}
if(compress == 1){
int f_src, f_dst = -1;
if(argc > optind){
if((f_src = open(argv[optind], O_RDONLY)) < 0){
fprintf(stderr, " -- Cannot open file: %s --\n", argv[optind]);
return 1;
}
if(pstdout){
f_dst = fileno(stdout);
} else {
char *name = malloc(sizeof(strlen(argv[optind]) + 5));
strcpy(name, argv[optind]);
strcat(name, ".rz");
f_dst = write_open(name, is_forced);
if (f_dst < 0) return 1;
free(name);
}
} else if(pstdout){
f_src = fileno(stdin);
f_dst = fileno(stdout);
} else return razf_main_usage();
rz = razf_dopen(f_dst, "w");
buffer = malloc(WINDOW_SIZE);
while((c = read(f_src, buffer, WINDOW_SIZE)) > 0) razf_write(rz, buffer, c);
razf_close(rz); // f_dst will be closed here
if (argc > optind && !pstdout) unlink(argv[optind]);
free(buffer);
close(f_src);
return 0;
} else {
if(argc <= optind) return razf_main_usage();
if(compress == 2){
rz = razf_open(argv[optind], "r");
if(rz->file_type == FILE_TYPE_RZ) {
printf("%20s%20s%7s %s\n", "compressed", "uncompressed", "ratio", "name");
printf("%20lld%20lld%6.1f%% %s\n", (long long)rz->end, (long long)rz->src_end, rz->end * 100.0f / rz->src_end,
argv[optind]);
} else fprintf(stdout, "%s is not a regular rz file\n", argv[optind]);
} else {
int f_dst;
if (argc > optind && !pstdout) {
char *name;
if (strstr(argv[optind], ".rz") - argv[optind] != strlen(argv[optind]) - 3) {
printf("razip: %s: unknown suffix -- ignored\n", argv[optind]);
return 1;
}
name = strdup(argv[optind]);
name[strlen(name) - 3] = '\0';
f_dst = write_open(name, is_forced);
free(name);
} else f_dst = fileno(stdout);
rz = razf_open(argv[optind], "r");
buffer = malloc(WINDOW_SIZE);
razf_seek(rz, start, SEEK_SET);
while(1){
if(end < 0) c = razf_read(rz, buffer, WINDOW_SIZE);
else c = razf_read(rz, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
if(c <= 0) break;
start += c;
write(f_dst, buffer, c);
if(end >= 0 && start >= end) break;
}
free(buffer);
if (!pstdout) unlink(argv[optind]);
}
razf_close(rz);
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;
}
