int main(int argc, char *argv[]){
char*gcf_name;
archive_t gcf=NULL;
RTinitPopt(&argc,&argv,options,1,-1,&gcf_name,NULL,"([-c] <gcf> (<dir>|<file>)*) | (-x <gcf> [<dir>|<pattern>])",
"Tool for creating and extracting GCF archives\n\nOptions");
compression_policy_compile(policy);
if (operation==GCF_EXTRACT) {
char *out_name=RTinitNextArg();
archive_t dir;
if(out_name){
if(RTinitNextArg()){
Fatal(1,error,"extraction uses gcf -x <gcf> [<dir>|<pattern>]");
}
if (strstr(out_name,"%s")) {
dir=arch_fmt(out_name,file_input,file_output,blocksize);
} else {
dir=arch_dir_create(out_name,blocksize,force?DELETE_ALL:DELETE_NONE);
}
} else {
dir=arch_dir_open(".",blocksize);
}
if (is_a_dir(gcf_name)){
gcf=arch_dir_open(gcf_name,blocksize);
} else {
gcf=arch_gcf_read(raf_unistd(gcf_name));
}
archive_copy(gcf,"auto",dir,NULL,blocksize);
arch_close(&dir);
arch_close(&gcf);
} else {
if (operation==GCF_FILE){
gcf=arch_gcf_create(raf_unistd(gcf_name),blocksize,blocksize*blockcount,0,1);
} else {
gcf=arch_dir_create(gcf_name,blocksize,force?DELETE_ALL:DELETE_NONE);
}
for(;;){
char *input_name=RTinitNextArg();
if (!input_name) break;
if (is_a_dir(input_name)){
Warning(info,"copying contents of %s",input_name);
archive_t dir=arch_dir_open(input_name,blocksize);
archive_copy(dir,NULL,gcf,get_compression,blocksize);
arch_close(&dir);
} else {
Warning(info,"copying %s",input_name);
stream_t is=file_input(input_name);
stream_t os=arch_write(gcf,input_name,get_compression(input_name),1);
char buf[blocksize];
for(;;){
int len=stream_read_max(is,buf,blocksize);
if (len) stream_write(os,buf,len);
if(len<blocksize) break;
}
stream_close(&is);
stream_close(&os);
}
}
arch_close(&gcf);
}
}
bool is_valid_vcf_file(std::istream &input,
const std::string &sourceName,
ValidationLevel validationLevel,
std::vector<std::unique_ptr<ebi::vcf::ReportWriter>> &outputs)
{
std::vector<char> line;
get_magic_num(input, line);
std::string file_extension = get_compression(sourceName, line);
check_readability_of_file(file_extension);
if (file_extension == NO_EXT) {
return process_vcf_stream(input, sourceName, validationLevel, outputs);
} else {
boost::iostreams::filtering_istream uncompressed_input;
create_uncompressed_stream(input, file_extension, uncompressed_input);
return process_vcf_stream(uncompressed_input, sourceName, validationLevel, outputs);
}
}
static int load_conf_field_and_value(struct conf **c,
const char *f, // field
const char *v, // value
const char *conf_path,
int line)
{
if(!strcmp(f, "compression"))
{
int compression=get_compression(v);
if(compression<0) return -1;
set_int(c[OPT_COMPRESSION], compression);
}
else if(!strcmp(f, "ssl_compression"))
{
int compression=get_compression(v);
if(compression<0) return -1;
set_int(c[OPT_SSL_COMPRESSION], compression);
}
else if(!strcmp(f, "ratelimit"))
{
float f=0;
f=atof(v);
// User is specifying Mega bits per second.
// Need to convert to bytes per second.
f=(f*1024*1024)/8;
if(!f)
{
logp("ratelimit should be greater than zero\n");
return -1;
}
set_float(c[OPT_RATELIMIT], f);
}
else
{
int i=0;
for(i=0; i<OPT_MAX; i++)
{
if(strcmp(c[i]->field, f)) continue;
switch(c[i]->conf_type)
{
case CT_STRING:
return set_string(c[i], v);
case CT_UINT:
return set_int(c[i], atoi(v));
case CT_FLOAT:
return set_float(c[i], atof(v));
break;
case CT_MODE_T:
return set_mode_t(c[i],
strtol(v, NULL, 8));
case CT_SSIZE_T:
{
uint64_t s=0;
return
get_file_size(v, &s, conf_path, line)
|| set_uint64_t(c[i], s);
}
case CT_E_BURP_MODE:
return set_e_burp_mode(c[i],
str_to_burp_mode(v));
case CT_E_PROTOCOL:
return set_e_protocol(c[i],
str_to_protocol(v));
case CT_E_RECOVERY_METHOD:
return set_e_recovery_method(c[i],
str_to_recovery_method(v));
case CT_STRLIST:
return add_to_strlist(c[i], v,
!strcmp(c[i]->field, "include"));
case CT_E_RSHASH:
break;
case CT_CNTR:
break;
// No default so we get a warning if something
// was missed;
}
}
}
return 0;
}
/* Make and init a Write.
*/
static Write *
write_new( VipsImage *im, const char *filename,
VipsForeignTiffCompression compression, int Q,
VipsForeignTiffPredictor predictor,
char *profile,
gboolean tile, int tile_width, int tile_height,
gboolean pyramid,
gboolean squash,
gboolean miniswhite,
VipsForeignTiffResunit resunit, double xres, double yres,
gboolean bigtiff,
gboolean rgbjpeg,
gboolean properties,
gboolean strip )
{
Write *write;
if( !(write = VIPS_NEW( im, Write )) )
return( NULL );
write->im = im;
write->filename = vips_strdup( VIPS_OBJECT( im ), filename );
write->layer = NULL;
write->tbuf = NULL;
write->compression = get_compression( compression );
write->jpqual = Q;
write->predictor = predictor;
write->tile = tile;
write->tilew = tile_width;
write->tileh = tile_height;
write->pyramid = pyramid;
write->onebit = squash;
write->miniswhite = miniswhite;
write->icc_profile = vips_strdup( NULL, profile );
write->bigtiff = bigtiff;
write->rgbjpeg = rgbjpeg;
write->properties = properties;
write->strip = strip;
write->resunit = get_resunit( resunit );
write->xres = xres;
write->yres = yres;
/* In strip mode we use tileh to set rowsperstrip, and that does not
* have the multiple-of-16 restriction.
*/
if( tile ) {
if( (write->tilew & 0xf) != 0 ||
(write->tileh & 0xf) != 0 ) {
vips_error( "vips2tiff",
"%s", _( "tile size not a multiple of 16" ) );
return( NULL );
}
}
/* We can only pyramid LABQ and non-complex images.
*/
if( write->pyramid ) {
if( im->Coding == VIPS_CODING_NONE &&
vips_band_format_iscomplex( im->BandFmt ) ) {
vips_error( "vips2tiff",
"%s", _( "can only pyramid LABQ and "
"non-complex images" ) );
return( NULL );
}
}
/* Only 1-bit-ize 8 bit mono images.
*/
if( write->onebit &&
(im->Coding != VIPS_CODING_NONE ||
im->BandFmt != VIPS_FORMAT_UCHAR ||
im->Bands != 1) ) {
vips_warn( "vips2tiff",
"%s", _( "can only squash 1 band uchar images -- "
"disabling squash" ) );
write->onebit = 0;
}
if( write->onebit &&
write->compression == COMPRESSION_JPEG ) {
vips_warn( "vips2tiff",
"%s", _( "can't have 1-bit JPEG -- disabling JPEG" ) );
write->compression = COMPRESSION_NONE;
}
/* We can only MINISWHITE non-complex images of 1 or 2 bands.
*/
if( write->miniswhite &&
(im->Coding != VIPS_CODING_NONE ||
vips_band_format_iscomplex( im->BandFmt ) ||
im->Bands > 2) ) {
vips_warn( "vips2tiff",
"%s", _( "can only save non-complex greyscale images "
"as miniswhite -- disabling miniswhite" ) );
write->miniswhite = FALSE;
}
/* Sizeof a line of bytes in the TIFF tile.
*/
if( im->Coding == VIPS_CODING_LABQ )
write->tls = write->tilew * 3;
else if( write->onebit )
write->tls = VIPS_ROUND_UP( write->tilew, 8 ) / 8;
else
write->tls = VIPS_IMAGE_SIZEOF_PEL( im ) * write->tilew;
/* Build the pyramid framework.
*/
write->layer = pyramid_new( write, NULL, im->Xsize, im->Ysize );
/* Fill all the layers.
*/
if( pyramid_fill( write ) ) {
write_free( write );
return( NULL );
}
if( tile )
write->tbuf = vips_malloc( NULL,
TIFFTileSize( write->layer->tif ) );
else
write->tbuf = vips_malloc( NULL,
TIFFScanlineSize( write->layer->tif ) );
if( !write->tbuf ) {
write_free( write );
return( NULL );
}
return( write );
}
void ReadBinaryRaster(
char *file,
IHEAD **head,
unsigned char **data,
int *bpi,int *width,int *height)
{
FILE *fp;
IHEAD *ihead;
int outbytes, depth, comp, filesize, complen, n;
unsigned char *indata, *outdata;
/* open the image file */
fp = fopen(file,"rb");
if (fp == NULL)
syserr("ReadBinaryRaster",file,"fopen");
/* read in the image header */
(*head) = readihdr(fp);
ihead = *head;
depth = get_depth(ihead);
if(depth != 1)
fatalerr("ReadBinaryRaster",file,"not a binary file");
(*width) = get_width(ihead);
(*height) = get_height(ihead);
(*bpi) = get_density(ihead);
comp = get_compression(ihead);
complen = get_complen(ihead);
/* allocate a raster data buffer */
filesize = SizeFromDepth(*width, *height, depth);
malloc_uchar(&outdata, filesize, "ReadIheadRaster : outdata");
/* read in the raster data */
if(comp == UNCOMP) { /* file is uncompressed */
n = fread(outdata,1,filesize,fp);
if (n != filesize) {
(void) fprintf(stderr,
"ReadBinaryRaster: %s: fread returned %d (expected %d)\n",
file,n,filesize);
exit(1);
} /* IF */
} else {
malloc_uchar(&indata, complen, "ReadBinaryRaster : indata");
n = fread(indata,1,complen,fp); /* file compressed */
if (n != complen) {
(void) fprintf(stderr,
"ReadBinaryRaster: %s: fread returned %d (expected %d)\n",
file,n,complen);
} /* IF */
}
switch (comp) {
case RL:
rldecomp(indata,complen,outdata,&outbytes,filesize);
set_compression(ihead, UNCOMP);
set_complen(ihead, 0);
free((char *)indata);
break;
case CCITT_G4:
if((*head)->sigbit == LSBF) {
inv_bytes(indata, complen);
(*head)->sigbit = MSBF;
(*head)->byte_order = HILOW;
}
grp4decomp(indata,complen,*width,*height,outdata,&outbytes);
set_compression(ihead, UNCOMP);
set_complen(ihead, 0);
free((char *)indata);
break;
case UNCOMP:
break;
default:
fatalerr("ReadBinaryRaster",file,"Invalid compression code");
break;
}
*data = outdata;
/* close the image file */
(void) fclose(fp);
}
