void link(void) {
int i;
FILE *fp;
if ( ( obj_file_cnt() + lib_file_cnt() ) > 0 ) {
if ( get_dosex() != OPT_PMODE )
fprintf( stderr, "LINK use only with PMODE!\n" );
sprintf( args, "/NOIGNORECASE %s @" RESPONSE " ",
get_option(OPT_MAPFILE) ? "/MAP" : "" );
fp = response( RESPONSE );
if (! get_option(OPT_NODEFLIB) ) {
if ( get_option(OPT_DEBUG) )
fprintf(fp,"%s\\C0DOSD.OBJ", get_syslib_path() );
else
fprintf(fp,"%s\\C0DOS.OBJ", get_syslib_path() );
}
for ( i = 0; i < obj_file_cnt(); i++ )
fprintf( fp, " %s", obj_file(i) );
fprintf( fp, "\n%s\n%s\n",
get_exe_name(),
get_option( OPT_MAPFILE) ? get_exe_name() : "NUL"
);
if (! get_option(OPT_NODEFLIB) )
fprintf(fp,"%s\\CLDOS.LIB", get_syslib_path() );
for ( i = 0; i < lib_file_cnt(); i++ )
fprintf( fp, " %s", lib_file(i) );
fprintf( fp, "\n" );
fclose(fp);
exec("LINK", args );
if (! get_option(OPT_KEEPRSP) )
unlink( RESPONSE );
}
}
void wlink(void) {
int i;
char *dosx;
FILE *fp;
if ( ( obj_file_cnt() + lib_file_cnt() ) > 0 ) {
switch ( get_dosex() ) {
case OPT_PMODEW:dosx = "pmodew.exe"; break;
case OPT_DOS4G: dosx = "4gs.exe"; break;
case OPT_WDOSX: dosx = "wdosxle.exe"; break;
case OPT_DOS32A:dosx = "dos32a.exe"; break;
case OPT_ZRDX: dosx = "zrdx.exe"; break;
case OPT_CAUSEWAY: dosx = "cwstub.exe"; break;
case OPT_D3X: dosx = "d3xw.exe"; break;
case OPT_PMODE:
default:
fprintf( stderr, "WLINK NO use with PMODE!\n" );
dosx = "4gs.exe";
break;
}
fp = response( RESPONSE );
fprintf( fp,
"op osname=CC386[%s]\n"
"format os2 le\n"
"op nod\n"
"op quiet\n"
"op stub=%s\\%s\n"
"name %s\n",
dosx,
get_syslib_path(),
dosx,
get_exe_name()
);
if ( get_option(OPT_MAPFILE) )
fprintf( fp, "op map\n" );
if ( get_option(OPT_DEBUG) )
fprintf( fp, "debug all \nop symf\n" );
if (! get_option(OPT_NODEFLIB) )
fprintf( fp, "file %s\\C0DOSW.OBJ\n", get_syslib_path() );
for( i = 0; i < obj_file_cnt(); i++)
fprintf( fp, "file %s\n", obj_file(i) );
if (! get_option(OPT_NODEFLIB) )
fprintf( fp, "library %s\\CLDOS.LIB\n", get_syslib_path() );
for( i = 0; i < lib_file_cnt(); i++)
fprintf( fp, "library %s\n", lib_file(i) );
fclose(fp);
exec("WLINK", "@" RESPONSE );
if (! get_option(OPT_KEEPRSP) )
unlink( RESPONSE );
}
}
void tlink(void) {
int i;
FILE *fp;
if ( ( obj_file_cnt() + lib_file_cnt() ) > 0 ) {
if ( get_dosex() != OPT_PMODE )
fprintf( stderr, "TLINK use only with PMODE!\n" );
fp = response( RESPONSE );
fprintf( fp, "/3/c/d%s%s",
get_option(OPT_MAPFILE) ? "/m/l/s" : "/x",
get_option(OPT_DEBUG) ? "/v" : ""
);
if ( lib_file_cnt() > 0 )
fprintf(fp, "/L%s ", get_lib_path() );
if (! get_option(OPT_NODEFLIB) ) {
if ( get_option(OPT_DEBUG) )
fprintf(fp,"%s\\C0DOSD.OBJ", get_syslib_path() );
else
fprintf(fp,"%s\\C0DOS.OBJ", get_syslib_path() );
}
for ( i = 0; i < obj_file_cnt(); i++ )
fprintf( fp, " %s", obj_file(i) );
fprintf( fp, ",%s,%s,",
get_exe_name(),
get_option( OPT_MAPFILE) ? get_exe_name() : "NUL"
);
if (! get_option(OPT_NODEFLIB) )
fprintf(fp,"%s\\CLDOS.LIB", get_syslib_path() );
for ( i = 0; i < lib_file_cnt(); i++ )
fprintf( fp, " %s", lib_file(i) );
fprintf( fp, "\n" );
fclose(fp);
exec("TLINK", "@" RESPONSE );
if (! get_option(OPT_KEEPRSP) )
unlink( RESPONSE );
}
}
/**
* Non-Windows shared library constructor. This ensures that the environment
* variable \c TWEEK_BASE_DIR is set as soon as this shared library is loaded.
* If it is not set, then it sets it based on an assumption about the
* structure of a Tweek installation. More specifically, an assumption is made
* that this shared library lives in the \c lib subdirectory of the Tweek
* installation. Therefore, the root of the Tweek installation is the parent
* of the directory containing this shared library.
*/
extern "C" void __attribute ((constructor)) tweekLibraryInit()
{
fs::path base_dir;
const char* env_dir = std::getenv("TWEEK_BASE_DIR");
// If TWEEK_BASE_DIR is not set, look up the path to this shared library
// and use it to provide a default setting for that environment variable.
if ( NULL == env_dir )
{
Dl_info info;
info.dli_fname = 0;
const int result =
#if defined(__GNUC__) && __GNUC_MAJOR__ < 4
dladdr((void*) &tweekLibraryInit, &info);
#else
dladdr(reinterpret_cast<void*>(&tweekLibraryInit), &info);
#endif
// NOTE: dladdr(3) really does return a non-zero value on success.
if ( 0 != result )
{
try
{
fs::path lib_file(info.dli_fname, fs::native);
lib_file = fs::system_complete(lib_file);
#if defined(VPR_OS_IRIX) && defined(_ABIN32)
const std::string bit_suffix("32");
#elif defined(VPR_OS_IRIX) && defined(_ABI64) || \
defined(VPR_OS_Linux) && defined(__x86_64__)
const std::string bit_suffix("64");
#else
const std::string bit_suffix("");
#endif
// Get the directory containing this shared library.
const fs::path lib_path = lib_file.branch_path();
// Start the search for the root of the Tweek installation in the
// parent of the directory containing this shared library.
base_dir = lib_path.branch_path();
// Use the lib subdirectory to figure out when we have found the
// root of the Tweek installation tree.
const fs::path lib_subdir(std::string("lib") + bit_suffix);
bool found(false);
while ( ! found && ! base_dir.empty() )
{
try
{
if ( ! fs::exists(base_dir / lib_subdir) )
{
base_dir = base_dir.branch_path();
}
else
{
found = true;
}
}
catch (fs::filesystem_error&)
{
base_dir = base_dir.branch_path();
}
}
if ( found )
{
setenv("TWEEK_BASE_DIR",
base_dir.native_directory_string().c_str(), 1);
}
}
catch (fs::filesystem_error& ex)
{
std::cerr << "Automatic assignment of TWEEK_BASE_DIR failed:\n"
<< ex.what() << std::endl;
}
}
}
else
{
try
{
base_dir = fs::path(env_dir, fs::native);
}
catch (fs::filesystem_error& ex)
{
std::cerr << "Invalid path set in TWEEK_BASE_DIR environment "
<< "variable:\n" << ex.what() << std::endl;
}
}
if ( ! base_dir.empty() )
{
// If base_dir were empty, this would result in data_dir being relative
// to the current working directory.
const fs::path data_dir = base_dir / TWEEK_SHARE_DIR;
// We use the overwrite value of 0 as a way around testing whether the
// environment variable is already set.
setenv("TWEEK_DATA_DIR", data_dir.native_directory_string().c_str(), 0);
}
}
/**
* Non-Windows shared library constructor. This ensures that the environment
* variable \c GADGET_BASE_DIR is set as soon as this shared library is loaded.
* If it is not set, then it sets it based on an assumption about the
* structure of a Gadgeteer installation. More specifically, an assumption is
* made that this shared library lives in the \c lib subdirectory of the
* Gadgeteer installation. Therefore, the root of the Gadgeteer installation
* is the parent of the directory containing this shared library.
*/
extern "C" void __attribute ((constructor)) gadgetLibraryInit()
{
fs::path base_dir;
const char* env_dir = std::getenv("GADGET_BASE_DIR");
// If GADGET_BASE_DIR is not set, look up the path to this shared library
// and use it to provide a default setting for that environment variable.
if ( NULL == env_dir )
{
Dl_info info;
info.dli_fname = 0;
const int result =
#if defined(__GNUC__) && __GNUC_MAJOR__ < 4
dladdr((void*) &gadgetLibraryInit, &info);
#else
dladdr(reinterpret_cast<void*>(&gadgetLibraryInit), &info);
#endif
// NOTE: dladdr(3) really does return a non-zero value on success.
if ( 0 != result )
{
try
{
fs::path lib_file(
#if BOOST_VERSION >= 104600 && BOOST_FILESYSTEM_VERSION == 3
info.dli_fname
#else
info.dli_fname, fs::native
#endif
);
lib_file = fs::system_complete(lib_file);
#if defined(GADGET_LIBDIR_NAME)
const std::string lib_dir_name(GADGET_LIBDIR_NAME);
#else
const std::string lib_dir_name("lib");
#endif
// Get the directory containing this shared library.
const fs::path lib_path = lib_file.branch_path();
// Start the search for the root of the Gadgeteer installation in
// the parent of the directory containing this shared library.
base_dir = lib_path.branch_path();
// Use the lib subdirectory to figure out when we have found the
// root of the Gadgeteer installation tree.
const fs::path lib_subdir(lib_dir_name);
bool found(false);
while ( ! found && ! base_dir.empty() )
{
try
{
if ( ! fs::exists(base_dir / lib_subdir) )
{
base_dir = base_dir.branch_path();
}
else
{
found = true;
}
}
catch (fs::filesystem_error&)
{
base_dir = base_dir.branch_path();
}
}
if ( found )
{
setenv("GADGET_BASE_DIR",
#if BOOST_VERSION >= 104600 && BOOST_FILESYSTEM_VERSION == 3
base_dir.native().c_str(),
#else
base_dir.native_directory_string().c_str(),
#endif
1);
}
}
catch (fs::filesystem_error& ex)
{
std::cerr << "Automatic assignment of GADGET_BASE_DIR failed:\n"
<< ex.what() << std::endl;
}
}
}
else
{
try
{
base_dir =
#if BOOST_VERSION >= 104600 && BOOST_FILESYSTEM_VERSION == 3
fs::path(env_dir);
#else
fs::path(env_dir, fs::native);
#endif
}
catch (fs::filesystem_error& ex)
{
std::cerr << "Invalid path set in GADGET_BASE_DIR environment "
<< "variable:\n" << ex.what() << std::endl;
}
}
if ( ! base_dir.empty() )
{
// If base_dir were empty, this would result in data_dir being relative
// to the current working directory.
const fs::path data_dir = base_dir / GADGET_SHARE_DIR;
// We use the overwrite value of 0 as a way around testing whether the
// environment variable is already set.
setenv("GADGET_DATA_DIR",
#if BOOST_VERSION >= 104600 && BOOST_FILESYSTEM_VERSION == 3
data_dir.native().c_str(),
#else
data_dir.native_directory_string().c_str(),
#endif
0);
}
}
bool SRAssembler::read_library_file() {
ifstream lib_file(this->library_file.c_str());
string line;
Library* lib = NULL;
while (getline(lib_file, line)){
line = trim(line);
if (line == "[LIBRARY]") {
if (lib != NULL){
if (lib->get_left_read() == ""){
print_message("r1 file is expected in config file!");
return false;
}
this->libraries.push_back(*lib);
}
lib = new Library(this->libraries.size(), this->data_dir, this->tmp_dir, this->logger);
} else {
vector<string> tokens;
tokenize(line, tokens, "=");
if (tokens.size() == 2){
string param = trim(tokens[0]);
string value = trim(tokens[1]);
if (param == "r1" && lib != NULL) {
lib->set_left_read(value);
if (!file_exists(lib->get_left_read())) {
print_message("r1 file in config file: " + lib->get_left_read() + " does not exist!");
return false;
}
}
if (param == "r2" && lib != NULL) {
lib->set_right_read(value);
if (!file_exists(lib->get_right_read())) {
print_message("r2 file in config file: " + lib->get_right_read() + " does not exist!");
return false;
}
lib->set_paired_end(true);
}
if (param == "insert_size" && lib != NULL) {
lib->set_insert_size(str2int(value));
}
if (param == "direction" && lib != NULL) {
lib->set_reversed(str2int(value));
}
if (param == "format" && lib != NULL) {
if (value == "fastq") {
lib->set_format(FORMAT_FASTQ);
}
else if (value == "fasta") {
lib->set_format(FORMAT_FASTA);
} else {
print_message("format in config file should be 'fastq' or 'fasta'!");
return false;
}
}
}
}
}
if (lib != NULL){
if (lib->get_left_read() == ""){
print_message("r1 file is expected in config file!");
return false;
}
this->libraries.push_back(*lib);
}
if (this->libraries.size() == 0){
print_message(" No [LIBRARY] section found in config file!");
return false;
}
return true;
}
void valx(void) {
int i;
FILE *fp;
char *c0 = "C0DOS.OBJ";
char *c0d= "C0DOSD.OBJ";
char *cl = "CLDOS.LIB";
char *ci = NULL;
char *dosx = NULL;
char *lnk_op = "/NCI /32";
if ( ( obj_file_cnt() + lib_file_cnt() ) > 0 ) {
int sys = get_dosex();
switch ( sys ) {
case OPT_W32CON:
c0d = c0 = "C0xwin.obj"; cl = "CLWIN.LIB"; ci = "CLIMP.LIB";
lnk_op = "/NCI /PE";
break;
case OPT_W32GUI:
c0d = c0 = "C0win.obj"; cl = "CLWIN.LIB"; ci = "CLIMP.LIB";
lnk_op = "/NCI /PE /WIN";
break;
case OPT_W32DLL:
c0d = c0 = "C0dwin.obj"; cl = "CLWIN.LIB"; ci = "CLIMP.LIB";
lnk_op = "/NCI /PE /BDL";
break;
case OPT_DOS32A:
c0d = "c0doswd.obj" ;
c0 = "c0dosw.obj" ;
lnk_op = "/NCI /LE" ;
dosx = "stub32a.exe" ;
break ;
case OPT_PMODEW:
c0d = "c0doswd.obj" ;
c0 = "c0dosw.obj" ;
lnk_op = "/NCI /LE" ;
dosx = "pmodew.exe";
break;
case OPT_DOS4G:
c0d = "c0doswd.obj" ;
c0 = "c0dosw.obj" ;
lnk_op = "/NCI /LE" ;
dosx = "4gstub.exe";
break;
case OPT_WDOSX:
c0d = "c0doswd.obj" ;
c0 = "c0dosw.obj" ;
lnk_op = "/NCI /LE" ;
dosx = "wdosxle.exe";
break;
case OPT_ZRDX:
c0d = "c0doswd.obj" ;
c0 = "c0dosw.obj" ;
lnk_op = "/NCI /LE" ;
dosx = "zrdx.exe";
break;
case OPT_CAUSEWAY:
c0d = "c0doswd.obj" ;
c0 = "c0dosw.obj" ;
lnk_op = "/NCI /LE" ;
dosx = "cwstub.exe";
break;
case OPT_HXDOS:
c0d = c0 = "C0xwin.obj";
cl = "CLWIN.LIB";
ci = "CLIMP.LIB";
lnk_op = "/NCI /PE";
dosx = "dpmist32.bin";
break;
case OPT_WHXDOS:
c0d = c0 = "C0doswhx.obj";
lnk_op = "/NCI /PE";
dosx = "hdld32.bin";
break;
case OPT_D3X:
c0d = "c0doswd.obj";
c0 = "c0dos.obj";
lnk_op = "/NCI /LE" ;
dosx = "d3xw.exe";
break;
default:
fprintf( stderr, "VALX use only with PMODE!\n" );
case OPT_PMODE:
break;
}
fp = response( RESPONSE );
fprintf( fp, "-NOCA -USE32 %s ",
get_option(OPT_MAPFILE) ? "-MAP" : "-NOMAP" );
if ( lnk_op )
fprintf( fp, "%s ", lnk_op);
if (dosx)
fprintf(fp, "-STB:(%s\\%s) ", get_syslib_path(), dosx);
if (! get_option(OPT_NODEFLIB) ) {
if ( get_option(OPT_DEBUG) )
fprintf(fp,"\"%s\\%s\"", get_syslib_path(), c0d );
else
fprintf(fp,"\"%s\\%s\"", get_syslib_path(), c0 );
}
for ( i = 0; i < obj_file_cnt(); i++ )
fprintf( fp, " %s", obj_file(i) );
fprintf( fp, ",%s,%s,",
get_exe_name(),
get_option( OPT_MAPFILE) ? get_exe_name() : "NUL"
);
if (! get_option(OPT_NODEFLIB) )
fprintf(fp,"\"%s\\%s\"", get_syslib_path(), cl );
if (ci)
fprintf(fp," \"%s\\%s\"", get_syslib_path(), ci );
for ( i = 0; i < lib_file_cnt(); i++ )
fprintf( fp, " %s", lib_file(i) );
fprintf( fp, "\n" );
for ( i = 0; i < res_file_cnt(); i++ )
fprintf( fp, " %s", res_file(i) );
fprintf( fp, "\n\n" );
fclose(fp);
exec("VALX", "@" RESPONSE );
if (! get_option(OPT_KEEPRSP) )
unlink( RESPONSE );
if ( !get_option(OPT_KEEPGEN) )
{
del_res_tmpfiles();
}
if (sys == OPT_WHXDOS)
{
exec("PATCHPE", get_exe_name());
}
}
}
void olink(void) {
int i;
FILE *fp;
char *c0 = "c0pm.o";
char *c0d= "c0pmd.o";
char *cl = "cldos.l";
char *ci = NULL;
char *lnk_op = "/T:PM";
if ( ( obj_file_cnt() + lib_file_cnt() ) > 0 ) {
int sys = get_dosex();
switch ( sys ) {
case OPT_W32CON:
c0d = c0 = "c0xpe.o"; cl = "clwin.l"; ci = "climp.l";
lnk_op = "/T:CON32";
break;
case OPT_W32GUI:
c0d = c0 = "c0pe.o"; cl = "clwin.l"; ci = "climp.l";
lnk_op = "/T:GUI32";
break;
case OPT_W32DLL:
c0d = c0 = "c0dpe.o"; cl = "clwin.l"; ci = "climp.l";
lnk_op = "/T:DLL32";
break;
case OPT_DOS32A:
c0d = "c0watd.o" ;
c0 = "c0wat.o" ;
lnk_op = "/T:DOS32;sstub32a.exe" ;
break ;
case OPT_PMODEW:
c0d = "c0watd.o" ;
c0 = "c0wat.o" ;
lnk_op = "/T:DOS32;spmodew.exe" ;
break;
case OPT_DOS4G:
c0d = "c0watd.o" ;
c0 = "c0wat.o" ;
lnk_op = "/T:DOS32;s4gstub.exe" ;
break;
case OPT_WDOSX:
c0d = "c0watd.o" ;
c0 = "c0wat.o" ;
lnk_op = "/T:DOS32;swdosxle.exe" ;
break;
case OPT_ZRDX:
c0d = "c0watd.o" ;
c0 = "c0wat.o" ;
lnk_op = "/T:DOS32;szrdx.exe" ;
break;
case OPT_CAUSEWAY:
c0d = "c0watd.o" ;
c0 = "c0wat.o" ;
lnk_op = "/T:DOS32;scwstub.exe" ;
break;
case OPT_HXDOS:
c0d = c0 = "c0xpe.o";
cl = "CLWIN.L";
ci = "CLIMP.L";
lnk_op = "/T:CON32;sdpmist32.bin";
break;
case OPT_WHXDOS:
c0d = "c0hxd.o";
c0 = "c0hx.o";
lnk_op = "/T:CON32;shdld32.bin /DOBJECTALIGN=10000";
break;
case OPT_D3X:
c0d = "c0watd.o" ;
c0 = "c0wat.o" ;
lnk_op = "/T:DOS32;sd3xw.exe" ;
break;
default:
fprintf( stderr, "VALX use only with PMODE!\n" );
case OPT_PMODE:
break;
}
fp = response( RESPONSE );
fprintf( fp, "-c%s",
get_option(OPT_MAPFILE) ? " -m" : "" );
fprintf( fp, " -o%s%s", get_exe_name(), get_option( OPT_MAPFILE) ? get_exe_name() : "");
if ( lnk_op )
{
fprintf( fp, " %s", lnk_op);
}
if (! get_option(OPT_NODEFLIB) ) {
if ( get_option(OPT_DEBUG) )
fprintf(fp," \"%s\\%s\"", get_syslib_path(), c0d );
else
fprintf(fp," \"%s\\%s\"", get_syslib_path(), c0 );
}
for ( i = 0; i < obj_file_cnt(); i++ )
fprintf( fp, " %s", obj_file(i) );
for ( i = 0; i < lib_file_cnt(); i++ )
fprintf( fp, " %s", lib_file(i) );
if (! get_option(OPT_NODEFLIB) )
{
if (cl)
{
fprintf(fp," \"%s\\%s\"", get_syslib_path(), cl );
}
if (ci)
{
fprintf(fp," \"%s\\%s\"", get_syslib_path(), ci );
}
}
for ( i = 0; i < res_file_cnt(); i++ )
fprintf( fp, " %s", res_file(i) );
fclose(fp);
exec("olink", "@" RESPONSE );
if (! get_option(OPT_KEEPRSP) )
unlink( RESPONSE );
if ( !get_option(OPT_KEEPGEN) )
{
del_res_tmpfiles();
}
if (sys == OPT_WHXDOS)
{
exec("PATCHPE", get_exe_name());
}
}
}