int main(int argc, char * argv[]) {
void* argtable[] = {
input = arg_filen( "i", "input", "<string>", 0, 100, "input file")
, o_validate = arg_strn( "v", "validate", "<string>", 0, 10, "validate operations")
, o_h = arg_file0( NULL, "output-h", "<string>", "output h file dir")
, o_lib_c = arg_file0( NULL, "output-lib-c", "<string>", "output c lib file")
, o_lib_c_arg = arg_str0( NULL, "output-lib-c-arg", "<string>", "output c lib file")
, o_lib_bin = arg_file0( NULL, "output-lib-bin", "<string>", "output c lib file")
, help = arg_lit0( NULL, "help", "print this help and exit")
, end = arg_end(20)
};
struct error_monitor em_buf;
error_monitor_t em;
int rv;
int nerrors;
cpe_error_monitor_init(&em_buf, cpe_error_log_to_consol, 0);
em = &em_buf;
rv = -1;
if (arg_nullcheck(argtable) != 0) {
CPE_ERROR(em, "init arg table fail!");
goto exit;
}
nerrors = arg_parse(argc,argv,argtable);
if (help->count > 0) {
printf("Usage: %s", argv[0]);
arg_print_syntax(stdout,argtable,"\n");
rv = 0;
goto exit;
}
if (nerrors > 0) {
arg_print_errors(stdout, end, argv[0]);
printf("Try '%s --help' for more information.\n", argv[0]);
goto exit;
}
rv = tools_main(em);
exit:
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return rv;
}
void parse_command_line(int argc, char* argv[])
{
// if the parsing of the arguments was unsuccessful
int nerrors;
// Define argument table structs
python_folder = arg_file0 ( NULL, "py-folder", "<path to file>", "Path to folder (relative or absolute) that contains python script (default: lpfw-pygui)" );
log_debug = arg_int0 ( NULL, "log-debug", "<1/0 for yes/no>", "Enable debug messages logging" );
struct arg_lit *help = arg_lit0 ( NULL, "help", "Display this help screen" );
struct arg_lit *version = arg_lit0 ( NULL, "version", "Display the current version" );
struct arg_end *end = arg_end ( 10 );
void *argtable[] = {python_folder, log_debug, help, version, end};
// Set default values
char *python_folder_pointer = malloc(strlen("lpfw-pygui")+1);
strcpy (python_folder_pointer, "lpfw-pygui");
python_folder->filename[0] = python_folder_pointer;
* ( log_debug->ival ) = 0;
if ( arg_nullcheck ( argtable ) != 0 )
{
printf ( "Error: insufficient memory\n" );
exit(0);
}
nerrors = arg_parse ( argc, argv, argtable );
if ( nerrors == 0 )
{
if ( help->count == 1 )
{
printf ( "Leopard Flower frontend :\n Syntax and help:\n" );
arg_print_glossary ( stdout, argtable, "%-43s %s\n" );
exit (0);
}
else if ( version->count == 1 )
{
printf ( "%s\n", VERSION );
exit (0);
}
}
else if ( nerrors > 0 )
{
arg_print_errors ( stdout, end, "Leopard Flower frontend" );
printf ( "Leopard Flower frontend:\n Syntax and help:\n" );
arg_print_glossary ( stdout, argtable, "%-43s %s\n" );
exit (1);
}
// Free memory - don't do this cause args needed later on
// arg_freetable(argtable, sizeof (argtable) / sizeof (argtable[0]));
}
int main(int argc, char *argv[])
{
/* the global arg_xxx structs are initialised within the argtable */
void *argtable[] = {
help = arg_lit0(NULL, "help", "display this help and exit"),
version = arg_lit0(NULL, "version", "display version info and exit"),
a = arg_lit0("a", NULL,"the -a option"),
b = arg_lit0("b", NULL, "the -b option"),
c = arg_lit0("c", NULL, "the -c option"),
scal = arg_int0(NULL, "scalar", "<n>", "foo value"),
verb = arg_lit0("v", "verbose", "verbose output"),
o = arg_file0("o", NULL, "myfile", "output file"),
file = arg_filen(NULL, NULL, "<file>", 0, 100, "input files"),
end = arg_end(20),
};
int exitcode = 0;
char progname[] = "testargtable3.exe";
int nerrors;
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("List information about the FILE(s) "
"(the current directory by default).\n\n");
arg_print_glossary(stdout, argtable, " %-25s %s\n");
exitcode = 0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0)
{
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
exitcode = 1;
goto exit;
}
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return exitcode;
}
/*
* All code below is "unimportant", it's only argument and file handling
*/
int main(int argc, char *argv[]) {
struct arg_file *ifile = arg_file1("i", "input-file", "INPUT_FILE", "Set Input File");
struct arg_file *ofile = arg_file0("o", "output-file", "OUTPUT_FILE", "Set Output File");
struct arg_str *pass = arg_str0("p", "password", "PASSWORD", "Set Encryption Password");
struct arg_int *pas = arg_int0("c", "passes", "PASSES", "Set number of passes (To decrypt you'll need the same number of passes)");
struct arg_int *buf = arg_int0("b", "buffer-size", "BUFFER_SIZE", "Set Buffer Size");
struct arg_end *end = arg_end(20);
void *argtable[] = {
ifile, ofile, pass, pas, buf, end};
int nerrors = arg_parse(argc, argv, argtable);
if (nerrors > 0) {
arg_print_errors(stdout, end, "rxe");
printf("\nUsage: rxe");
arg_print_syntax(stdout, argtable, "\n");
arg_print_glossary(stdout, argtable, " %-10s %s\n");
} else {
if (buf->count > 0) {
BUFFER_SIZE = buf->ival[0];
}
FILE *outfile, *infile = fopen(ifile->filename[0], "rb");
if (ofile->count > 0) outfile = fopen(ofile->filename[0], "wb");
else {
char farr[2048];
char *ptr;
strcpy(farr, ifile->filename[0]);
if ((ptr = strstr(farr, ".rxe")) != NULL) {
farr[0] = '\0';
farr[1] = '\0';
farr[2] = '\0';
farr[3] = '\0';
} else strcat(farr, ".rxe");
outfile = fopen(farr, "wb");
}
if(pas->count > 0) PASSES = pas->ival[0];
if(pass->count > 0) RXE_Main(infile, outfile, (char *)pass->sval[0]);
else RXE_Main(infile, outfile, "DEFAULT");
fclose(outfile);
fclose(infile);
}
return 0;
}
int main(int argc, char* argv[])
{
// Define our variables.
FILE* load;
uint16_t flash[0x10000];
char leading[0x100];
unsigned int i;
bool uread = true;
vm_t* vm;
int nerrors;
bstring ss, st;
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_file* input_file = arg_file1(NULL, NULL, "<file>", "The input file, or - to read from standard input.");
struct arg_file* execution_dump_file = arg_file0("e", "execution-dump", "<file>", "Produce a very large execution dump file.");
struct arg_lit* debug_mode = arg_lit0("d", "debug", "Show each executed instruction.");
struct arg_lit* terminate_mode = arg_lit0("t", "show-on-terminate", "Show state of machine when program is terminated.");
struct arg_lit* legacy_mode = arg_lit0("l", "legacy", "Automatically initialize hardware to legacy values.");
struct arg_lit* little_endian_mode = arg_lit0(NULL, "little-endian", "Use little endian serialization (for compatibility with older versions).");
struct arg_lit* verbose = arg_litn("v", NULL, 0, LEVEL_EVERYTHING - LEVEL_DEFAULT, "Increase verbosity.");
struct arg_lit* quiet = arg_litn("q", NULL, 0, LEVEL_DEFAULT - LEVEL_SILENT, "Decrease verbosity.");
struct arg_end* end = arg_end(20);
void* argtable[] = { input_file, debug_mode, execution_dump_file, terminate_mode, legacy_mode, little_endian_mode, verbose, quiet, end };
// Parse arguments.
nerrors = arg_parse(argc, argv, argtable);
version_print(bautofree(bfromcstr("Emulator")));
if (nerrors != 0 || show_help->count != 0)
{
if (show_help->count != 0)
arg_print_errors(stdout, end, "emulator");
printd(LEVEL_DEFAULT, "syntax:\n dtemu");
arg_print_syntax(stderr, argtable, "\n");
printd(LEVEL_DEFAULT, "options:\n");
arg_print_glossary(stderr, argtable, " %-25s %s\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Set verbosity level.
debug_setlevel(LEVEL_DEFAULT + verbose->count - quiet->count);
// Set global path variable.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
// Set endianness.
isetmode(little_endian_mode->count == 0 ? IMODE_BIG : IMODE_LITTLE);
// Zero out the flash space.
for (i = 0; i < 0x10000; i++)
flash[i] = 0x0;
// Zero out the leading space.
for (i = 0; i < 0x100; i++)
leading[i] = 0x0;
// Load from either file or stdin.
if (strcmp(input_file->filename[0], "-") != 0)
{
// Open file.
load = fopen(input_file->filename[0], "rb");
if (load == NULL)
{
fprintf(stderr, "emulator: unable to load %s from disk.\n", argv[1]);
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
}
else
{
// Windows needs stdin in binary mode.
#ifdef _WIN32
_setmode(_fileno(stdin), _O_BINARY);
#endif
// Set load to stdin.
load = stdin;
}
// Read up to 0x10000 words.
for (i = 0; i < 0x10000 && !feof(load); i++)
iread(&flash[i], load);
fclose(load);
// Check to see if the first X bytes matches the header
// for intermediate code and stop if it does.
ss = bfromcstr("");
st = bfromcstr(ldata_objfmt);
for (i = 0; i < strlen(ldata_objfmt); i++)
bconchar(ss, leading[i]);
if (biseq(ss, st))
{
fprintf(stderr, "emulator: it appears you passed intermediate code for execution. link\n");
fprintf(stderr, " the input code with the toolchain linker to execute it.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// And then use the VM.
vm = vm_create();
vm->debug = (debug_mode->count > 0);
vm_flash(vm, flash);
vm_hw_timer_init(vm);
vm_hw_io_init(vm);
vm_hw_lem1802_init(vm);
vm_hw_lua_init(vm);
if (legacy_mode->count > 0)
{
vm_hw_lem1802_mem_set_screen(vm, 0x8000);
vm_hw_io_set_legacy(true);
}
vm_execute(vm, execution_dump_file->count > 0 ? execution_dump_file->filename[0] : NULL);
#ifdef __EMSCRIPTEN__
printd(LEVEL_WARNING, "warning: not cleaning up resources in Emscripten.\n");
#else
if (terminate_mode->count > 0)
{
fprintf(stderr, "\n");
fprintf(stderr, "A: 0x%04X [A]: 0x%04X\n", vm->registers[REG_A], vm->ram[vm->registers[REG_A]]);
fprintf(stderr, "B: 0x%04X [B]: 0x%04X\n", vm->registers[REG_B], vm->ram[vm->registers[REG_B]]);
fprintf(stderr, "C: 0x%04X [C]: 0x%04X\n", vm->registers[REG_C], vm->ram[vm->registers[REG_C]]);
fprintf(stderr, "X: 0x%04X [X]: 0x%04X\n", vm->registers[REG_X], vm->ram[vm->registers[REG_X]]);
fprintf(stderr, "Y: 0x%04X [Y]: 0x%04X\n", vm->registers[REG_Y], vm->ram[vm->registers[REG_Y]]);
fprintf(stderr, "Z: 0x%04X [Z]: 0x%04X\n", vm->registers[REG_Z], vm->ram[vm->registers[REG_Z]]);
fprintf(stderr, "I: 0x%04X [I]: 0x%04X\n", vm->registers[REG_I], vm->ram[vm->registers[REG_I]]);
fprintf(stderr, "J: 0x%04X [J]: 0x%04X\n", vm->registers[REG_J], vm->ram[vm->registers[REG_J]]);
fprintf(stderr, "PC: 0x%04X SP: 0x%04X\n", vm->pc, vm->sp);
fprintf(stderr, "EX: 0x%04X IA: 0x%04X\n", vm->ex, vm->ia);
}
vm_hw_lua_free(vm);
vm_hw_timer_free(vm);
vm_hw_io_free(vm);
vm_hw_lem1802_free(vm);
vm_free(vm);
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 0;
#endif
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
int Idx;
int iMode = 0; // processing mode
int iRandSeed = 0; // random base seed to use (if < 0 then current time used to seed generator)
int KMerLen; // what length kmer to generate for 1..cMaxKMerLen
int NumInFileSpecs; // number of input file specs
char *pszInFiles[cMaxInFileSpecs]; // input control aligned reads files
char szOutputFile[_MAX_PATH];
// command line args
struct arg_lit *help = arg_lit0("hH","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *Mode = arg_int0("m","mode","<int>", "processing mode - 0 randomise genome");
struct arg_int *kmerlen = arg_int0("k","kmerlen","<int>", "maintain frequency composition of K-mer length (default = 1, range 1..15)");
struct arg_file *InFiles = arg_filen("i",NULL,"<file>",1,cMaxInFileSpecs, "input genome assembly multifasta files (s) to randomise");
struct arg_file *OutFile= arg_file1("o",NULL,"<file>", "output randomised assembly to this file as multifasta");
struct arg_int *RandSeed = arg_int0("s","randseed","<int>", "random seed to use (default is use system time)");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,LogFile,Mode,kmerlen,InFiles,OutFile,RandSeed,end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s Kanga randomise genome K-mers, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n",gszProcName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>\n'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d\n",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
// now that log parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem\n");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created\n",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s",cpszProgVer);
iMode = Mode->count ? Mode->ival[0] : 0;
if(iMode < 0 || iMode >= cMaxSupportedModes)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Unsupported Mode '-m%d' requested",iMode);
exit(1);
}
KMerLen = 0;
switch(iMode) {
case 0: // generate random species fasta sequence
for(NumInFileSpecs=Idx=0;NumInFileSpecs < cMaxInFileSpecs && Idx < InFiles->count; Idx++)
{
pszInFiles[Idx] = NULL;
if(pszInFiles[NumInFileSpecs] == NULL)
pszInFiles[NumInFileSpecs] = new char [_MAX_PATH];
strncpy(pszInFiles[NumInFileSpecs],InFiles->filename[Idx],_MAX_PATH);
pszInFiles[NumInFileSpecs][_MAX_PATH-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(pszInFiles[NumInFileSpecs]);
if(pszInFiles[NumInFileSpecs][0] != '\0')
NumInFileSpecs++;
}
if(!NumInFileSpecs)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no input file(s) specified with '-i<filespec>' option)\n");
exit(1);
}
KMerLen = kmerlen->count ? kmerlen->ival[0] : cDfltKMerLen;
if(KMerLen < 1 || KMerLen > cMaxKMerLen)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: K-mer length specified with '-k%d' is outside of range 1..10",KMerLen);
exit(1);
}
if(!OutFile->count || OutFile->filename[0][0] == '\0')
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: No output fasta file specified with '-o<filename>'");
exit(1);
}
strncpy(szOutputFile,OutFile->filename[0],_MAX_PATH);
szOutputFile[_MAX_PATH] = '\0';
if(!RandSeed->count)
iRandSeed = -1;
else
{
iRandSeed = RandSeed->ival[0];
if(iRandSeed < 0 || iRandSeed > 32767)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Random seed specified as '-s%d' must be between 0 and 32767",iRandSeed);
exit(1);
}
}
break;
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
switch(iMode) {
case 0:
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Mode: 0 (randomise genome K-mers)");
for(Idx=0; Idx < NumInFileSpecs; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Use frequency compositions from these genome multifasta file(s) (%d): '%s'",Idx+1,pszInFiles[Idx]);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maintain K-mer composition of length: %d",KMerLen);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Genome output file: '%s'",szOutputFile);
if(iRandSeed >= 0)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Random seed: %d",iRandSeed);
else
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Random seed: will use current time as seed");
break;
}
gStopWatch.Start();
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
Rslt = GenerateRandFasta(iMode,KMerLen,NumInFileSpecs,pszInFiles,szOutputFile,iRandSeed);
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s Kanga randomise genome K-mers, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
return 0;
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
etPMode PMode; // processing mode
int Idx;
int NumInputFiles; // number of input sequence files
char *pszInFastaFile[cMaxInFileSpecs]; // names of input sequence files (wildcards allowed)
char szRsltsFile[_MAX_PATH]; // output stats to this file
// command line args
struct arg_lit *help = arg_lit0("h","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *pmode = arg_int0("m","mode","<int>", "Processing mode: 0 - BED output, single exon");
struct arg_file *pinputfiles = arg_filen("i","infasta","<file>",1,cMaxInFileSpecs,"input fasta file(s)");
struct arg_file *RsltsFile = arg_file0("o","output","<file>", "output BED file");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,LogFile,
pmode,pinputfiles,RsltsFile,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s Generate BED file from multifasta file, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n",gszProcName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>\n'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d\n",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
// now that log parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem\n");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created\n",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s",cpszProgVer);
PMode = (etPMode)(pmode->count ? pmode->ival[0] : ePMdefault);
if(PMode < ePMdefault || PMode >= ePMplaceholder)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Processing mode '-m%d' specified outside of range %d..%d\n",PMode,ePMdefault,(int)ePMplaceholder-1);
exit(1);
}
NumInputFiles = 0;
for(NumInputFiles=Idx=0;NumInputFiles < cMaxInFileSpecs && Idx < pinputfiles->count; Idx++)
{
pszInFastaFile[Idx] = NULL;
if(pszInFastaFile[NumInputFiles] == NULL)
pszInFastaFile[NumInputFiles] = new char [_MAX_PATH];
strncpy(pszInFastaFile[NumInputFiles],pinputfiles->filename[Idx],_MAX_PATH);
pszInFastaFile[NumInputFiles][_MAX_PATH-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(pszInFastaFile[NumInputFiles]);
if(pszInFastaFile[NumInputFiles][0] != '\0')
NumInputFiles++;
}
if(!NumInputFiles)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no input file(s) specified with '-i<filespec>' option)\n");
exit(1);
}
if(!RsltsFile->count)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: No output BED file specified");
exit(1);
}
strncpy(szRsltsFile,RsltsFile->filename[0],_MAX_PATH);
szRsltsFile[_MAX_PATH-1] = '\0';
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
for(Idx=0; Idx < NumInputFiles; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"input fasta sequence files (%d): '%s'",Idx+1,pszInFastaFile[Idx]);
if(szRsltsFile[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output to BED file: '%s'",szRsltsFile);
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
// processing here...
gStopWatch.Start();
Rslt = Process(PMode,NumInputFiles,pszInFastaFile,szRsltsFile);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s Generate BED file from multifasta file, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
return 0;
}
int main(int argc, char **argv)
{
struct arg_lit *list = arg_lit0("lL",NULL, "list files");
struct arg_lit *recurse = arg_lit0("R",NULL, "recurse through subdirectories");
struct arg_int *repeat = arg_int0("k","scalar",NULL, "define scalar value k (default is 3)");
struct arg_str *defines = arg_strn("D","define","MACRO",0,argc+2, "macro definitions");
struct arg_file *outfile = arg_file0("o",NULL,"<output>", "output file (default is \"-\")");
struct arg_lit *verbose = arg_lit0("v","verbose,debug", "verbose messages");
struct arg_lit *help = arg_lit0(NULL,"help", "print this help and exit");
struct arg_lit *version = arg_lit0(NULL,"version", "print version information and exit");
struct arg_file *infiles = arg_filen(NULL,NULL,NULL,1,argc+2, "input file(s)");
struct arg_end *end = arg_end(20);
void* argtable[] = {list,recurse,repeat,defines,outfile,verbose,help,version,infiles,end};
const char* progname = "myprog";
int nerrors;
int exitcode=0;
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0)
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n",progname);
exitcode=1;
goto exit;
}
/* set any command line default values prior to parsing */
repeat->ival[0]=3;
outfile->filename[0]="-";
/* Parse the command line as defined by argtable[] */
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s", progname);
arg_print_syntax(stdout,argtable,"\n");
printf("This program demonstrates the use of the argtable2 library\n");
printf("for parsing command line arguments.\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
exitcode=0;
goto exit;
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("'%s' example program for the \"argtable\" command line argument parser.\n",progname);
printf("September 2003, Stewart Heitmann\n");
exitcode=0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0)
{
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout,end,progname);
printf("Try '%s --help' for more information.\n",progname);
exitcode=1;
goto exit;
}
/* special case: uname with no command line options induces brief help */
if (argc==1)
{
printf("Try '%s --help' for more information.\n",progname);
exitcode=0;
goto exit;
}
/* normal case: take the command line options at face value */
exitcode = mymain(list->count, recurse->count, repeat->ival[0],
defines->sval, defines->count,
outfile->filename[0], verbose->count,
infiles->filename, infiles->count);
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
return exitcode;
}
int main(int argc, char* argv[]) {
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "Input altpals file");
struct arg_int *pal = arg_int1("p", "palette", "<number>", "Select a palette");
struct arg_file *export = arg_file0("e", "export", "<file>", "Export selected palette to GPL file");
struct arg_file *import = arg_file0("i", "import", "<file>", "Import selected palette from GPL file");
struct arg_file *output = arg_file0("o", "output", "<file>", "Output altpals file");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,pal,output,import,export,end};
const char* progname = "altpaltool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 Altpals file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2014 Tuomas Virtanen\n");
goto exit_0;
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Need import or export ...
if(pal->count > 0 && import->count == 0 && export->count == 0) {
printf("Define either --import or --export with --palette!\n");
goto exit_0;
}
// Make sure output is set
if(import->count > 0 && output->count <= 0) {
printf("Define --output with --import.\n");
goto exit_0;
}
// Load file
sd_altpal_file alt;
sd_altpal_create(&alt);
int ret = sd_altpals_load(&alt, file->filename[0]);
if(ret != SD_SUCCESS) {
printf("Unable to load altpals file %s: %s.\n",
file->filename[0],
sd_get_error(ret));
goto exit_1;
}
// Check ID
int pal_id = pal->ival[0];
if(pal_id < 0 || pal_id > SD_ALTPALS_PALETTES) {
printf("Palette index %d does not exist!\n", pal_id);
goto exit_1;
}
// Check what to do
if(export->count > 0) {
ret = sd_palette_to_gimp_palette(&alt.palettes[pal_id], export->filename[0]);
if(ret == SD_SUCCESS) {
printf("Palette %d exported to file %s succesfully.\n",
pal_id,
export->filename[0]);
} else {
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
bool bSkipFirst; // true if first line contains header and should be skipped
int iMinLength; // core elements must be of at least this length
int iMaxLength; // and no longer than this length
char szInLociFile[_MAX_PATH]; // input element loci from this file
char szInSeqFile[_MAX_PATH]; // input bioseq file containing assembly
char szRsltsFile[_MAX_PATH]; // output stats to this file
// command line args
struct arg_lit *help = arg_lit0("hH","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_int *ScreenLogLevel=arg_int0("S", "ScreenLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_file *InLociFile = arg_file1("i","inloci","<file>", "element loci CSV file");
struct arg_file *InSeqFile = arg_file1("I","assembly","<file>", "genome assembly bioseq file");
struct arg_file *RsltsFile = arg_file1("o","output","<file>", "output file");
struct arg_lit *SkipFirst = arg_lit0("x","skipfirst", "skip first line of CSV - header line");
struct arg_int *MinLength = arg_int0("l","minlength","<int>", "minimum element length (default 10)");
struct arg_int *MaxLength = arg_int0("L","maxlength","<int>", "maximum element length (default 1000000000)");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,ScreenLogLevel,LogFile,
InLociFile,InSeqFile,RsltsFile,SkipFirst,MinLength,MaxLength,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s csv2stats, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
bSkipFirst = SkipFirst->count ? true : false;
iMinLength = MinLength->count ? MinLength->ival[0] : cDfltMinLengthRange;
if(iMinLength < 1 || iMinLength > cMaxLengthRange)
{
printf("Error: Mininum element length '-l%d' is not in range 1..%d",iMinLength,cMaxLengthRange);
exit(1);
}
iMaxLength = MaxLength->count ? MaxLength->ival[0] : cMaxLengthRange;
if(iMaxLength < iMinLength || iMaxLength > cMaxLengthRange)
{
printf("Error: Maximum element length '-L%d' is not in range %d..%d",iMaxLength,iMinLength,cMaxLengthRange);
exit(1);
}
strncpy(szInLociFile,InLociFile->filename[0],_MAX_PATH);
szInLociFile[_MAX_PATH-1] = '\0';
strncpy(szInSeqFile,InSeqFile->filename[0],_MAX_PATH);
szInSeqFile[_MAX_PATH-1] = '\0';
strncpy(szRsltsFile,RsltsFile->filename[0],_MAX_PATH);
szRsltsFile[_MAX_PATH-1] = '\0';
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input CSV element loci file: '%s'",szInLociFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input bioseq genome assembly file: '%s'",szInSeqFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output to file: '%s'",szRsltsFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"First line contains header: %s",bSkipFirst ? "yes" : "no");
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum element length: %d",iMinLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum element length: %d",iMaxLength);
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
// processing here...
Rslt = Process(bSkipFirst,iMinLength,iMaxLength,szInLociFile,szInSeqFile,szRsltsFile);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s csv2stats, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
}
int main(int argc, char **argv)
{
/* SYNTAX 1: insert [-nvR] <file> [file]... -o <file> */
struct arg_rex *cmd1 = arg_rex1(NULL, NULL, "insert", NULL, REG_ICASE, NULL);
struct arg_lit *noact1 = arg_lit0("n", NULL, "take no action");
struct arg_lit *verbose1 = arg_lit0("v", "verbose", "verbose messages");
struct arg_lit *recurse1 = arg_lit0("R", NULL, "recurse through subdirectories");
struct arg_file *infiles1 = arg_filen(NULL, NULL, NULL, 1,argc+2, "input file(s)");
struct arg_file *outfile1 = arg_file0("o", NULL, "<output>", "output file (default is \"-\")");
struct arg_end *end1 = arg_end(20);
void* argtable1[] = {cmd1,noact1,verbose1,recurse1,infiles1,outfile1,end1};
int nerrors1;
/* SYNTAX 2: remove [-nv] <file> */
struct arg_rex *cmd2 = arg_rex1(NULL, NULL, "remove", NULL, REG_ICASE, NULL);
struct arg_lit *noact2 = arg_lit0("n", NULL, NULL);
struct arg_lit *verbose2 = arg_lit0("v", "verbose", NULL);
struct arg_file *infiles2 = arg_file1(NULL, NULL, NULL, NULL);
struct arg_end *end2 = arg_end(20);
void* argtable2[] = {cmd2,noact2,verbose2,infiles2,end2};
int nerrors2;
/* SYNTAX 3: search [-v] <pattern> [-o <file>] [--help] [--version] */
struct arg_rex *cmd3 = arg_rex1(NULL, NULL, "search", NULL, REG_ICASE, NULL);
struct arg_lit *verbose3 = arg_lit0("v", "verbose", NULL);
struct arg_str *pattern3 = arg_str1(NULL, NULL, "<pattern>", "search string");
struct arg_file *outfile3 = arg_file0("o", NULL, "<output>", NULL);
struct arg_end *end3 = arg_end(20);
void* argtable3[] = {cmd3,verbose3,pattern3,outfile3,end3};
int nerrors3;
/* SYNTAX 4: [-help] [-version] */
struct arg_lit *help4 = arg_lit0(NULL,"help", "print this help and exit");
struct arg_lit *version4 = arg_lit0(NULL,"version", "print version information and exit");
struct arg_end *end4 = arg_end(20);
void* argtable4[] = {help4,version4,end4};
int nerrors4;
const char* progname = "multisyntax";
int exitcode=0;
/* verify all argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable1)!=0 ||
arg_nullcheck(argtable2)!=0 ||
arg_nullcheck(argtable3)!=0 ||
arg_nullcheck(argtable4)!=0 )
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n",progname);
exitcode=1;
goto exit;
}
/* set any command line default values prior to parsing */
outfile1->filename[0]="-";
outfile3->filename[0]="-";
/* Above we defined a separate argtable for each possible command line syntax */
/* and here we parse each one in turn to see if any of them are successful */
nerrors1 = arg_parse(argc,argv,argtable1);
nerrors2 = arg_parse(argc,argv,argtable2);
nerrors3 = arg_parse(argc,argv,argtable3);
nerrors4 = arg_parse(argc,argv,argtable4);
/* Execute the appropriate main<n> routine for the matching command line syntax */
/* In this example program our alternate command line syntaxes are mutually */
/* exclusive, so we know in advance that only one of them can be successful. */
if (nerrors1==0)
exitcode = mymain1(noact1->count, verbose1->count, recurse1->count,
outfile1->filename[0], infiles1->filename, infiles1->count);
else if (nerrors2==0)
exitcode = mymain2(noact2->count, verbose2->count, infiles2->filename[0]);
else if (nerrors3==0)
exitcode = mymain3(verbose3->count, pattern3->sval[0], outfile3->filename[0]);
else if (nerrors4==0)
exitcode = mymain4(help4->count, version4->count, progname,
argtable1, argtable2, argtable3, argtable4);
else
{
/* We get here if the command line matched none of the possible syntaxes */
if (cmd1->count > 0)
{
/* here the cmd1 argument was correct, so presume syntax 1 was intended target */
arg_print_errors(stdout,end1,progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout,argtable1,"\n");
}
else if (cmd2->count > 0)
{
/* here the cmd2 argument was correct, so presume syntax 2 was intended target */
arg_print_errors(stdout,end2,progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout,argtable2,"\n");
}
else if (cmd3->count > 0)
{
/* here the cmd3 argument was correct, so presume syntax 3 was intended target */
arg_print_errors(stdout,end3,progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout,argtable3,"\n");
}
else
{
/* no correct cmd literals were given, so we cant presume which syntax was intended */
printf("%s: missing <insert|remove|search> command.\n",progname);
printf("usage 1: %s ", progname); arg_print_syntax(stdout,argtable1,"\n");
printf("usage 2: %s ", progname); arg_print_syntax(stdout,argtable2,"\n");
printf("usage 3: %s ", progname); arg_print_syntax(stdout,argtable3,"\n");
printf("usage 4: %s", progname); arg_print_syntax(stdout,argtable4,"\n");
}
}
exit:
/* deallocate each non-null entry in each argtable */
arg_freetable(argtable1,sizeof(argtable1)/sizeof(argtable1[0]));
arg_freetable(argtable2,sizeof(argtable2)/sizeof(argtable2[0]));
arg_freetable(argtable3,sizeof(argtable3)/sizeof(argtable3[0]));
arg_freetable(argtable4,sizeof(argtable4)/sizeof(argtable4[0]));
return exitcode;
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
int Idx;
int iProcMode;
char Strand; // process features on this strand
int MinLen;
int JoinLen;
int LenFileList;
int NumIncludeChroms;
char *pszIncludeChroms[cMaxIncludeChroms];
int NumExcludeChroms;
char *pszExcludeChroms[cMaxExcludeChroms];
etBEDRegion Region; // process for this functional region only
int NumInFiles; // number of control input files
char *pszInFileSpecs[cMaxNumBedFiles]; // input (wildcards allowed) BED files
char szOutFile[_MAX_PATH]; // write merged to this file
// command line args
struct arg_lit *help = arg_lit0("h","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *ProcMode = arg_int0("m","mode","<int>", "merge processing mode: 0 - Strand independent union, 1 - Strand dependent union");
struct arg_int *strand = arg_int0("s","strand","<int>", "filter for this strand: 0 - any, 1 - Watson '+', 2 - Crick '-' (default is any)");
struct arg_int *region = arg_int0("r","genomicregion","<int>", "Retain annotated regions 0:ALL,1:Intergenic,2:Exons,3:Introns,4:CDS,5:UTRs,6:5'UTR,7:3'UTR (default = ALL)");
struct arg_int *minlen = arg_int0("l","minlen","<int>", "generated merged features must be of at least this length (default is 20)");
struct arg_int *joinlen = arg_int0("j","joinlen","<int>", "merge features which are separated by at most this length, 0 if no merging (default is 1)");
struct arg_str *excludechroms = arg_strn("Z","chromexclude","<string>",0,cMaxExcludeChroms,"regular expressions defining chromosomes to always exclude");
struct arg_str *includechroms = arg_strn("z","chromeinclude","<string>",0,cMaxIncludeChroms,"regular expressions defining chromosomes to explicitly include if not already excluded");
struct arg_file *infiles = arg_filen("i","srcfiles","<file>",0, cMaxNumBedFiles,"merge features contained in these BED files (wildcards alllowed)");
struct arg_file *OutFile = arg_file1("o",NULL,"<file>", "output merged features to this BED file");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,LogFile,
ProcMode,strand,minlen,joinlen,region,excludechroms,includechroms,infiles,OutFile,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s BED Merge Blocks, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n",gszProcName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
iProcMode = ProcMode->count ? ProcMode->ival[0] : ePMDefault;
if(iProcMode < ePMDefault || iProcMode >= ePMplaceholder)
{
printf("Error: Processing mode '-p%d' is not in range 0..%d",iProcMode,ePMplaceholder-1);
exit(1);
}
MinLen = minlen->count ? minlen->ival[0] : cDfltMergeLen;
if(MinLen < cMinMergeLen || MinLen > cMaxMergeLen)
{
printf("Error: minimum length '-l%d' is not in range %d..%d",MinLen,cMinMergeLen,cMaxMergeLen);
exit(1);
}
JoinLen = joinlen->count ? joinlen->ival[0] : 1;
if(JoinLen < 0 || JoinLen > cMaxMergeLen)
{
printf("Error: Join length '-j%d' is not in range 0..%d",JoinLen,cMaxMergeLen);
exit(1);
}
Strand = strand->count ? strand->ival[0] : 0;
if(Strand < 0 || Strand > 2)
{
printf("\nError: Strand '-s%d' specified outside of range 0..2",Strand);
exit(1);
}
switch(Strand) {
case 1: Strand = (int)'+'; break;
case 2: Strand = (int)'-'; break;
case 0: Strand = (int)'*'; break;
}
Region = (etBEDRegion)(region->count ? region->ival[0] : eMEGRAny); // default as being any region
if(Region < eMEGRAny || Region > eMEG3UTR)
{
printf("\nSpecified region '-g%d' outside of range 0..%d",Region,eMEG3UTR);
exit(1);
}
NumIncludeChroms = includechroms->count;
for(Idx=0;Idx < includechroms->count; Idx++)
{
LenFileList = (int)strlen(includechroms->sval[Idx]);
pszIncludeChroms[Idx] = new char [LenFileList+1];
strcpy(pszIncludeChroms[Idx],includechroms->sval[Idx]);
TrimQuotes(pszIncludeChroms[Idx]);
}
NumExcludeChroms = excludechroms->count;
for(Idx=0;Idx < excludechroms->count; Idx++)
{
LenFileList = (int)strlen(excludechroms->sval[Idx]);
pszExcludeChroms[Idx] = new char [LenFileList+1];
strcpy(pszExcludeChroms[Idx],excludechroms->sval[Idx]);
TrimQuotes(pszExcludeChroms[Idx]);
}
if(!infiles->count)
{
printf("\nError: No input file(s) specified with with '-i<filespec>' option)");
exit(1);
}
for(NumInFiles=Idx=0;NumInFiles < cMaxNumBedFiles && Idx < infiles->count; Idx++)
{
pszInFileSpecs[Idx] = NULL;
if(pszInFileSpecs[NumInFiles] == NULL)
pszInFileSpecs[NumInFiles] = new char [_MAX_PATH];
strncpy(pszInFileSpecs[NumInFiles],infiles->filename[Idx],_MAX_PATH);
pszInFileSpecs[NumInFiles][_MAX_PATH-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(pszInFileSpecs[NumInFiles]);
if(pszInFileSpecs[NumInFiles][0] != '\0')
NumInFiles++;
}
if(!NumInFiles)
{
printf("\nError: After removal of whitespace, no input file(s) specified with '-i<filespec>' option)");
exit(1);
}
strncpy(szOutFile,OutFile->filename[0],_MAX_PATH);
szOutFile[_MAX_PATH-1] = '\0';
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing Mode: %d (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
gDiagnostics.DiagOutMsgOnly(eDLInfo,"process for this strand only: '%c'",(char)Strand);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"generated merged features will be at least this length: %d",MinLen);
if(JoinLen == 0)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"keep separate features, no merging");
else
gDiagnostics.DiagOutMsgOnly(eDLInfo,"merge features separated by upto: %d",JoinLen);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Retain Region: %s",Region2Txt((etBEDRegion)Region));
for(Idx = 0; Idx < NumIncludeChroms; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"reg expressions defining chroms to include: '%s'",pszIncludeChroms[Idx]);
for(Idx = 0; Idx < NumExcludeChroms; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"reg expressions defining chroms to exclude: '%s'",pszExcludeChroms[Idx]);
for(Idx=0;Idx < NumInFiles; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"merge features from this input BED file (%d): '%s'",Idx+1,pszInFileSpecs[Idx]);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output merged features into BED file: '%s'",szOutFile);
gStopWatch.Start();
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
Rslt = Process((etProcMode)iProcMode,Strand,MinLen,JoinLen,Region,
NumIncludeChroms, // number of chromosome regular expressions to include
pszIncludeChroms, // array of include chromosome regular expressions
NumExcludeChroms, // number of chromosome expressions to exclude
pszExcludeChroms, // array of exclude chromosome regular expressions
NumInFiles,pszInFileSpecs,szOutFile);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s BED Merge Blocks, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
}
void processArgs(int argc, char **argv) {
int nerrors, i;
char *savptr, str[1024], *str1, machName[1024], sessIDstr[1024];
struct arg_str *arg_sessionID = arg_str1( "S", "sessionID", "<mach.sessionID>", "session ID of run to be processed\n");
struct arg_str *arg_propIDs = arg_str0( "P", "proposals", "<int [,int [,int]]>", "quoted string of proposal numbers to use\n");
struct arg_str *arg_skipDays = arg_str0( "D", "days", "<skip [,length]>", "skip days at start, do length days after\n");
struct arg_lit *arg_Check = arg_lit0( NULL, "checkobs", "check observations for basic errors\n");
struct arg_lit *arg_TimeSummary = arg_lit0( NULL, "timesummary", "time summary");
struct arg_lit *arg_PeriodSearch = arg_lit0( NULL, "periodsearch", "make periodogram plots\n");
struct arg_lit *arg_Hourglass = arg_lit0( "H", "hourglass", "make hourglass plot\n");
struct arg_lit *arg_Opposition = arg_lit0( NULL, "opposition", "make solar angle (opposition) plot\n");
struct arg_str *arg_Airmass = arg_str0( NULL, "airmass", "<int>", "make per-field airmass plot (0 is max, 1 is median)\n");
struct arg_lit *arg_SixVisits = arg_lit0( "V", "sixvisitnum", "make all-filter visit numbers plot\n");
struct arg_lit *arg_5sigma = arg_lit0( "V", "5sigma", "make aitoff plot for median 5sigma also per proposal\n");
struct arg_lit *arg_skyb = arg_lit0( "V", "skyb", "make aitoff plot for median skyb also per proposal\n");
struct arg_lit *arg_seeing = arg_lit0( "V", "seeing", "make aitoff plot for median seeing also per proposal\n");
struct arg_lit *arg_Visits = arg_lit0( "v", "visitnum", "make visit numbers plot for specified filters\n \
(requires -f|--filters)\n");
struct arg_str *arg_reqFilters = arg_str0( "f", "filters", "<f [,f [,f]]>", "which filters to use; f in {ugrizy}\n");
struct arg_lit *arg_NEOrevisits = arg_lit0( "R", "revisits", "make NEO revisit numbers plot\n");
struct arg_lit *arg_Slew = arg_lit0( NULL, "slew", "make slew time histogram\n");
struct arg_lit *arg_SNtiming = arg_lit0( NULL, "sntiming", "make SN Ia cadence plots\n");
struct arg_file *arg_plotfileRoot = arg_file0(NULL, "plotfile", "harcopy file", "root name of plotfile for hardcopy\n");
struct arg_file *arg_plotTitle = arg_file0(NULL, "plottitle", "<string>", "title for plots\n");
struct arg_lit *arg_help = arg_lit0( "h", "help", "show usage\n");
struct arg_lit *arg_debug = arg_lit0( "d", "debug", "debugging output\n");
struct arg_str *arg_hostname = arg_str1( "N", "hostname", "<string>", "if you know hostname \n");
struct arg_str *arg_databasename = arg_str1( "DB", "database", "<string>", "if you know the db name \n");
struct arg_str *arg_designstretch = arg_str1( NULL, "designstretch", "<int>", "design or stretch value\n");
struct arg_end *arg_endp = arg_end(20);
void *argtable[] = {arg_sessionID, arg_propIDs, arg_skipDays, arg_TimeSummary, arg_Check, arg_PeriodSearch,
arg_Hourglass, arg_Opposition, arg_Airmass, arg_SixVisits, arg_5sigma, arg_skyb, arg_seeing,
arg_Slew, arg_Visits, arg_reqFilters, arg_NEOrevisits, arg_SNtiming, arg_plotfileRoot,
arg_plotTitle, arg_debug, arg_help, arg_hostname, arg_designstretch, arg_databasename, arg_endp};
if (arg_nullcheck(argtable) != 0) fprintf(stderr, "error: insufficient memory\n");
nerrors = arg_parse(argc,argv,argtable);
// process arguments
// render assistance when asked
if(arg_help->count>0) {
fprintf(stderr,"Usage: %s [options]\n where [options] are:\n\n",argv[0]);
arg_print_glossary(stderr, argtable, "%-45s %s");
// arg_print_syntaxv(stderr, argtable, "\n");
exit(1);
}
// list errors
if (nerrors > 0) {
arg_print_errors(stdout,arg_endp,argv[0]);
fprintf(stderr,"\nUsage: %s [options]\n where [options] are:\n\n",argv[0]);
arg_print_glossary(stderr, argtable, "%-45s %s");
// arg_print_syntaxv(stderr, argtable, "\n");
exit(1);
}
// set database tableName and sessionID from sessionID argument
//strcpy(str, *arg_sessionID->sval);
//strcpy(machName, strtok_r(str,".",&savptr));
//strcpy(sessIDstr, strtok_r(NULL,".",&savptr));
strcpy(sessIDstr, *arg_sessionID->sval);
sessionID = atoi(sessIDstr);
if ( *arg_databasename->sval == NULL ) {
sprintf(database, "%s", "OpsimDB");
} else {
sprintf(database, "%s", *arg_databasename->sval);
}
if ( *arg_hostname->sval == NULL ) {
if ( gethostname(identifier, identifier_length) == 0 ) {
sprintf(hostname, "%s", identifier);
} else {
printf( "Hostname : %s\n", strerror(errno));
exit(1);
}
} else {
sprintf (hostname, "%s", *arg_hostname->sval);
}
sprintf(tableName, "output_%s_%d", hostname, sessionID);
// set action flags
if(arg_5sigma->count>0) do5sigma=1;
if(arg_skyb->count>0) doskyb=1;
if(arg_seeing->count>0) doSeeing=1;
if(arg_TimeSummary->count>0) doTimeSummary=1;
if(arg_Check->count>0) doCheck=1;
if(arg_PeriodSearch->count>0) doPeriodSearch=1;
if(arg_Hourglass->count>0) doHourglass=1;
if(arg_Opposition->count>0) doOpposition=1;
if(arg_designstretch->count>0) {
if ( strcmp(*arg_designstretch->sval, "0") == 0) {
useDesignStretch = 0;
} else {
useDesignStretch = 1;
}
}
if(arg_Airmass->count>0) {
doAirmass=1;
if(strcmp(*arg_Airmass->sval, "0") != 0) {
useMaxAirmass=0;
}
else {
useMaxAirmass=1;
}
}
if(arg_SixVisits->count>0) doSixVisits=1;
if(arg_Visits->count>0) {
doVisits=1;
if(arg_reqFilters->count==0) {
fprintf(stderr,"Error: with -v|--visitsnum must give -f|--filters\n");
exit(1);
}
strcpy(str, *arg_reqFilters->sval);
i = 0;
strcpy(desiredFilters[i],strtok_r(str," ,",&savptr));
i++;
while((str1=strtok_r(NULL," ,",&savptr))!= NULL) {
strcpy(desiredFilters[i],str1);
i++;
}
ndesiredFilters = i;
}
if(arg_NEOrevisits->count>0) doNEOrevisits=1;
if(arg_SNtiming->count>0) doSNtiming=1;
if(arg_Slew->count>0) doSlew=1;
if(arg_propIDs->count>0) {
strcpy(str, *arg_propIDs->sval);
i = 0;
propIDs[i] = atoi(strtok_r(str," ,",&savptr));
i++;
while((str1=strtok_r(NULL," ,",&savptr))!= NULL) {
propIDs[i] = atoi(str1);
i++;
}
nIDs = i;
}
if(arg_plotfileRoot->count>0) {
strcpy(plotfileRoot,arg_plotfileRoot->filename[0]);
doHardcopy = 1;
}
if(arg_plotTitle->count>0) {
strcpy(plotTitle,arg_plotTitle->filename[0]);
}
if(arg_skipDays->count>0) {
strcpy(str, *arg_skipDays->sval);
skipDays = atoi(strtok_r(str," ,",&savptr));
str1 = strtok_r(NULL," ,",&savptr);
if(str1 != (char *) NULL) lengthDays = atoi(str1);
}
if(arg_debug->count>0) {
debug = 1;
}
#if 0
printf(" sessionID: %d\n", sessionID);
printf(" skipDays: %d\n", skipDays);
printf(" lengthDays: %d\n", lengthDays);
printf(" nIDs: %d\n", nIDs);
if(nIDs>0) {
printf(" using IDs: "); for(i=0; i<nIDs; i++) printf(" %d",propIDs[i]); printf("\n");
}
printf(" doCheck: %d\n", doCheck);
printf("doPeriodSearch: %d\n", doPeriodSearch);
printf(" doHourglass: %d\n", doHourglass);
printf(" doOpposition: %d\n", doOpposition);
printf(" doSixVisits: %d\n", doSixVisits);
printf(" doVisits: %d\n", doVisits);
if(doVisits) {
printf(" using filters: "); for(i=0; i<ndesiredFilters; i++) printf(" %s",desiredFilters[i]); printf("\n");
}
printf(" doNEOrevisits: %d\n", doNEOrevisits);
printf(" doSNtiming: %d\n", doSNtiming);
if(strlen(plotfileRoot)>0) printf(" hardcopy file: \"%s\"\n", plotfileRoot);
if(strlen(plotTitle)>0) printf(" plot title: \"%s\"\n", plotTitle);
printf(" debug: %d\n", debug);
#endif
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
}
int main(int argc, char *argv[]) {
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "Input .BK file");
struct arg_file *output = arg_file0("o", "output", "<file>", "Output .BK file");
struct arg_int *anim = arg_int0("a", "anim", "<animation_id>", "Select animation");
struct arg_lit *all_anims = arg_lit0("A", "all_anims", "All animations");
struct arg_int *sprite = arg_int0("s", "sprite", "<sprite_id>", "Select sprite (requires --anim)");
struct arg_lit *keylist = arg_lit0(NULL, "keylist", "Prints a list of valid fields for --key.");
struct arg_str *key = arg_strn("k", "key", "<key>", 0, 2, "Select key");
struct arg_str *value = arg_str0(NULL, "value", "<value>", "Set value (requires --key)");
struct arg_lit *play = arg_lit0(NULL, "play", "Play animation or sprite (requires --anim)");
struct arg_int *scale = arg_int0(NULL, "scale", "<factor>", "Scales sprites (requires --play)");
struct arg_lit *parse = arg_lit0(NULL, "parse", "Parse value (requires --key)");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,output,anim,all_anims,sprite,keylist,key,value,play,scale,parse,end};
const char* progname = "bktool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-30s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 .BK file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2013 Tuomas Virtanen\n");
goto exit_0;
}
// Argument dependencies
if(anim->count == 0) {
if(sprite->count > 0) {
printf("--sprite requires --anim\n");
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
if(play->count > 0) {
printf("--play requires --anim\n");
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
}
if(key->count == 0) {
if(value->count > 0) {
printf("--value requires --key\n");
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
}
if(output->count == 0) {
if(value->count > 0) {
printf("--value requires --output\n");
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
}
if(play->count == 0) {
if(scale->count > 0) {
printf("--scale requires --play\n");
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Init SDL
SDL_Init(SDL_INIT_VIDEO);
// Load file
sd_bk_file *bk = sd_bk_create();
int ret = sd_bk_load(bk, file->filename[0]);
if(ret) {
printf("Unable to load BK file! Make sure the file exists and is a valid BK file.\n");
goto exit_1;
}
// Scaling variable
int _sc = 1;
if(scale->count > 0) {
_sc = scale->ival[0];
if(_sc > 4) _sc = 4;
if(_sc < 1) _sc = 1;
}
// Handle args
if(sprite->count > 0) {
// Make sure sprite exists.
if(!check_anim_sprite(bk, anim->ival[0], sprite->ival[0])) {
goto exit_1;
}
sd_sprite *sp = bk->anims[anim->ival[0]]->animation->sprites[sprite->ival[0]];
// Handle arguments
if(key->count > 0) {
if(value->count > 0) {
sprite_set_key(sp, key->sval, key->count, value->sval[0]);
} else {
sprite_get_key(sp, key->sval, key->count);
}
} else if(keylist->count > 0) {
sprite_keylist();
} else if(play->count > 0) {
sprite_play(bk, _sc, anim->ival[0], sprite->ival[0]);
} else {
sprite_info(sp, anim->ival[0], sprite->ival[0]);
}
} else if(anim->count > 0) {
// Make sure the bkanim exists
if(!check_anim(bk, anim->ival[0])) {
goto exit_1;
}
sd_bk_anim *bka = bk->anims[anim->ival[0]];
sd_animation *ani = bka->animation;
if(key->count > 0) {
if(value->count > 0) {
bkanim_set_key(bka, ani, key->sval, key->count, value->sval[0]);
} else {
bkanim_get_key(bka, ani, key->sval, key->count, parse->count);
}
} else if(keylist->count > 0) {
bkanim_keylist();
} else if(play->count > 0) {
anim_play(bk, _sc, anim->ival[0]);
} else {
bkanim_info(bka, ani, anim->ival[0]);
}
} else if(all_anims->count > 0) {
sd_bk_anim *bka;
sd_animation *ani;
for(int i = 0; i < 50; i++) {
if (bk->anims[i]) {
bka = bk->anims[i];
ani = bka->animation;
if(key->count > 0) {
if(value->count > 0) {
bkanim_set_key(bka, ani, key->sval, key->count, value->sval[0]);
} else {
printf("Animation %2u: ", i);
bkanim_get_key(bka, ani, key->sval, key->count, parse->count);
}
} else {
printf("\n");
bkanim_info(bka, ani, i);
}
}
}
} else {
if(key->count > 0) {
if(value->count > 0) {
bk_set_key(bk, key->sval, key->count, value->sval[0]);
} else {
bk_get_key(bk, key->sval, key->count);
}
} else if(keylist->count > 0) {
bk_keylist();
} else {
bk_info(bk);
}
}
// Write output file
if(output->count > 0) {
sd_bk_save(bk, output->filename[0]);
}
// Quit
exit_1:
sd_bk_delete(bk);
SDL_Quit();
exit_0:
arg_freetable(argtable, sizeof(argtable)/sizeof(argtable[0]));
return 0;
}
int main (int argc, char **argv) {
void *argtable[] = {
help = arg_lit0("h","help","print this screen"),
verbose = arg_lit0("v","verbose","tell me everything"),
fsyslog = arg_lit0(NULL,"syslog","use syslog"),
cachepath = arg_file1(NULL,NULL,"cachepath","directory or .cdb database file"),
netaddress0 = arg_file0(NULL,NULL,"address","zmq address"),
end = arg_end(20),
};
int32_t nerrors = arg_parse(argc,argv,argtable);
if (help->count) {
fprintf(stdout,"tmpcache %s - version 0\n",__FUNCTION__); /*FIXME*/
arg_print_syntaxv(stdout,argtable,"\n\n");
arg_print_glossary (stdout,argtable,"%-25s %s\n");
goto finish;
}
if (verbose->count) {
fprintf(stdout,"tmpcache host - version 0\n");
int32_t major,minor,patch;
zmq_version (&major,&minor,&patch);
fprintf(stdout,"compiled with zmq support %d.%d.%d\n",major,minor,patch);
goto finish;
}
if (nerrors) {
arg_print_errors (stdout,end,"");
arg_print_syntaxv(stdout,argtable,"\n\n");
goto finish;
}
u_term = 0;
signal (SIGINT,signalhandler);
signal (SIGTERM,signalhandler);
tc_snapshotconfig_t config;
/* check if there is an address or not */
if (netaddress0->count == 0) {
config.cachepath = bfromcstr (cachepath->filename[0]);
config.signalf = checksignal;
config.errorf = (fsyslog->count) ? logerror : printerror;
if (fsyslog->count) {
openlog (NULL,LOG_PID|LOG_NDELAY,LOG_USER);
syslog (LOG_INFO,"writing cache %s to stdout",btocstr(config.cachepath));
}
tc_snapshotcachetostdout (&config);
if (fsyslog->count) {
syslog (LOG_INFO,"done writing cache %s to stdout",btocstr(config.cachepath));
closelog();
}
bdestroy (config.cachepath);
} else {
config.cachepath = bfromcstr (cachepath->filename[0]);
/*TODO: check for .cdb*/
config.address = bfromcstr (netaddress0->filename[0]);
/*TODO: check for correct address*/
config.signalf = checksignal;
config.errorf = (fsyslog->count) ? logerror : printerror;
if (fsyslog->count) {
openlog (NULL,LOG_PID|LOG_NDELAY,LOG_USER);
syslog (LOG_INFO,"writing cache from %s @ %s",btocstr(config.cachepath),btocstr(config.address));
}
tc_snapshotcachetoaddress (&config);
if (fsyslog->count) {
syslog (LOG_INFO,"closing cache %s @ %s for reading",btocstr(config.cachepath),btocstr(config.address));
closelog();
}
bdestroy (config.address);
bdestroy (config.cachepath);
}
finish:
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
exit(0);
}
int main(int argc, char **argv)
{
const char* progname = "z-connector";
struct arg_file *device = arg_file1("dD", "device", NULL, "path to the serial port of Z-Wave dongle");
struct arg_str *server = arg_str1("sS", "server", NULL, "IP address or host name to connect to");
struct arg_int *port = arg_int0("pP", "port", NULL, "port number (defaults to 9087)");
struct arg_file *cert = arg_file0(NULL, "cert", NULL, "personal certificate");
struct arg_file *key = arg_file0(NULL, "key", NULL, "personal certificate key");
struct arg_file *cacert = arg_file0(NULL, "cacert", NULL, "CA certificate");
struct arg_file *log = arg_file0("lL", "log", NULL, "file to write log to (defaults to stdout)");
struct arg_lit *debug = arg_lit0(NULL, "debug", "log debugging information");
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_end *end = arg_end(20);
void* argTable[] = {device, server, port, cert, key, cacert, log, debug, help, end};
#ifdef WIN32
WSADATA wsa;
WORD wsaVersion = MAKEWORD(2, 2);
int wsaError;
DWORD win32err;
#endif
int retCode, nErrors;
if (arg_nullcheck(argTable) != 0)
{
printf("%s: insufficient memory\n", progname);
CLEAN_RETURN(1);
}
nErrors = arg_parse(argc, argv, argTable);
if (IS_ARG_SET(help))
{
printf("Usage: %s", progname);
arg_print_syntax(stdout, argTable, "\n");
//printf("Print certain system information. With no options, same as -s.\n\n");
arg_print_glossary(stdout, argTable," %-25s %s\n");
printf("\nReport bugs to <*****@*****.**>.\n");
CLEAN_RETURN(0);
}
LogLevel = (IS_ARG_SET(debug)) ? 3 : 2;
if (nErrors > 0)
{
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
CLEAN_RETURN(2);
}
#ifdef WIN32
hStoppingEvent = CreateEvent(NULL, TRUE, FALSE, "Local\\Z-Agent-Stop");
if (hStoppingEvent == NULL)
{
win32err = GetLastError();
if (win32err == ERROR_INVALID_HANDLE)
{
printf("Another instance is already running\n");
CLEAN_RETURN(0);
}
else
{
printf("Failed to create synchronization event: %d\n", win32err);
CLEAN_RETURN(3);
}
}
wsaError = WSAStartup(wsaVersion, &wsa);
if (wsaError != 0)
{
printf("WSA Startup failed with code %d\n", wsaError);
CloseHandle(hStoppingEvent);
CLEAN_RETURN(3);
}
if (wsa.wVersion != wsaVersion)
{
printf("Required WSA version not found\n");
CloseHandle(hStoppingEvent);
CLEAN_RETURN(3);
}
#endif
retCode = main_impl(device->filename[0],
server->sval[0], SAFE_INT(port, 9087),
SAFE_FILE(cert, ""), SAFE_FILE(key, ""), SAFE_FILE(cacert, ""),
SAFE_FILE(log, "-"));
#ifdef WIN32
WSACleanup();
CloseHandle(hStoppingEvent);
#endif
CLEAN_RETURN(retCode);
}
int main(int argc, char *argv[]) {
struct arg_str *cblOpt = arg_str1("c", "cable", "nero:<VID>:<PID> | xil3 | dusb", "cable driver to use");
struct arg_lit *scanOpt = arg_lit0("s", "scan", " scan the JTAG chain");
struct arg_file *bitOpt = arg_file0("b", "bitfile", "<fileName>", " bit file to load");
struct arg_uint *devOpt = arg_uint0("d", "device", "<device>", " target device (default \"1\")");
struct arg_lit *helpOpt = arg_lit0("h", "help", " print this help and exit\n");
struct arg_end *endOpt = arg_end(20);
void* argTable[] = {cblOpt, scanOpt, bitOpt, devOpt, helpOpt, endOpt};
const char *progName = "xilprg";
uint32 exitCode = 0;
int numErrors;
const char *cable, *bitFile;
uint32 devNum;
char line[1024];
char configFileName[4097]; // TODO: Fix, somehow.
if ( arg_nullcheck(argTable) != 0 ) {
fprintf(stderr, "%s: insufficient memory\n", progName);
fail(1);
}
numErrors = arg_parse(argc, argv, argTable);
if ( helpOpt->count > 0 ) {
printf("Xilinx Programmer 0.6 Copyright (C) 2006-2011 Zoltan Csizmadia & Chris McClelland\n\nUsage: %s", progName);
arg_print_syntax(stdout, argTable, "\n");
printf("\nProgram a Xilinx FPGA.\n\n");
arg_print_glossary(stdout, argTable," %-10s %s\n");
fail(0);
}
if ( numErrors > 0 ) {
arg_print_errors(stdout, endOpt, progName);
fprintf(stderr, "Try '%s --help' for more information.\n", progName);
fail(2);
}
if ( (scanOpt->count == 0 && bitOpt->count == 0) ||
(scanOpt->count != 0 && bitOpt->count != 0) )
{
fprintf(stderr, "%s: you must specify either -s|--scan or -b|--bitfile, but not both\n", progName);
fprintf(stderr, "Try '%s --help' for more information.\n", progName);
fail(3);
}
cable = cblOpt->sval[0];
bitFile = bitOpt->count ? bitOpt->filename[0] : NULL;
devNum = devOpt->count ? devOpt->ival[0] : 1;
if ( initialize() ) {
fprintf(stderr, "%s failed to initialize!\n", progName);
fail(4);
}
if ( getConfigFullPath("xilprg.conf", configFileName, sizeof(configFileName)) ) {
fprintf(stderr, "%s failed to determine the location of its config file!\n", progName);
fail(5);
}
if ( load_config_file(configFileName) ) {
fprintf(stderr, "%s failed to load its config file from %s!\n", progName, configFileName);
fail(6);
}
try {
sprintf(line, "cable %s", cable);
process_command_line(line);
if ( scanOpt->count ) {
process_command_line("detect");
} else {
sprintf(line, "program %lu \"%s\"", devNum, bitFile);
process_command_line(line);
}
}
catch ( const std::exception &ex ) {
fprintf(stderr, "%s failed: %s!\n", progName, ex.what());
fail(7);
}
cleanup:
uninitialize();
arg_freetable(argTable, sizeof(argTable)/sizeof(argTable[0]));
return exitCode;
}
int main(int argc, char* argv[]) {
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "font file");
struct arg_int *fh = arg_int1("g", "height", "<value>", "font height in pixels (6 or 8)");
struct arg_str *text = arg_str0("t", "text", "<value>", "text to show");
struct arg_int *scale = arg_int0("s", "scale", "<value>", "scaling for the window");
struct arg_file *export = arg_file0("e", "export", "<file>", "Export the full font to a PNG file");
struct arg_lit *split = arg_lit0(NULL, "split", "Split to separate PNG files (set path in -e).");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,fh,text,scale,export,split,end};
const char* progname = "fonttool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 Font file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2013 Tuomas Virtanen\n");
goto exit_0;
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Requite either export or text
if(export->count <= 0 && text->count <= 0) {
printf("Use either --export or --text arguments!\n");
goto exit_0;
}
// Font size
int _fs = fh->ival[0];
if(_fs < 6 || _fs > 8 || _fs == 7) {
printf("Only valid values for fontsize are 6 and 8.\n");
goto exit_0;
}
// Load fonts
sd_font font;
sd_font_create(&font);
int ret = sd_font_load(&font, file->filename[0], _fs);
if(ret != SD_SUCCESS) {
printf("Couldn't load small font file! Error [%d] %s.\n", ret, sd_get_error(ret));
goto exit_1;
}
// Export or display
if(export->count > 0) {
export_to(&font, export->filename[0], (split->count > 0));
} else {
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
etFMode FMode; // format output mode
char szOutputFileSpec[_MAX_PATH];
char szInputFileSpec[_MAX_PATH];
// command line args
struct arg_lit *help = arg_lit0("h","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *format = arg_int0("M","format","<int>", "output format: 0 - multifasta, 1 - CSV format only, 2 - BED format, 3 - XML entries only (default: 0)");
struct arg_file *InFile = arg_file1("i","input","<file>", "input from bioseq files");
struct arg_file *OutFile = arg_file1("o","result","<file>", "output entry dump file");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,LogFile,LogFile,format,InFile,OutFile,end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s Dump biosequence (generated by genbioseq) file contents, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n",gszProcName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
FMode = (etFMode)(format->count ? format->ival[0] : eFMdefault);
if(FMode < eFMdefault || FMode >= eFMplaceholder)
{
printf("\nError: Requested output format '-M%d' not supported, must be in range %d..%d",FMode,eFMdefault,eFMplaceholder-1);
exit(1);
}
strcpy(szInputFileSpec,InFile->filename[0]);
strcpy(szOutputFileSpec,OutFile->filename[0]);
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
const char *pszDescr;
switch(FMode) {
case eFMdefault: // default is for multifasta
pszDescr = "Multifasta";
break;
case eFMcsv: // CSV entries
pszDescr = "CSV format";
break;
case eFMbed: // BED entries
pszDescr = "BED format";
break;
case eFMxml: // XML entries
pszDescr = "XML format";
break;
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"dump output format: %s",pszDescr);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"input biosequence file: '%s'",szInputFileSpec);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"output to file: '%s'",szOutputFileSpec);
gStopWatch.Start();
Rslt = Process(szInputFileSpec,szOutputFileSpec,FMode);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s Dump biosequence (generated by genbioseq) file contents, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
}
int main(int argc, char *argv[]) {
int retcode = 1;
int nerrors = 0;
streamer_t streamer;
memset(&streamer, 0, sizeof(streamer_t));
// Signal handlers
signal(SIGINT, sig_fn);
signal(SIGTERM, sig_fn);
// Initialize SDL2
if (SDL_Init(SDL_INIT_AUDIO) != 0) {
fprintf(stderr, "%s\n", SDL_GetError());
return 1;
}
// Defaults
streamer.freq = 44100;
streamer.n_channels = 2;
streamer.bits = 16;
streamer.volume = 1.0f;
streamer.quality = DUMB_RQ_CUBIC;
// commandline argument parser options
struct arg_lit *arg_help =
arg_lit0("h", "help", "print this help and exits");
struct arg_dbl *arg_volume =
arg_dbl0("v", "volume", "<volume",
"sets the output volume (-8.0 to +8.0, default 1.0)");
struct arg_int *arg_samplerate = arg_int0(
"s", "samplerate", "<freq>", "sets the sampling rate (default 44100)");
struct arg_int *arg_quality = arg_int0(
"r", "quality", "<quality>", "specify the resampling quality to use");
struct arg_lit *arg_mono =
arg_lit0("m", "mono", "generate mono output instead of stereo");
struct arg_lit *arg_eight =
arg_lit0("8", "eight", "generate 8-bit instead of 16-bit");
struct arg_lit *arg_noprogress =
arg_lit0("n", "noprogress", "hide progress bar");
struct arg_file *arg_output =
arg_file0("o", "output", "<file>", "output file");
struct arg_file *arg_input =
arg_file1(NULL, NULL, "<file>", "input module file");
struct arg_end *arg_fend = arg_end(20);
void *argtable[] = {arg_help, arg_input, arg_volume,
arg_samplerate, arg_quality, arg_mono,
arg_eight, arg_noprogress, arg_fend};
const char *progname = "dumbplay";
// Make sure everything got allocated
if (arg_nullcheck(argtable) != 0) {
fprintf(stderr, "%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse inputs
nerrors = arg_parse(argc, argv, argtable);
// Handle help
if (arg_help->count > 0) {
fprintf(stderr, "Usage: %s", progname);
arg_print_syntax(stderr, argtable, "\n");
fprintf(stderr, "\nArguments:\n");
arg_print_glossary(stderr, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle libargtable errors
if (nerrors > 0) {
arg_print_errors(stderr, arg_fend, progname);
fprintf(stderr, "Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Handle the switch options
streamer.input = arg_input->filename[0];
if (arg_eight->count > 0) {
streamer.bits = 8;
}
if (arg_mono->count > 0) {
streamer.n_channels = 1;
}
if (arg_noprogress->count > 0) {
streamer.no_progress = true;
}
if (arg_volume->count > 0) {
streamer.volume = arg_volume->dval[0];
if (streamer.volume < -8.0f || streamer.volume > 8.0f) {
fprintf(stderr, "Volume must be between -8.0f and 8.0f.\n");
goto exit_0;
}
}
if (arg_samplerate->count > 0) {
streamer.freq = arg_samplerate->ival[0];
if (streamer.freq < 1 || streamer.freq > 96000) {
fprintf(stderr, "Sampling rate must be between 1 and 96000.\n");
goto exit_0;
}
}
if (arg_quality->count > 0) {
streamer.quality = arg_quality->ival[0];
if (streamer.quality < 0 || streamer.quality >= DUMB_RQ_N_LEVELS) {
fprintf(stderr, "Quality must be between %d and %d.\n", 0,
DUMB_RQ_N_LEVELS - 1);
goto exit_0;
}
}
// Load source file.
dumb_register_stdfiles();
streamer.src = dumb_load_any(streamer.input, 0, 0);
if (!streamer.src) {
fprintf(stderr, "Unable to load file %s for playback!\n",
streamer.input);
goto exit_0;
}
// Set up playback
streamer.renderer =
duh_start_sigrenderer(streamer.src, 0, streamer.n_channels, 0);
streamer.delta = 65536.0f / streamer.freq;
streamer.sbytes = (streamer.bits / 8) * streamer.n_channels;
streamer.ssize = duh_get_length(streamer.src);
// Stop producing samples on module end
DUMB_IT_SIGRENDERER *itsr = duh_get_it_sigrenderer(streamer.renderer);
dumb_it_set_loop_callback(itsr, &dumb_it_callback_terminate, NULL);
dumb_it_set_xm_speed_zero_callback(itsr, &dumb_it_callback_terminate, NULL);
dumb_it_set_resampling_quality(itsr, streamer.quality);
// Set up the SDL2 format we want for playback.
SDL_AudioSpec want;
SDL_zero(want);
want.freq = streamer.freq;
want.format = (streamer.bits == 16) ? AUDIO_S16 : AUDIO_S8;
want.channels = streamer.n_channels;
want.samples = SAMPLES;
want.callback = stream_audio;
want.userdata = &streamer;
// Find SDL2 audio device, and request the format we just set up.
// SDL2 will tell us what we got in the "have" struct.
SDL_AudioSpec have;
streamer.dev = SDL_OpenAudioDevice(NULL, 0, &want, &have, 0);
if (streamer.dev == 0) {
fprintf(stderr, "%s\n", SDL_GetError());
goto exit_1;
}
// Make sure we got the format we wanted. If not, stop here.
if (have.format != want.format) {
fprintf(stderr, "Could not get correct playback format.\n");
goto exit_2;
}
// Play file
SDL_PauseAudioDevice(streamer.dev, 0);
// Show initial state of the progress bar (if it is enabled)
int time_start = SDL_GetTicks();
float seek = 0.0f;
int ms_played = 0;
if (!streamer.no_progress) {
show_progress(PROGRESSBAR_LENGTH, seek, ms_played);
}
// Loop while dumb is still giving data. Update progressbar if enabled.
while (!stop_signal && !streamer.ended) {
if (!streamer.no_progress) {
seek = ((float)streamer.spos) / ((float)streamer.ssize);
ms_played = SDL_GetTicks() - time_start;
show_progress(PROGRESSBAR_LENGTH, seek, ms_played);
}
SDL_Delay(100);
}
// We made it this far without crashing, so let's just exit with no error :)
retcode = 0;
// Free up resources and exit.
if (streamer.sig_samples) {
destroy_sample_buffer(streamer.sig_samples);
}
exit_2:
SDL_CloseAudioDevice(streamer.dev);
exit_1:
if (streamer.renderer) {
duh_end_sigrenderer(streamer.renderer);
}
if (streamer.src) {
unload_duh(streamer.src);
}
exit_0:
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
SDL_Quit();
return retcode;
}
int genkmarkers(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
genkmarkers(int argc, char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt = 0; // function result code >= 0 represents success, < 0 on failure
int NumberOfProcessors; // number of installed CPUs
int NumThreads; // number of threads (0 defaults to number of CPUs)
int PMode; // processing mode
int KMerLen; // this length K-mers
int PrefixLen; // inter-cultivar shared prefix length
int SuffixLen; // cultivar specific suffix length
int MinWithPrefix; // minimum number of cultivars required to have the shared prefix
int MinHamming; // must be at least this Hamming away from any other K-mer in other species
char szCultivarName[cMaxDatasetSpeciesChrom+1]; // cultivar name
char szPartialCultivarsList[(cMaxDatasetSpeciesChrom + 10) * cMaxTargCultivarChroms]; // individual species parsed from this comma/tab/space separated list
int NumPartialCultivars; // there are this many pseudo chromosomes for targeted cultivar for which K-mer markers are required
char *pszPartialCultivars[cMaxTargCultivarChroms+1]; // pseudo chromosome names which identify targeted cultivar
char szSfxPseudoGenome[_MAX_PATH]; // contains assembly + suffix array over all psuedo-chromosomes for all cultivars
char szMarkerFile[_MAX_PATH]; // output potential markers to this file
char szMarkerReadsFile[_MAX_PATH]; // output reads containing potential markers to this file
char szSQLiteDatabase[_MAX_PATH]; // results summaries to this SQLite file
char szExperimentName[cMaxDatasetSpeciesChrom+1]; // experiment name
char szExperimentDescr[1000]; // describes experiment
// command line args
struct arg_lit *help = arg_lit0("h","help", "Print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "Print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "Diagnostics log file");
struct arg_int *pmode = arg_int0("m","mode","<int>", "Processing mode : 0 - default with K-mer extension, 1 - no K-mer extension, 2 - inter-cultivar shared prefix sequences ");
struct arg_int *kmerlen = arg_int0("k","kmer","<int>", "Cultivar specific K-mers of this length (default 50, range 25..100)");
struct arg_int *prefixlen = arg_int0("p","prefixlen","<int>", "Cultivar specific K-mers to contain inter-cultivar shared prefix sequences of this length (Mode 2 only");
struct arg_int *minwithprefix = arg_int0("s","minshared","<int>","Inter-cultivar shared prefix sequences must be present in this many cultivars (Mode 2 only, default all)");
struct arg_int *minhamming = arg_int0("K","minhamming","<int>", "Minimum Hamming separation distance in other non-target cultivars (default 2, range 1..5)");
struct arg_str *cultivar = arg_str1("c","cultivar","<str>", "Cultivar name to associate with identified marker K-mers");
struct arg_str *chromnames = arg_str1("C","chromnames","<str>", "Comma/space separated list of pseudo-chrom names specific to cultivar for which markers are required");
struct arg_file *infile = arg_file1("i","in","<file>", "Use this suffix indexed pseudo-chromosomes file");
struct arg_file *outfile = arg_file1("o","markers","<file>", "Output accepted marker K-mer sequences to this multifasta file");
struct arg_file *outreadsfile = arg_file0("O","markerreads","<file>", "Output reads containing accepted marker K-mers to this multifasta file");
struct arg_int *numthreads = arg_int0("T","threads","<int>", "number of processing threads 0..128 (defaults to 0 which sets threads to number of CPU cores)");
struct arg_file *summrslts = arg_file0("q","sumrslts","<file>", "Output results summary to this SQLite3 database file");
struct arg_str *experimentname = arg_str0("w","experimentname","<str>", "experiment name SQLite3 database file");
struct arg_str *experimentdescr = arg_str0("W","experimentdescr","<str>", "experiment description SQLite3 database file");
struct arg_end *end = arg_end(200);
void *argtable[] = {help,version,FileLogLevel,LogFile,
summrslts,experimentname,experimentdescr,
pmode,kmerlen,prefixlen,minwithprefix,minhamming,cultivar,chromnames,infile,outfile,outreadsfile,
numthreads,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s %s %s, Version %s\nOptions ---\n", gszProcName,gpszSubProcess->pszName,gpszSubProcess->pszFullDescr,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s %s @myparams.txt\n",gszProcName,gpszSubProcess->pszName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
return(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s %s Version %s\n",gszProcName,gpszSubProcess->pszName,cpszProgVer);
return(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>\n'",FileLogLevel->ival[0]);
return(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d\n",iFileLogLevel,eDLNone,eDLDebug);
return(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
// now that log parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem\n");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created\n",szLogFile);
return(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Subprocess %s Version %s starting",gpszSubProcess->pszName,cpszProgVer);
gExperimentID = 0;
gProcessID = 0;
gProcessingID = 0;
szSQLiteDatabase[0] = '\0';
szExperimentName[0] = '\0';
szExperimentDescr[0] = '\0';
if(experimentname->count)
{
strncpy(szExperimentName,experimentname->sval[0],sizeof(szExperimentName));
szExperimentName[sizeof(szExperimentName)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szExperimentName);
CUtility::ReduceWhitespace(szExperimentName);
}
else
szExperimentName[0] = '\0';
gExperimentID = 0;
gProcessID = 0;
gProcessingID = 0;
szSQLiteDatabase[0] = '\0';
szExperimentDescr[0] = '\0';
if(summrslts->count)
{
strncpy(szSQLiteDatabase,summrslts->filename[0],sizeof(szSQLiteDatabase)-1);
szSQLiteDatabase[sizeof(szSQLiteDatabase)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szSQLiteDatabase);
if(strlen(szSQLiteDatabase) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite database specified with '-q<filespec>' option");
return(1);
}
if(strlen(szExperimentName) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite experiment name specified with '-w<str>' option");
return(1);
}
if(experimentdescr->count)
{
strncpy(szExperimentDescr,experimentdescr->sval[0],sizeof(szExperimentDescr)-1);
szExperimentDescr[sizeof(szExperimentDescr)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szExperimentDescr);
}
if(strlen(szExperimentDescr) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite experiment description specified with '-W<str>' option");
return(1);
}
gExperimentID = gSQLiteSummaries.StartExperiment(szSQLiteDatabase,false,true,szExperimentName,szExperimentName,szExperimentDescr);
if(gExperimentID < 1)
return(1);
gProcessID = gSQLiteSummaries.AddProcess((char *)gpszSubProcess->pszName,(char *)gpszSubProcess->pszName,(char *)gpszSubProcess->pszFullDescr);
if(gProcessID < 1)
return(1);
gProcessingID = gSQLiteSummaries.StartProcessing(gExperimentID,gProcessID,(char *)cpszProgVer);
if(gProcessingID < 1)
return(1);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Initialised SQLite database '%s' for results summary collection",szSQLiteDatabase);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database experiment identifier for '%s' is %d",szExperimentName,gExperimentID);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database process identifier for '%s' is %d",(char *)gpszSubProcess->pszName,gProcessID);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database processing instance identifier is %d",gProcessingID);
}
else
{
szSQLiteDatabase[0] = '\0';
szExperimentDescr[0] = '\0';
}
// show user current resource limits
#ifndef _WIN32
gDiagnostics.DiagOut(eDLInfo, gszProcName, "Resources: %s",CUtility::ReportResourceLimits());
#endif
#ifdef _WIN32
SYSTEM_INFO SystemInfo;
GetSystemInfo(&SystemInfo);
NumberOfProcessors = SystemInfo.dwNumberOfProcessors;
#else
NumberOfProcessors = sysconf(_SC_NPROCESSORS_CONF);
#endif
int MaxAllowedThreads = min(cMaxWorkerThreads,NumberOfProcessors); // limit to be at most cMaxWorkerThreads
if((NumThreads = numthreads->count ? numthreads->ival[0] : MaxAllowedThreads)==0)
NumThreads = MaxAllowedThreads;
if(NumThreads < 0 || NumThreads > MaxAllowedThreads)
{
gDiagnostics.DiagOut(eDLWarn,gszProcName,"Warning: Number of threads '-T%d' specified was outside of range %d..%d",NumThreads,1,MaxAllowedThreads);
gDiagnostics.DiagOut(eDLWarn,gszProcName,"Warning: Defaulting number of threads to %d",MaxAllowedThreads);
NumThreads = MaxAllowedThreads;
}
PMode = (etPMode)(pmode->count ? pmode->ival[0] : ePMExtdKMers);
if(PMode < ePMExtdKMers || PMode >= ePMplaceholder)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Processing mode '-m%d' specified outside of range %d..%d\n",PMode,ePMExtdKMers,(int)ePMplaceholder-1);
exit(1);
}
KMerLen = kmerlen->count ? kmerlen->ival[0] : cDfltKMerLen;
if(KMerLen < cMinKMerLen || KMerLen > cMaxKMerLen)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: K-mer core length '-k%d' must be in range %d..%d",KMerLen,cMinKMerLen,cMaxKMerLen);
return(1);
}
if(PMode == 2)
{
PrefixLen = prefixlen->count ? prefixlen->ival[0] : KMerLen/2;
if(PrefixLen < cMinKMerLen/2 || PrefixLen > KMerLen-(cMinKMerLen/2))
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Prefix length '-p%d' must be in range %d..%d",KMerLen,cMinKMerLen/2,KMerLen-(cMinKMerLen/2));
return(1);
}
SuffixLen = KMerLen - PrefixLen;
MinWithPrefix = minwithprefix->count ? minwithprefix->ival[0] : 0;
if(MinWithPrefix != 0 && MinWithPrefix < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum cultivars sharing prefix sequence '-s%d' must be either 0 (all) or at least 1",MinWithPrefix);
return(1);
}
}
MinHamming = minhamming->count ? minhamming->ival[0] : cDfltHamming;
if(MinHamming < cMinHamming || MinHamming > cMaxHamming)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum Hamming separation '-K%d' must be in range %d..%d",MinHamming,cMinHamming,cMaxHamming);
return(1);
}
strncpy(szCultivarName,cultivar->sval[0],cMaxDatasetSpeciesChrom);
szCultivarName[cMaxDatasetSpeciesChrom]= '\0';
CUtility::TrimQuotedWhitespcExtd(szCultivarName);
if(strlen(szCultivarName) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected cultivar name '-c<name>' is empty");
return(1);
}
strncpy(szPartialCultivarsList,chromnames->sval[0],sizeof(szPartialCultivarsList));
szPartialCultivarsList[sizeof(szPartialCultivarsList)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szPartialCultivarsList);
CUtility::ReduceWhitespace(szPartialCultivarsList);
char *pChr = szPartialCultivarsList;
char *pStartChr;
char Chr;
int CurSpeciesLen;
NumPartialCultivars=0;
CurSpeciesLen = 0;
pStartChr = pChr;
while((Chr = *pChr++) != '\0')
{
if(Chr == ' ' || Chr == '\t' || Chr == ',') // treat any of these as delimiters
{
pChr[-1] = '\0';
if(CurSpeciesLen != 0)
{
pszPartialCultivars[NumPartialCultivars++] = pStartChr;
CurSpeciesLen = 0;
}
pStartChr = pChr;
continue;
}
CurSpeciesLen += 1;
}
if(CurSpeciesLen)
pszPartialCultivars[NumPartialCultivars++] = pStartChr;
if(!NumPartialCultivars)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected at least one ('-C<names>') targeted cultivar chromosme name");
return(1);
}
strcpy(szSfxPseudoGenome,infile->filename[0]);
CUtility::TrimQuotedWhitespcExtd(szSfxPseudoGenome);
if(strlen(szSfxPseudoGenome) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected input pseudo-genome suffix array filename '-i<name>' is empty");
return(1);
}
strcpy(szMarkerFile,outfile->filename[0]);
CUtility::TrimQuotedWhitespcExtd(szMarkerFile);
if(strlen(szMarkerFile) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected marker file to generate filename '-o<name>' is empty");
return(1);
}
if(outreadsfile->count)
{
strcpy(szMarkerReadsFile,outreadsfile->filename[0]);
CUtility::TrimQuotedWhitespcExtd(szMarkerReadsFile);
if(strlen(szMarkerReadsFile) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Reads containing markers filename '-O<name>' is empty");
return(1);
}
}
else
szMarkerReadsFile[0] = '\0';
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
const char *pszDescr;
switch(PMode) {
case ePMExtdKMers:
pszDescr = "Extended K-mer markers";
break;
case ePMNoExtdKMers:
pszDescr = "Non-extended K-mer markers";
break;
case ePMPrefixKMers:
pszDescr = "K-mers to share prefix sequence with other cultivars";
break;
}
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode is : '%s'",pszDescr);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Targeted cultivar name : '%s'",szCultivarName);
for(int Idx = 0; Idx < NumPartialCultivars; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Targeted cultivar chromosome name (%d) : '%s'", Idx + 1,pszPartialCultivars[Idx]);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Core K-mer length : %d",KMerLen);
if(PMode == ePMPrefixKMers)
{
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Inter-cultivar shared prefix sequence length : %d",PrefixLen);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Cultivar specific suffix sequence length : %d",SuffixLen);
if(MinWithPrefix)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Min number cultivars sharing prefix : %d",MinWithPrefix);
else
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Min number cultivars sharing prefix : 'All'");
}
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum Hamming separation : %d",MinHamming);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input indexed pseudo-genome file: '%s'",szSfxPseudoGenome);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Write marker K-mers to file: '%s'",szMarkerFile);
if(szMarkerReadsFile[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Write marker containing reads to file: '%s'",szMarkerReadsFile);
if(szExperimentName[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"This processing reference: %s",szExperimentName);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Number of processing threads: %d",NumThreads);
if(gExperimentID > 0)
{
int ParamID;
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szLogFile),"log",szLogFile);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(PMode),"mode",&PMode);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(KMerLen),"kmer",&KMerLen);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(PrefixLen),"prefixlen",&PrefixLen);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(SuffixLen),"suffixlen",&SuffixLen);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(MinWithPrefix),"minwithprefix",&MinWithPrefix);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(MinHamming),"minhamming",&MinHamming);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(NumThreads),"threads",&NumThreads);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(NumberOfProcessors),"cpus",&NumberOfProcessors);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szCultivarName),"cultivar",szCultivarName);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(NumPartialCultivars),"NumPartialCultivars",&NumPartialCultivars);
for(int Idx = 0; Idx < NumPartialCultivars; Idx++)
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(pszPartialCultivars[Idx]),"chromnames",pszPartialCultivars[Idx]);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szSfxPseudoGenome),"in",szSfxPseudoGenome);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szMarkerFile),"markers",szMarkerFile);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szMarkerReadsFile),"markerreads",szMarkerReadsFile);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szSQLiteDatabase),"sumrslts",szSQLiteDatabase);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szExperimentName),"experimentname",szExperimentName);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szExperimentDescr),"experimentdescr",szExperimentDescr);
}
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
gStopWatch.Start();
Rslt = LocMarkers((etPMode)PMode,KMerLen,PrefixLen,SuffixLen,MinWithPrefix,MinHamming,szCultivarName,NumPartialCultivars,pszPartialCultivars,szSfxPseudoGenome,szMarkerFile,szMarkerReadsFile,NumThreads);
Rslt = Rslt >=0 ? 0 : 1;
if(gExperimentID > 0)
{
if(gProcessingID)
gSQLiteSummaries.EndProcessing(gProcessingID,Rslt);
gSQLiteSummaries.EndExperiment(gExperimentID);
}
gStopWatch.Stop();
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
return(Rslt);
}
else
{
printf("\n%s %s %s, Version %s\n", gszProcName,gpszSubProcess->pszName,gpszSubProcess->pszFullDescr,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
return(1);
}
return 0;
}
int GRTCLCrackCommandLineData::ParseCommandLine(int argc, char *argv[]) {
int deviceCount, i;
std::vector<std::string> webTableFilenames;
// Command line argument parsing with argtable
struct arg_lit *verbose = arg_lit0("v", "verbose", "verbose output");
struct arg_lit *silent = arg_lit0(NULL, "silent", "silence all output");
// Table related options
struct arg_file *table_file = arg_filen(NULL,NULL,"<file>", 0, 10000, "GRT Tables to use");
struct arg_file *hash_file = arg_file0("f","hashfile","<file>", "Hashfile to use");
struct arg_str *hash_value = arg_str0("s", "hashstring", "hashstring", "The hash string");
struct arg_str *hash_type = arg_str1("h", "hashtype", "{NTLM, MD4, MD5, SHA1}", "hash type to crack");
// CUDA related params
struct arg_int *device = arg_int0("d", "device", "<n>", "OpenCL device to use");
struct arg_int *platform = arg_int0("p", "platform", "<n>", "OpenCL platform to use");
struct arg_int *m = arg_int0("m", "ms", "<n>", "target step time in ms");
struct arg_int *blocks = arg_int0("b", "blocks", "<n>", "number of thread blocks to run");
struct arg_int *threads = arg_int0("t", "threads", "<n>", "number of threads per block");
struct arg_lit *zerocopy = arg_lit0("z", "zerocopy", "use zerocopy memory");
struct arg_file *o = arg_file0("o", "outputfile", "outputfile", "output file for results");
// hexoutput: Adds hex output to all password outputs.
struct arg_lit *hex_output = arg_lit0(NULL, "hexoutput", "Adds hex output to all hash outputs");
struct arg_lit *amd_kernels = arg_lit0(NULL, "amd", "use AMD vector kernels");
struct arg_int *vector_width = arg_int0(NULL, "vectorwidth", "<n>", "vector width");
struct arg_lit *debug = arg_lit0(NULL, "debug", "Use debug display class");
struct arg_lit *devdebug = arg_lit0(NULL, "devdebug", "Developer debugging output");
struct arg_str *debugfiles = arg_str0(NULL, "debugdumpfiles", "<filename>", "Filename base to dump candidates and chains to");
struct arg_int *prefetch_count = arg_int0(NULL, "prefetch", "<n>", "number of prefetch threads");
struct arg_int *candidates_to_skip = arg_int0(NULL, "skip", "<n>", "number of candidate hashes to skip");
struct arg_str *table_url = arg_str0(NULL, "tableurl", "<URL>", "URL of the web table script");
struct arg_str *table_username = arg_str0(NULL, "tableusername", "<username>", "Username, if required, for the web table script");
struct arg_str *table_password = arg_str0(NULL, "tablepassword", "<password>", "Password, if required, for the web table script");
struct arg_end *end = arg_end(20);
void *argtable[] = {verbose,silent,table_file,hash_value,hash_file,hash_type,
device,platform,m,blocks,threads,zerocopy,o,amd_kernels,vector_width,
debug, devdebug, prefetch_count,table_url,table_username,table_password,
candidates_to_skip,debugfiles,hex_output,end};
// Get arguments, collect data, check for basic errors.
if (arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
}
// Look for errors
int nerrors = arg_parse(argc,argv,argtable);
if (nerrors > 0) {
// Print errors, exit.
arg_print_errors(stdout,end,argv[0]);
//arg_print_syntax(stdout,argtable,"\n\n");
printf("\n\nOptions: \n");
arg_print_glossary(stdout,argtable," %-20s %s\n");
exit(1);
}
// Verbose & silent
if (verbose->count) {
this->Verbose = 1;
}
if (silent->count) {
this->Silent = 1;
}
if (zerocopy->count) {
this->CUDAUseZeroCopy = 1;
}
if (debug->count) {
this->Debug = 1;
}
if (devdebug->count) {
this->Debug = 1;
this->DeveloperDebug = 1;
}
if (debugfiles->count) {
this->DebugDump = 1;
this->DebugDumpFilenameBase = *debugfiles->sval;
}
if (prefetch_count->count) {
this->NumberPrefetchThreads = *prefetch_count->ival;
}
if (candidates_to_skip->count) {
this->CandidateHashesToSkip = *candidates_to_skip->ival;
}
// Web table stuff
if (table_url->count) {
this->useWebTable = 1;
this->tableURL = *table_url->sval;
// If someone has NOT specified the candidates to skip, set to default.
if (!candidates_to_skip->count) {
this->CandidateHashesToSkip = DEFAULT_CANDIDATES_TO_SKIP;
}
}
if (table_username->count) {
this->tableUsername = *table_username->sval;
}
if (table_password->count) {
this->tablePassword = *table_password->sval;
}
this->HashType = this->GRTHashTypes->GetHashIdFromString(*hash_type->sval);
if (this->HashType == -1) {
printf("Unknown hash type %s: Exiting.\n\n", *hash_type->sval);
exit(1);
}
int correct_length = this->GRTHashTypes->GetHashLengthFromId(this->HashType);
// if we know the correct length, we make sure the hash is the correct length
if (correct_length != 0) {
if ((hash_value->count) && (strlen(*hash_value->sval) != correct_length)) {
printf("Hash string is not %d hex characters. Exiting.\n\n", correct_length);
exit(1);
}
}
if (hash_value->count) {
convertAsciiToBinary(*hash_value->sval, this->Hash, 16);
} else if (hash_file->count) {
this->hashFileName = hash_file->filename[0];
this->useHashFile = 1;
} else {
printf("Must provide a hash value or a hash file!\n");
exit(1);
}
if (o->count) {
this->outputHashFileName = o->filename[0];
this->useOutputHashFile = 1;
}
// Desired kernel time
if (m->count) {
this->KernelTimeMs = *m->ival;
}
// Do this to emulate CUDA behavior for now...
// Threads - if not set, leave at default 0
if (threads->count) {
this->OpenCLWorkitems = *threads->ival;
}
// Blocks - if not set, leave at default 0
if (blocks->count) {
this->OpenCLWorkgroups = *blocks->ival * this->OpenCLWorkitems;
}
if (hex_output->count) {
this->AddHexOutput = 1;
}
// Allocate space for the list of pointers
// Create the table header type
if (this->useWebTable) {
this->TableHeader = new GRTTableHeaderVWeb();
this->TableHeader->setWebURL(this->tableURL);
this->TableHeader->setWebUsername(this->tableUsername);
this->TableHeader->setWebPassword(this->tablePassword);
GRTTableHeaderVWeb *WebTableHeader =
(GRTTableHeaderVWeb *)this->TableHeader;
webTableFilenames = WebTableHeader->getHashesFromServerByType(this->HashType);
} else {
// V1 will work for both V1 & V2 types
this->TableHeader = new GRTTableHeaderV1();
}
// If we don't have any table filenames, get the ones from the web.
// Note: The script ONLY reutrns valid tables.
if ((table_file->count == 0) && this->useWebTable) {
this->Table_File_Count = webTableFilenames.size();
this->Table_Filenames = (char **)malloc(this->Table_File_Count * sizeof(char *));
for (i = 0; i < this->Table_File_Count; i++) {
// Increment size by 1 for null termination
this->Table_Filenames[i] = (char *)malloc((webTableFilenames.at(i).size() + 1) * sizeof(char));
strcpy(this->Table_Filenames[i], webTableFilenames.at(i).c_str());
}
} else {
this->Table_File_Count = table_file->count;
this->Table_Filenames = (char **)malloc(this->Table_File_Count * sizeof(char *));
// Handle the file list sanely
for (i = 0; i < table_file->count; i++) {
// Check to ensure the file is valid
if (!this->TableHeader->isValidTable(table_file->filename[i], -1)) {
printf("%s is not a valid GRT table! Exiting.\n", table_file->filename[i]);
exit(1);
}
// Check to ensure the file is of the right type
if (!this->TableHeader->isValidTable(table_file->filename[i], this->HashType)) {
printf("%s is not a valid %s GRT table!\n", table_file->filename[i],
this->GRTHashTypes->GetHashStringFromId(this->HashType));
exit(1);
}
// Increment size by 1 for null termination
this->Table_Filenames[i] = (char *)malloc((strlen(table_file->filename[i]) + 1) * sizeof(char));
strcpy(this->Table_Filenames[i], table_file->filename[i]);
}
}
// Finally, set the CUDA device and look for errors.
if (device->count) {
this->OpenCLDevice = *device->ival;
}
if (platform->count) {
this->OpenCLPlatform = *platform->ival;
}
if (amd_kernels->count) {
this->useAmdKernels = 1;
this->vectorWidth = 4;
}
if (vector_width->count) {
this->vectorWidth = *vector_width->ival;
}
}
int main(int argc, char* argv[])
{
// Define our variables.
FILE* load;
uint16_t flash[0x10000];
char leading[0x100];
unsigned int i;
bool uread = true;
vm_t* vm;
int nerrors;
bstring ss, st;
host_context_t* dtemu = malloc(sizeof(host_context_t));
const char* warnprefix = "no-";
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_file* input_file = arg_file1(NULL, NULL, "<file>", "The input file, or - to read from standard input.");
struct arg_file* execution_dump_file = arg_file0("e", "execution-dump", "<file>", "Produce a very large execution dump file.");
struct arg_lit* debug_mode = arg_lit0("d", "debug", "Show each executed instruction.");
struct arg_lit* terminate_mode = arg_lit0("t", "show-on-terminate", "Show state of machine when program is terminated.");
struct arg_lit* headless_mode = arg_lit0("h", "headless", "Run machine witout displaying monitor and SPED output");
struct arg_lit* legacy_mode = arg_lit0("l", "legacy", "Automatically initialize hardware to legacy values.");
struct arg_str* warning_policies = arg_strn("W", NULL, "policy", 0, _WARN_COUNT * 2 + 10, "Modify warning policies.");
struct arg_lit* little_endian_mode = arg_lit0(NULL, "little-endian", "Use little endian serialization (for compatibility with older versions).");
struct arg_lit* verbose = arg_litn("v", NULL, 0, LEVEL_EVERYTHING - LEVEL_DEFAULT, "Increase verbosity.");
struct arg_lit* quiet = arg_litn("q", NULL, 0, LEVEL_DEFAULT - LEVEL_SILENT, "Decrease verbosity.");
struct arg_int* radiation = arg_intn("r", NULL, "<n>", 0, 1, "Radiation factor (higher is less radiation)");
struct arg_lit* catch_fire = arg_lit0("c", "catch-fire", "The virtual machine should catch fire instead of halting.");
struct arg_end* end = arg_end(20);
void* argtable[] = { input_file, warning_policies, debug_mode, execution_dump_file, terminate_mode, headless_mode, legacy_mode, little_endian_mode, radiation, catch_fire, verbose, quiet, end };
// Parse arguments.
nerrors = arg_parse(argc, argv, argtable);
if (nerrors != 0 || show_help->count != 0)
{
if (show_help->count != 0)
arg_print_errors(stdout, end, "emulator");
printd(LEVEL_DEFAULT, "syntax:\n dtemu");
arg_print_syntax(stderr, argtable, "\n");
printd(LEVEL_DEFAULT, "options:\n");
arg_print_glossary(stderr, argtable, " %-25s %s\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Set verbosity level.
debug_setlevel(LEVEL_DEFAULT + verbose->count - quiet->count);
// Show version information.
version_print(bautofree(bfromcstr("Emulator")));
// Set global path variable.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
// Set endianness.
isetmode(little_endian_mode->count == 0 ? IMODE_BIG : IMODE_LITTLE);
// Set up warning policies.
dsetwarnpolicy(warning_policies);
// Set up error handling.
if (dsethalt())
{
// Handle the error.
dautohandle();
printd(LEVEL_ERROR, "emulator: error occurred.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Zero out the flash space.
for (i = 0; i < 0x10000; i++)
flash[i] = 0x0;
// Zero out the leading space.
for (i = 0; i < 0x100; i++)
leading[i] = 0x0;
// Load from either file or stdin.
if (strcmp(input_file->filename[0], "-") != 0)
{
// Open file.
load = fopen(input_file->filename[0], "rb");
if (load == NULL)
dhalt(ERR_EMU_LOAD_FILE_FAILED, input_file->filename[0]);
}
else
{
// Windows needs stdin in binary mode.
#ifdef _WIN32
_setmode(_fileno(stdin), _O_BINARY);
#endif
// Set load to stdin.
load = stdin;
}
// Read leading component.
for (i = 0; i < strlen(ldata_objfmt); i++)
leading[i] = fgetc(load);
fseek(load, 0, SEEK_SET);
// Read up to 0x10000 words.
for (i = 0; i < 0x10000 && !feof(load); i++)
iread(&flash[i], load);
fclose(load);
// Check to see if the first X bytes matches the header
// for intermediate code and stop if it does.
ss = bfromcstr("");
st = bfromcstr(ldata_objfmt);
for (i = 0; i < strlen(ldata_objfmt); i++)
bconchar(ss, leading[i]);
if (biseq(ss, st))
dhalt(ERR_INTERMEDIATE_EXECUTION, NULL);
// Set up the host context.
glfwInit();
dtemu->create_context = &dtemu_create_context;
dtemu->activate_context = &dtemu_activate_context;
dtemu->swap_buffers = &dtemu_swap_buffers;
dtemu->destroy_context = &dtemu_destroy_context;
dtemu->get_ud = &dtemu_get_ud;
// And then use the VM.
vm = vm_create();
vm->debug = (debug_mode->count > 0);
vm_flash(vm, flash);
// Set radiation and catch fire settings.
if (radiation->count == 1)
vm->radiation_factor = radiation->ival[0];
if (catch_fire->count == 1)
vm->can_fire = true;
// Init hardware.
vm_hw_clock_init(vm);
if (headless_mode->count < 1)
vm->host = dtemu;
vm_hw_sped3_init(vm);
vm_hw_lem1802_init(vm);
vm_hw_m35fd_init(vm);
vm_hw_lua_init(vm);
if (legacy_mode->count > 0)
{
for (i = 0; i < vm_hw_count(vm); i++) {
hw_t* device = vm_hw_get_device(vm, i);
if (device == NULL)
continue;
if (device->id == 0x7349F615 && device->manufacturer == 0x1C6C8B36)
{
vm_hw_lem1802_mem_set_screen((struct lem1802_hardware*)device->userdata, 0x8000);
break;
}
}
}
vm_execute(vm, execution_dump_file->count > 0 ? execution_dump_file->filename[0] : NULL);
if (terminate_mode->count > 0)
{
fprintf(stderr, "\n");
fprintf(stderr, "A: 0x%04X [A]: 0x%04X\n", vm->registers[REG_A], vm->ram[vm->registers[REG_A]]);
fprintf(stderr, "B: 0x%04X [B]: 0x%04X\n", vm->registers[REG_B], vm->ram[vm->registers[REG_B]]);
fprintf(stderr, "C: 0x%04X [C]: 0x%04X\n", vm->registers[REG_C], vm->ram[vm->registers[REG_C]]);
fprintf(stderr, "X: 0x%04X [X]: 0x%04X\n", vm->registers[REG_X], vm->ram[vm->registers[REG_X]]);
fprintf(stderr, "Y: 0x%04X [Y]: 0x%04X\n", vm->registers[REG_Y], vm->ram[vm->registers[REG_Y]]);
fprintf(stderr, "Z: 0x%04X [Z]: 0x%04X\n", vm->registers[REG_Z], vm->ram[vm->registers[REG_Z]]);
fprintf(stderr, "I: 0x%04X [I]: 0x%04X\n", vm->registers[REG_I], vm->ram[vm->registers[REG_I]]);
fprintf(stderr, "J: 0x%04X [J]: 0x%04X\n", vm->registers[REG_J], vm->ram[vm->registers[REG_J]]);
fprintf(stderr, "PC: 0x%04X SP: 0x%04X\n", vm->pc, vm->sp);
fprintf(stderr, "EX: 0x%04X IA: 0x%04X\n", vm->ex, vm->ia);
}
vm_hw_lua_free(vm);
vm_free(vm);
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
glfwTerminate();
return 0;
}
int main(int argc, char* argv[])
{
struct arg_lit *help;
struct arg_file *input, *output;
struct arg_str *rotation;
struct arg_end *end;
/* command line parsing through argtable package */
void* argtable[] = {
help = arg_lit0("h", "help", "display this help and exit"),
input = arg_file0("i", "input", "input", "name of the input file (default stdin"),
output = arg_file0("o", "output", "file", "name of the output file (default stdout)"),
rotation = arg_str1(NULL, NULL, "\"x y z w\"", "rotate w degrees around axis x y z"),
end = arg_end(20) };
const char* progname = "xyztk-rotate";
int rc = 0;
int nerrors;
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0)
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n", progname);
rc=1;
goto exit;
}
/* set default values */
/* parse the command line flags, overriding default values */
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s", progname);
arg_print_syntax(stdout,argtable,"\n");
printf("\n");
arg_print_glossary(stdout,argtable," %-40s %s\n");
printf("\n");
rc=0;
goto exit;
}
/* special case: no command line options induces brief help */
if (argc==1) {
printf("Try '%s --help' for more information.\n",progname);
rc=0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0)
{
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout,end,progname);
printf("Try '%s --help' for more information.\n",progname);
rc=1;
goto exit;
}
/* set global structures */
/* initialize I/O pointers */
FILE* in;
if (input->count) {
in = fopen(input->filename[0], "r");
} else {
in = stdin;
}
FILE* out;
if (output->count) {
out = fopen(output->filename[0], "w");
} else {
out = stdout;
}
/* initialize molecule structure */
xyztk_molecule_t molecule;
xyztk_molecule_load (&molecule, in);
/* read rotation from string */
xyztk_quat_t r;
sscanf (rotation->sval[0], "%lf%lf%lf%lf", &r.x, &r.y, &r.z, &r.w);
xyztk_molecule_rotate (&molecule, &r);
/* print output */
int i;
fprintf(out, "%d\n", molecule.n_atoms);
fprintf(out, "%s", molecule.name);
for (i = 0; i < molecule.n_atoms; ++i)
{
fprintf(out, "%-8s %20.14lf %20.14lf %20.14lf \n",
molecule.label[i].s, molecule.coord[i].x, molecule.coord[i].y, molecule.coord[i].z);
}
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
return rc;
}
int main(int argc, char *argv[]) {
SDL_AudioSpec want, have;
SDL_AudioDeviceID dev;
Streamer streamer;
int retcode = 0;
// Init SDL Audio
if(SDL_Init(SDL_INIT_AUDIO) != 0) {
fprintf(stderr, "Error: %s\n", SDL_GetError());
return 1;
}
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "SOUNDS.DAT file");
struct arg_file *output = arg_file0("o", "output", "<file>", "Output sounds file");
struct arg_int *sid = arg_int0("s", "sound", "<int>", "Sound ID");
struct arg_int *sampleprint = arg_int0(NULL, "print", "<int>", "Print first n bytes from selected sound");
struct arg_lit *play = arg_lit0("p", "play", "Play selected sound");
struct arg_file *export = arg_file0("e", "export", "<file>", "Export selected sound to AU file");
struct arg_file *import = arg_file0("i", "import", "<file>", "Import selected sound from AU file");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,output,sid,sampleprint,play,export,import,end};
const char* progname = "soundtool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 SOUNDS.DAT file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2013 Tuomas Virtanen\n");
goto exit_0;
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Open sounds.dat
sd_sound_file sf;
sd_sounds_create(&sf);
retcode = sd_sounds_load(&sf, file->filename[0]);
if(retcode) {
printf("Error %d: %s\n", retcode, sd_get_error(retcode));
goto exit_1;
}
if(sid->count > 0) {
// Sound ID to handle
int sound_id = sid->ival[0];
const sd_sound *sound = sd_sounds_get(&sf, sound_id-1);
if(sound == NULL) {
printf("Invalid sound ID");
goto exit_1;
}
if(sampleprint->count > 0) {
int count = (sampleprint->ival[0] > sound->len) ? sound->len : sampleprint->ival[0];
printf("Sample size = %d\n", sound->len);
printf("Unknown = %d\n", sound->unknown);
printf("Attempting to print %d first bytes.\n", count);
for(int i = 0; i < count; i++) {
unsigned int s = sound->data[i] & 0xFF;
printf("%2x ", s);
}
} else if(play->count > 0) {
printf("Attempting to play sample #%d.\n", sound_id);
// Make sure there is data at requested ID position
if(sound->len <= 0) {
printf("Sample does not contain data.\n");
goto exit_1;
}
// Streamer
streamer.size = sound->len;
streamer.pos = 0;
streamer.data = sound->data;
// Initialize required audio
SDL_zero(want);
want.freq = 8000;
want.format = AUDIO_U8;
want.channels = 1;
want.samples = 4096;
want.callback = stream;
want.userdata = &streamer;
// Open device, play file
dev = SDL_OpenAudioDevice(NULL, 0, &want, &have, 0);
if(dev == 0) {
printf("Failed to open audio dev: %s\n", SDL_GetError());
goto exit_0;
} else {
if(have.format != want.format) {
printf("Could not get correct playback format.\n");
} else {
printf("Starting playback ...\n");
SDL_PauseAudioDevice(dev, 0);
while(streamer.pos < streamer.size) {
SDL_Delay(100);
}
printf("All done.\n");
}
SDL_CloseAudioDevice(dev);
}
} else if(import->count > 0) {
if(sd_sound_from_au(&sf, sound_id, import->filename[0]) != SD_SUCCESS) {
printf("Importing sample %d from file %s failed.\n", sound_id, import->filename[0]);
} else {
printf("Importing sample %d from file %s succeeded.\n", sound_id, import->filename[0]);
}
} else if(export->count > 0) {
if(sd_sound_to_au(&sf, sound_id, export->filename[0]) != SD_SUCCESS) {
printf("Exporting sample %d to file %s failed.\n", sound_id, export->filename[0]);
} else {
printf("Exporting sample %d to file %s succeeded.\n", sound_id, export->filename[0]);
}
} else {
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
int iProcMode; // processing mode
char szRefFile[_MAX_PATH]; // nput from reference csv file
char szFilterRefIDFile[_MAX_PATH]; // exclude any RefIDs in this filter file
char szRelFile[_MAX_PATH]; // input from relative csv file(s)
char szRsltfile[_MAX_PATH]; // output to results CSV file
int iMinLen; // minimum accepted length
int iMaxLen; // maximum accepted length
// command line args
struct arg_lit *help = arg_lit0("hH","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_int *ScreenLogLevel=arg_int0("S", "ScreenLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *ProcMode = arg_int0("m", "mode","<int>", "processing mode (default 0) 0: Identities (Match/Match+Mismatches), 1: Identities (Match/CoreLength), 2: Aligned Length 3: Score");
struct arg_file *RefFile = arg_file1("i","in","<file>", "input from reference csv file");
struct arg_file *FilterRefIDFile = arg_file0("X",NULL,"<file>", "filter out any ref or rel loci with RefIDs in this filter file");
struct arg_file *RelFile = arg_file1("I","in","<file>", "input from relative csv file(s) - can use wildcards");
struct arg_file *Rsltfile= arg_file1("o","out","<file>", "output to results CSV file");
struct arg_int *MinLen=arg_int0("l", "MinLen", "<int>","minimum accepted length");
struct arg_int *MaxLen=arg_int0("L", "MaxLen", "<int>","maximum accepted length");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,ScreenLogLevel,LogFile,
ProcMode,RefFile,FilterRefIDFile,RelFile,Rsltfile,
MinLen,MaxLen,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s ", gszProcName);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %d.%2.2d",gszProcName,cProgVer/100,cProgVer%100);
exit(1);
}
if (!argerrors)
{
iScreenLogLevel = ScreenLogLevel->count ? ScreenLogLevel->ival[0] : eDLInfo;
if(iScreenLogLevel < eDLNone || iScreenLogLevel > eDLDebug)
{
printf("\nError: ScreenLogLevel '-S%d' specified outside of range %d..%d",iScreenLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
iProcMode = ProcMode->count ? ProcMode->ival[0] : eProcModeStandard;
if(iProcMode < eProcModeStandard || iProcMode > eProcModeScore)
{
printf("\nError: Requested processing mode '-x%d' not supported",iProcMode);
exit(1);
}
iMinLen = MinLen->count ? MinLen->ival[0] : 0;
if(iMinLen < 0)
{
printf("\nError: Requested minimum length '-l%d' is negative",iMinLen);
exit(1);
}
iMaxLen = MaxLen->count ? MaxLen->ival[0] : 1000000000;
if(iMaxLen < iMinLen)
{
printf("\nError: Requested maximum ength '-l%d' must be >= minimum %d",iMaxLen,iMinLen);
exit(1);
}
strcpy(szRefFile,RefFile->filename[0]);
strcpy(szRelFile,RelFile->filename[0]);
strcpy(szRsltfile,Rsltfile->filename[0]);
if(FilterRefIDFile->count)
{
strncpy(szFilterRefIDFile,FilterRefIDFile->filename[0],sizeof(szFilterRefIDFile));
szFilterRefIDFile[sizeof(szFilterRefIDFile)-1] = '\0';
}
else
szFilterRefIDFile[0] = '\0';
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %d.%2.2d Processing parameters:",cProgVer/100,cProgVer%100);
switch(iProcMode) {
case eProcModeStandard:
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode: Identity = Match/(Match+Mismatch)");
break;
case eProcModeIdentity:
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode: Identity = Match/(CoreLength)");
break;
case eProcModeAligned:
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode: Aligned = (Match+Mismatch)/CoreLength");
break;
case eProcModeScore:
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode: score");
break;
}
gDiagnostics.DiagOutMsgOnly(eDLInfo,"reference csv file to process: '%s'",szRefFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"relative csv file(s) to processs: '%s'",szRelFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"results file to generate: '%s'",szRsltfile);
if(szFilterRefIDFile[0])
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Exclude any RefIDs in this filter file: '%s'",szFilterRefIDFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"minimum length: %d",iMinLen);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"maximum length: %d",iMaxLen);
gStopWatch.Start();
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
Rslt = Process((etProcMode)iProcMode, // processing mode 0: default
szRefFile, // reference csv file to process
szFilterRefIDFile, // exclude any RefIDs in this filter file
szRelFile, // relative csv file(s) to processs
szRsltfile, // results file to generate
iMinLen, // minimum accepted ref length
iMaxLen); // maximum accepted ref length
gStopWatch.Stop();
Rslt = Rslt < 0 ? 1 : 0;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit Code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nend of help\n");
exit(1);
}
return 0;
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
int iProcMode;
int iMinLength;
int iMaxLength;
int iMinMergeLength;
int iMaxMergeLength;
char szRefFile[_MAX_PATH]; // process ref hypers from this file
char szRelFile[_MAX_PATH]; // process rel hypers from this file
char szOutLociFile[_MAX_PATH]; // write loci to this file
char szRefSpecies[cMaxDatasetSpeciesChrom]; // use this species as the ref species in generated szOutLociFile
char szRelSpecies[cMaxDatasetSpeciesChrom]; // use this species/list as the rel species in generated szOutLociFile
char szElType[cMaxDatasetSpeciesChrom]; // use this as the element type in generated szOutLociFile
int iRefExtend; // extend ref element lengths left+right by this many bases
int iRelExtend; // extend rel element lengths left+right by this many bases
int iJoinDistance; // if > 0 then join elements which only differ by at most this distance beween end of element i and start of element i+1
// command line args
struct arg_lit *help = arg_lit0("h","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_file *RefFile = arg_file1("i","reffile","<file>", "reference hyper element CSV file");
struct arg_file *RelFile = arg_file0("I","relfile","<file>", "relative hyper element CSV file");
struct arg_file *OutLociFile = arg_file1("o",NULL,"<file>", "output loci to file as CSV");
struct arg_str *RefSpecies = arg_str1("r","refspecies","<string>","output loci file ref species");
struct arg_str *RelSpecies = arg_str1("R","relspecies","<string>","output loci file rel species");
struct arg_str *ElType = arg_str0("t","eltype","<string>","output loci file element type");
struct arg_int *ProcMode = arg_int0("p","mode","<int>", "processing mode: 0:Intersect (Ref & Rel)\n\t\t1:Ref exclusive (Ref & !Rel)\n\t\t2:Rel exclusive (!Ref & Rel)\n\t\t3:Union (Ref | Rel)\n\t\t4:Neither (!(Ref | Rel))");
struct arg_int *MinLength = arg_int0("l","minlength","<int>", "minimum input ref/rel element length (default 4)");
struct arg_int *MaxLength = arg_int0("L","maxlength","<int>", "maximum input ref/rel element length (default 1000000)");
struct arg_int *MinMergeLength = arg_int0("m","minmergelength","<int>","minimum merged output element length (default 4)");
struct arg_int *MaxMergeLength = arg_int0("M","maxmergelength","<int>","maximum merged output element length (default 1000000)");
struct arg_int *RefExtend = arg_int0("e","refextend","<int>", "extend ref element flanks left+right by this many bases (default 0)");
struct arg_int *RelExtend = arg_int0("E","relextend","<int>", "extend rel element flanks left+right by this many bases (default 0)");
struct arg_int *JoinDistance = arg_int0("j","join","<int>", "merge output elements which are only separated by this number of bases (default 0)");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,LogFile,
ProcMode,
RefFile,RelFile,OutLociFile,
MinLength,MaxLength,RefExtend,RelExtend,JoinDistance,MinMergeLength,MaxMergeLength,
RefSpecies,RelSpecies,ElType,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s CSV Merge Elements, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n",gszProcName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
iProcMode = ProcMode->count ? ProcMode->ival[0] : ePMElIntersect;
if(iProcMode < ePMElIntersect || iProcMode > ePMElRefNotRefRel)
{
printf("Error: Processing mode '-p%d' is not in range 0..4",iProcMode);
exit(1);
}
strncpy(szOutLociFile,OutLociFile->filename[0],_MAX_PATH);
szOutLociFile[_MAX_PATH-1] = '\0';
strncpy(szRefSpecies,RefSpecies->sval[0],sizeof(szRefSpecies));
szRefSpecies[sizeof(szRefSpecies)-1] = '\0';
strncpy(szRelSpecies,RelSpecies->sval[0],sizeof(szRelSpecies));
szRelSpecies[sizeof(szRelSpecies)-1] = '\0';
if(ElType->count)
{
strncpy(szElType,ElType->sval[0],sizeof(szElType));
szElType[sizeof(szElType)-1] = '\0';
}
else
strcpy(szElType,"merged");
iMinLength = MinLength->count ? MinLength->ival[0] : cDfltMinLength;
if(iMinLength < 0 || iMinLength > cMaxLengthRange)
{
printf("Error: Minimum element length '-l%d' is not in range 0..%d",iMinLength,cMaxLengthRange);
exit(1);
}
iMaxLength = MaxLength->count ? MaxLength->ival[0] : cDfltMaxLength;
if(iMaxLength < iMinLength || iMaxLength > cMaxLengthRange)
{
printf("Error: Maximum element length '-L%d' is not in range %d..%d",iMaxLength,iMinLength,cMaxLengthRange);
exit(1);
}
iMinMergeLength = MinMergeLength->count ? MinMergeLength->ival[0] : cDfltMinLength;
if(iMinMergeLength < 0 || iMinMergeLength > cMaxLengthRange)
{
printf("Error: Minimum output merged element length '-m%d' is not in range 0..%d",iMinMergeLength,cMaxLengthRange);
exit(1);
}
iMaxMergeLength = MaxMergeLength->count ? MaxMergeLength->ival[0] : cDfltMaxLength;
if(iMaxMergeLength < iMinMergeLength || iMaxMergeLength > cMaxLengthRange)
{
printf("Error: Maximum element length '-M%d' is not in range %d..%d",iMaxMergeLength,iMinMergeLength,cMaxLengthRange);
exit(1);
}
iJoinDistance = JoinDistance->count ? JoinDistance->ival[0] : cDfltJoinOverlap;
if(iJoinDistance < 0 || iJoinDistance > cMaxJoinOverlap)
{
printf("Error: Join separation length '-j%d' is not in range %d..%d",iJoinDistance,0,cMaxJoinOverlap);
exit(1);
}
iRefExtend = RefExtend->count ? RefExtend->ival[0] : 0;
if(iRefExtend < (-1 * cMaxExtendLength) || iRefExtend > cMaxExtendLength)
{
printf("Error: Ref Extension length '-e%d' is not in range %d..%d",iRefExtend,(-1 * cMaxExtendLength),cMaxExtendLength);
exit(1);
}
iRelExtend = RelExtend->count ? RelExtend->ival[0] : 0;
if(iRelExtend < (-1 * cMaxExtendLength) || iRelExtend > cMaxExtendLength)
{
printf("Error: Rel Extension length '-E%d' is not in range %d..%d",iRelExtend,(-1 * cMaxExtendLength),cMaxExtendLength);
exit(1);
}
strncpy(szRefFile,RefFile->filename[0],_MAX_PATH);
szRefFile[_MAX_PATH-1] = '\0';
if(RelFile->count)
{
strncpy(szRelFile,RelFile->filename[0],_MAX_PATH);
szRelFile[_MAX_PATH-1] = '\0';
}
else
{
if(iProcMode == ePMElRefExclusive || iProcMode == ePMElRefRelUnion)
szRelFile[0] = '\0';
else
{
printf("Error: Rel loci file must be specified in processing mode '-p%d' (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
exit(1);
}
}
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing Mode: %d (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Reference CSV file: '%s'",szRefFile);
if(szRelFile[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Relative CSV file: '%s'",szRelFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output processed loci into CSV file: '%s'",szOutLociFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file ref species: '%s'",szRefSpecies);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file rel species: '%s'",szRelSpecies);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file element type: '%s'",szElType);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum input element length: %d",iMinLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum input element length: %d",iMaxLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Ref element flank extension length: %d",iRefExtend);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Rel element flank extension length: %d",iRelExtend);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Merge output elements separated by at most this many bases: %d",iJoinDistance);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum output merged element length: %d",iMinMergeLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum output merged element length: %d",iMaxMergeLength);
// processing here...
gStopWatch.Start();
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
Rslt = Process((etProcMode)iProcMode,iMinLength,iMaxLength,iRefExtend,iRelExtend,iJoinDistance,iMinMergeLength,iMaxMergeLength,szRefFile,szRelFile,szOutLociFile,
szRefSpecies,szRelSpecies,szElType);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s CSV Merge Elements, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
}
/**
* @brief Parse command line parameters. Will exit if help/usage etc
* are called or or call Log(&rLog, LOG_FATAL, ) if an error was detected.
*
* @param[out] user_opts
* User parameter struct, with defaults already set.
* @param[in] argc
* mains argc
* @param[in] argv
* mains argv
*
*/
void
ParseCommandLine(cmdline_opts_t *user_opts, int argc, char **argv)
{
/* argtable command line parsing:
* see
* http://argtable.sourceforge.net/doc/argtable2-intro.html
*
* basic structure is: arg_xxxN:
* xxx can be int, lit, db1, str, rex, file or date
* If N = 0, arguments may appear zero-or-once; N = 1 means
* exactly once, N = n means up to maxcount times
*
*
* @note: changes here, might also affect main.cpp:ConvertOldCmdLine()
*
*/
struct arg_rem *rem_seq_input = arg_rem(NULL, "\nSequence Input:");
struct arg_file *opt_seqin = arg_file0("i", "in,infile",
"{<file>,-}",
"Multiple sequence input file (- for stdin)");
struct arg_file *opt_hmm_in = arg_filen(NULL, "hmm-in", "<file>",
/*min*/ 0, /*max*/ 128,
"HMM input files");
struct arg_lit *opt_dealign = arg_lit0(NULL, "dealign",
"Dealign input sequences");
struct arg_file *opt_profile1 = arg_file0(NULL, "profile1,p1",
"<file>",
"Pre-aligned multiple sequence file (aligned columns will be kept fix)");
struct arg_file *opt_profile2 = arg_file0(NULL, "profile2,p2",
"<file>",
"Pre-aligned multiple sequence file (aligned columns will be kept fix)");
struct arg_str *opt_seqtype = arg_str0("t", "seqtype",
"{Protein, RNA, DNA}",
"Force a sequence type (default: auto)");
/* struct arg_lit *opt_force_protein = arg_lit0(NULL, "protein",
"Set sequence type to protein even if Clustal guessed nucleic acid"); */
struct arg_str *opt_infmt = arg_str0(NULL, "infmt",
"{a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]}",
"Forced sequence input file format (default: auto)");
struct arg_rem *rem_guidetree = arg_rem(NULL, "\nClustering:");
struct arg_str *opt_pairdist = arg_str0("p", "pairdist",
"{ktuple}",
"Pairwise alignment distance measure");
struct arg_file *opt_distmat_in = arg_file0(NULL, "distmat-in",
"<file>",
"Pairwise distance matrix input file (skips distance computation)");
struct arg_file *opt_distmat_out = arg_file0(NULL, "distmat-out",
"<file>",
"Pairwise distance matrix output file");
struct arg_file *opt_guidetree_in = arg_file0(NULL, "guidetree-in",
"<file>",
"Guide tree input file (skips distance computation and guide-tree clustering step)");
struct arg_file *opt_guidetree_out = arg_file0(NULL, "guidetree-out",
"<file>",
"Guide tree output file");
/* AW: mbed is default since at least R253
struct arg_lit *opt_mbed = arg_lit0(NULL, "mbed",
"Fast, Mbed-like clustering for guide-tree calculation");
struct arg_lit *opt_mbed_iter = arg_lit0(NULL, "mbed-iter",
"Use Mbed-like clustering also during iteration");
*/
/* Note: might be better to use arg_str (mbed=YES/NO) but I don't want to introduce an '=' into pipeline, FS, r250 -> */
struct arg_lit *opt_full = arg_lit0(NULL, "full",
"Use full distance matrix for guide-tree calculation (might be slow; mBed is default)");
struct arg_lit *opt_full_iter = arg_lit0(NULL, "full-iter",
"Use full distance matrix for guide-tree calculation during iteration (might be slowish; mBed is default)");
struct arg_str *opt_clustering = arg_str0("c", "clustering",
"{UPGMA}",
"Clustering method for guide tree");
struct arg_rem *rem_aln_output = arg_rem(NULL, "\nAlignment Output:");
struct arg_file *opt_outfile = arg_file0("o", "out,outfile",
"{file,-}",
"Multiple sequence alignment output file (default: stdout)");
struct arg_str *opt_outfmt = arg_str0(NULL, "outfmt",
"{a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]}",
"MSA output file format (default: fasta)");
struct arg_rem *rem_iteration = arg_rem(NULL, "\nIteration:");
struct arg_str *opt_num_iterations = arg_str0(NULL, "iterations,iter",
/* FIXME "{<n>,auto}", "Number of combined guide-tree/HMM iterations"); */
"<n>", "Number of (combined guide-tree/HMM) iterations");
struct arg_int *opt_max_guidetree_iterations = arg_int0(NULL, "max-guidetree-iterations",
"<n>", "Maximum number guidetree iterations");
struct arg_int *opt_max_hmm_iterations = arg_int0(NULL, "max-hmm-iterations",
"<n>", "Maximum number of HMM iterations");
struct arg_rem *rem_limits = arg_rem(NULL, "\nLimits (will exit early, if exceeded):");
struct arg_int *opt_max_seq = arg_int0(NULL, "maxnumseq", "<n>",
"Maximum allowed number of sequences");
struct arg_int *opt_max_seqlen = arg_int0(NULL, "maxseqlen", "<l>",
"Maximum allowed sequence length");
struct arg_rem *rem_misc = arg_rem(NULL, "\nMiscellaneous:");
struct arg_lit *opt_autooptions = arg_lit0(NULL, "auto",
"Set options automatically (might overwrite some of your options)");
struct arg_int *opt_threads = arg_int0(NULL, "threads", "<n>",
"Number of processors to use");
struct arg_file *opt_logfile = arg_file0("l", "log",
"<file>",
"Log all non-essential output to this file");
struct arg_lit *opt_help = arg_lit0("h", "help",
"Print this help and exit");
struct arg_lit *opt_version = arg_lit0(NULL, "version",
"Print version information and exit");
struct arg_lit *opt_long_version = arg_lit0(NULL, "long-version",
"Print long version information and exit");
struct arg_lit *opt_verbose = arg_litn("v", "verbose",
0, 3,
"Verbose output (increases if given multiple times)");
struct arg_lit *opt_force = arg_lit0(NULL, "force",
"Force file overwriting");
struct arg_int *opt_macram = arg_int0(NULL, "MAC-RAM", "<n>", /* keep this quiet for the moment, FS r240 -> */
NULL/*"maximum amount of RAM to use for MAC algorithm (in MB)"*/);
struct arg_end *opt_end = arg_end(10); /* maximum number of errors
* to store */
void *argtable[] = {rem_seq_input,
opt_seqin,
opt_hmm_in,
opt_dealign,
opt_profile1,
opt_profile2,
opt_seqtype,
/* opt_force_protein, */
opt_infmt,
rem_guidetree,
#if 0
/* no other options then default available or not implemented */
opt_pairdist,
#endif
opt_distmat_in,
opt_distmat_out,
opt_guidetree_in,
opt_guidetree_out,
opt_full, /* FS, r250 -> */
opt_full_iter, /* FS, r250 -> */
#if 0
/* no other options then default available */
opt_clustering,
#endif
rem_aln_output,
opt_outfile,
opt_outfmt,
rem_iteration,
opt_num_iterations,
opt_max_guidetree_iterations,
opt_max_hmm_iterations,
rem_limits,
opt_max_seq,
opt_max_seqlen,
rem_misc,
opt_autooptions,
opt_threads,
opt_logfile,
opt_help,
opt_verbose,
opt_version,
opt_long_version,
opt_force,
opt_macram, /* FS, r240 -> r241 */
opt_end};
int nerrors;
/* Verify the argtable[] entries were allocated sucessfully
*/
if (arg_nullcheck(argtable)) {
Log(&rLog, LOG_FATAL, "insufficient memory (for argtable allocation)");
}
/* Parse the command line as defined by argtable[]
*/
nerrors = arg_parse(argc, argv, argtable);
/* Special case: '--help' takes precedence over error reporting
*/
if (opt_help->count > 0) {
printf("%s - %s (%s)\n", PACKAGE_NAME, PACKAGE_VERSION, PACKAGE_CODENAME);
printf("\n");
printf("If you like Clustal-Omega please cite:\n%s\n", CITATION);
printf("If you don't like Clustal-Omega, please let us know why (and cite us anyway).\n");
/* printf("You can contact reach us under %s\n", PACKAGE_BUGREPORT); */
printf("\n");
printf("Check http://www.clustal.org for more information and updates.\n");
printf("\n");
printf("Usage: %s", basename(argv[0]));
arg_print_syntax(stdout,argtable, "\n");
printf("\n");
printf("A typical invocation would be: %s -i my-in-seqs.fa -o my-out-seqs.fa -v\n",
basename(argv[0]));
printf("See below for a list of all options.\n");
arg_print_glossary(stdout, argtable, " %-25s %s\n");
arg_freetable(argtable, sizeof(argtable)/sizeof(argtable[0]));
exit(EXIT_SUCCESS);
}
/* Special case: '--version' takes precedence over error reporting
*/
if (opt_version->count > 0) {
printf("%s\n", PACKAGE_VERSION);
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
exit(EXIT_SUCCESS);
}
/* Special case: '--long-version' takes precedence over error reporting
*/
if (opt_long_version->count > 0) {
char zcLongVersion[1024];
PrintLongVersion(zcLongVersion, sizeof(zcLongVersion));
printf("%s\n", zcLongVersion);
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
exit(EXIT_SUCCESS);
}
/* If the parser returned any errors then display them and exit
*/
if (nerrors > 0) {
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout, opt_end, PACKAGE);
fprintf(stderr, "For more information try: %s --help\n", argv[0]);
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
exit(EXIT_FAILURE);
}
/* ------------------------------------------------------------
*
* Command line successfully parsed. Now transfer values to
* user_opts. While doing so, make sure that given input files
* exist and given output files are writable do not exist, or if
* they do, should be overwritten.
*
* No logic checks here! They are done in a different function
*
* ------------------------------------------------------------*/
/* not part of user_opts because it declared in src/util.h */
if (0 == opt_verbose->count) {
rLog.iLogLevelEnabled = LOG_WARN;
} else if (1 == opt_verbose->count) {
rLog.iLogLevelEnabled = LOG_INFO;
} else if (2 == opt_verbose->count) {
rLog.iLogLevelEnabled = LOG_VERBOSE;
} else if (3 == opt_verbose->count) {
rLog.iLogLevelEnabled = LOG_DEBUG;
}
user_opts->aln_opts.bAutoOptions = opt_autooptions->count;
user_opts->bDealignInputSeqs = opt_dealign->count;
/* NOTE: full distance matrix used to be default - there was
--mbed flag but no --full flag after r250 decided that mBed
should be default - now need --full flag to turn off mBed.
wanted to retain mBed Boolean, so simply added --full flag. if
both flags set (erroneously) want --mbed to overwrite --full,
therefore do --full 1st, the --mbed, FS, r250 */
if (opt_full->count){
user_opts->aln_opts.bUseMbed = FALSE;
}
if (opt_full_iter->count){
user_opts->aln_opts.bUseMbedForIteration = FALSE;
}
user_opts->bForceFileOverwrite = opt_force->count;
/* log-file
*/
if (opt_logfile->count > 0) {
user_opts->pcLogFile = CkStrdup(opt_logfile->filename[0]);
/* warn if already exists or not writable */
if (FileExists(user_opts->pcLogFile) && ! user_opts->bForceFileOverwrite) {
Log(&rLog, LOG_FATAL, "%s '%s'. %s",
"Cowardly refusing to overwrite already existing file",
user_opts->pcLogFile,
"Use --force to force overwriting.");
}
if (! FileIsWritable(user_opts->pcLogFile)) {
Log(&rLog, LOG_FATAL, "Sorry, I do not have permission to write to file '%s'.",
user_opts->pcLogFile);
}
}
/* normal sequence input (no profile)
*/
if (opt_seqin->count > 0) {
user_opts->pcSeqInfile = CkStrdup(opt_seqin->filename[0]);
}
/* Input limitations
*/
/* maximum number of sequences */
if (opt_max_seq->count > 0) {
user_opts->iMaxNumSeq = opt_max_seq->ival[0];
}
/* maximum sequence length */
if (opt_max_seqlen->count > 0) {
user_opts->iMaxSeqLen = opt_max_seqlen->ival[0];
}
/* Output format
*/
if (opt_infmt->count > 0) {
/* avoid gcc warning about discarded qualifier */
char *tmp = (char *)opt_infmt->sval[0];
user_opts->iSeqInFormat = String2SeqfileFormat(tmp);
} else {
user_opts->iSeqInFormat = SQFILE_UNKNOWN;
}
/* Sequence type
*/
if (opt_seqtype->count > 0) {
if (STR_NC_EQ(opt_seqtype->sval[0], "protein")) {
user_opts->iSeqType = SEQTYPE_PROTEIN;
} else if (STR_NC_EQ(opt_seqtype->sval[0], "rna")) {
user_opts->iSeqType = SEQTYPE_RNA;
} else if (STR_NC_EQ(opt_seqtype->sval[0], "dna")) {
user_opts->iSeqType = SEQTYPE_DNA;
} else {
Log(&rLog, LOG_FATAL, "Unknown sequence type '%s'", opt_seqtype->sval[0]);
}
}
/* if (opt_force_protein->count > 0) {
user_opts->iSeqType = SEQTYPE_PROTEIN;
} */
/* Profile input
*/
if (opt_profile1->count > 0) {
user_opts->pcProfile1Infile = CkStrdup(opt_profile1->filename[0]);
if (! FileExists(user_opts->pcProfile1Infile)) {
Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->pcProfile1Infile);
}
}
if (opt_profile2->count > 0) {
user_opts->pcProfile2Infile = CkStrdup(opt_profile2->filename[0]);
if (! FileExists(user_opts->pcProfile2Infile)) {
Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->pcProfile2Infile);
}
}
/* HMM input
*/
user_opts->aln_opts.iHMMInputFiles = 0;
user_opts->aln_opts.ppcHMMInput = NULL;
if (opt_hmm_in->count>0) {
int iAux;
user_opts->aln_opts.iHMMInputFiles = opt_hmm_in->count;
user_opts->aln_opts.ppcHMMInput = (char **) CKMALLOC(
user_opts->aln_opts.iHMMInputFiles * sizeof(char*));
for (iAux=0; iAux<opt_hmm_in->count; iAux++) {
user_opts->aln_opts.ppcHMMInput[iAux] = CkStrdup(opt_hmm_in->filename[iAux]);
if (! FileExists(user_opts->aln_opts.ppcHMMInput[iAux])) {
Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->aln_opts.ppcHMMInput[iAux]);
}
}
}
/* Pair distance method
*/
if (opt_pairdist->count > 0) {
if (STR_NC_EQ(opt_pairdist->sval[0], "ktuple")) {
user_opts->aln_opts.iPairDistType = PAIRDIST_KTUPLE;
} else {
Log(&rLog, LOG_FATAL, "Unknown pairdist method '%s'", opt_pairdist->sval[0]);
}
}
/* Distance matrix input
*/
if (opt_distmat_in->count > 0) {
user_opts->aln_opts.pcDistmatInfile = CkStrdup(opt_distmat_in->filename[0]);
if (! FileExists(user_opts->aln_opts.pcDistmatInfile)) {
Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->aln_opts.pcDistmatInfile);
}
}
/* Distance matrix output
*/
if (opt_distmat_out->count > 0) {
user_opts->aln_opts.pcDistmatOutfile = CkStrdup(opt_distmat_out->filename[0]);
/* warn if already exists or not writable */
if (FileExists(user_opts->aln_opts.pcDistmatOutfile) && ! user_opts->bForceFileOverwrite) {
Log(&rLog, LOG_FATAL, "%s '%s'. %s",
"Cowardly refusing to overwrite already existing file",
user_opts->aln_opts.pcDistmatOutfile,
"Use --force to force overwriting.");
}
if (! FileIsWritable(user_opts->aln_opts.pcDistmatOutfile)) {
Log(&rLog, LOG_FATAL, "Sorry, I do not have permission to write to file '%s'.",
user_opts->aln_opts.pcDistmatOutfile);
}
}
/* Clustering
*
*/
if (opt_clustering->count > 0) {
if (STR_NC_EQ(opt_clustering->sval[0], "upgma")) {
user_opts->aln_opts.iClusteringType = CLUSTERING_UPGMA;
} else {
Log(&rLog, LOG_FATAL, "Unknown guide-tree clustering method '%s'", opt_clustering->sval[0]);
}
}
/* Guidetree input
*/
if (opt_guidetree_in->count > 0) {
user_opts->aln_opts.pcGuidetreeInfile = CkStrdup(opt_guidetree_in->filename[0]);
if (! FileExists(user_opts->aln_opts.pcGuidetreeInfile)) {
Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->aln_opts.pcGuidetreeInfile);
}
}
/* Guidetree output
*/
if (opt_guidetree_out->count > 0) {
user_opts->aln_opts.pcGuidetreeOutfile = CkStrdup(opt_guidetree_out->filename[0]);
/* warn if already exists or not writable */
if (FileExists(user_opts->aln_opts.pcGuidetreeOutfile) && ! user_opts->bForceFileOverwrite) {
Log(&rLog, LOG_FATAL, "%s '%s'. %s",
"Cowardly refusing to overwrite already existing file",
user_opts->aln_opts.pcGuidetreeOutfile,
"Use --force to force overwriting.");
}
if (! FileIsWritable(user_opts->aln_opts.pcGuidetreeOutfile)) {
Log(&rLog, LOG_FATAL, "Sorry, I do not have permission to write to file '%s'.",
user_opts->aln_opts.pcGuidetreeOutfile);
}
}
/* max guidetree iterations
*/
if (opt_max_guidetree_iterations->count > 0) {
user_opts->aln_opts.iMaxGuidetreeIterations = opt_max_guidetree_iterations->ival[0];
}
/* max guidetree iterations
*/
if (opt_max_hmm_iterations->count > 0) {
user_opts->aln_opts.iMaxHMMIterations = opt_max_hmm_iterations->ival[0];
}
/* number of iterations
*/
if (opt_num_iterations->count > 0) {
if (STR_NC_EQ(opt_num_iterations->sval[0], "auto")) {
Log(&rLog, LOG_FATAL, "Automatic iteration not supported at the moment.");
user_opts->aln_opts.bIterationsAuto = TRUE;
} else {
int iAux;
user_opts->aln_opts.bIterationsAuto = FALSE;
for (iAux=0; iAux<(int)strlen(opt_num_iterations->sval[0]); iAux++) {
if (! isdigit(opt_num_iterations->sval[0][iAux])) {
Log(&rLog, LOG_FATAL, "Couldn't iteration parameter: %s",
opt_num_iterations->sval[0]);
}
}
user_opts->aln_opts.iNumIterations = atoi(opt_num_iterations->sval[0]);
}
}
/* Alignment output
*/
if (opt_outfile->count > 0) {
user_opts->pcAlnOutfile = CkStrdup(opt_outfile->filename[0]);
/* warn if already exists or not writable */
if (FileExists(user_opts->pcAlnOutfile) && ! user_opts->bForceFileOverwrite) {
Log(&rLog, LOG_FATAL, "%s '%s'. %s",
"Cowardly refusing to overwrite already existing file",
user_opts->pcAlnOutfile,
"Use --force to force overwriting.");
}
if (! FileIsWritable(user_opts->pcAlnOutfile)) {
Log(&rLog, LOG_FATAL, "Sorry, I do not have permission to write to file '%s'.",
user_opts->pcAlnOutfile);
}
}
/* Output format
*/
if (opt_outfmt->count > 0) {
/* avoid gcc warning about discarded qualifier */
char *tmp = (char *)opt_outfmt->sval[0];
user_opts->iAlnOutFormat = String2SeqfileFormat(tmp);
if (SQFILE_UNKNOWN == user_opts->iAlnOutFormat) {
Log(&rLog, LOG_FATAL, "Unknown output format '%s'", opt_outfmt->sval[0]);
}
}
/* Number of threads
*/
#ifdef HAVE_OPENMP
if (opt_threads->count > 0) {
if (opt_threads->ival[0] <= 0) {
Log(&rLog, LOG_FATAL, "Changing number of threads to %d doesn't make sense.",
opt_threads->ival[0]);
}
user_opts->iThreads = opt_threads->ival[0];
}
#else
if (opt_threads->count > 0) {
if (opt_threads->ival[0] > 1) {
Log(&rLog, LOG_FATAL, "Cannot change number of threads to %d. %s was build without OpenMP support.",
opt_threads->ival[0], PACKAGE_NAME);
}
}
#endif
/* max MAC RAM (maximum amount of RAM set aside for MAC algorithm)
*/
if (opt_macram->count > 0) { /* FS, r240 -> r241 */
user_opts->aln_opts.rHhalignPara.iMacRamMB = opt_macram->ival[0];
}
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
UserOptsLogicCheck(user_opts);
return;
}
int main(int argc, char* argv[])
{
// Define our variables.
int nerrors, i;
int32_t saved = 0; // The number of words saved during compression and optimization.
struct errinfo* errval;
const char* prepend = "error: ";
const char* warnprefix = "no-";
int msglen;
char* msg;
int target;
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_str* target_arg = arg_str0("l", "link-as", "target", "Link as the specified object, can be 'image', 'static' or 'kernel'.");
struct arg_file* symbol_file = arg_file0("s", "symbols", "<file>", "Produce a combined symbol file (~triples memory usage!).");
struct arg_str* symbol_ext = arg_str0(NULL, "symbol-extension", "ext", "When -s is used, specifies the extension for symbol files. Defaults to \"dsym16\".");
struct arg_file* input_files = arg_filen(NULL, NULL, "<file>", 1, 100, "The input object files.");
struct arg_file* output_file = arg_file1("o", "output", "<file>", "The output file (or - to send to standard output).");
struct arg_file* kernel_file = arg_file0("k", "kernel", "<file>", "Directly link in the specified kernel.");
struct arg_file* jumplist_file = arg_file0("j", "jumplist", "<file>", "Link against the specified jumplist.");
struct arg_str* warning_policies = arg_strn("W", NULL, "policy", 0, _WARN_COUNT * 2 + 10, "Modify warning policies.");
struct arg_lit* keep_output_arg = arg_lit0(NULL, "keep-outputs", "Keep the .OUTPUT entries in the final static library (used for stdlib).");
struct arg_lit* little_endian_mode = arg_lit0(NULL, "little-endian", "Use little endian serialization (for compatibility with older versions).");
struct arg_lit* no_short_literals_arg = arg_lit0(NULL, "no-short-literals", "Do not compress literals to short literals.");
struct arg_int* opt_level = arg_int0("O", NULL, "<level>", "The optimization level.");
struct arg_lit* opt_mode = arg_lit0("S", NULL, "Favour runtime speed over size when optimizing.");
struct arg_lit* verbose = arg_litn("v", NULL, 0, LEVEL_EVERYTHING - LEVEL_DEFAULT, "Increase verbosity.");
struct arg_lit* quiet = arg_litn("q", NULL, 0, LEVEL_DEFAULT - LEVEL_SILENT, "Decrease verbosity.");
struct arg_end* end = arg_end(20);
void* argtable[] = { show_help, target_arg, keep_output_arg, little_endian_mode, opt_level, opt_mode, no_short_literals_arg,
symbol_ext, symbol_file, kernel_file, jumplist_file, warning_policies, output_file, input_files, verbose, quiet, end
};
// Parse arguments.
nerrors = arg_parse(argc, argv, argtable);
version_print(bautofree(bfromcstr("Linker")));
if (nerrors != 0 || show_help->count != 0)
{
if (show_help->count != 0)
arg_print_errors(stdout, end, "linker");
printd(LEVEL_DEFAULT, "syntax:\n dtld");
arg_print_syntax(stderr, argtable, "\n");
printd(LEVEL_DEFAULT, "options:\n");
arg_print_glossary(stderr, argtable, " %-25s %s\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Set verbosity level.
debug_setlevel(LEVEL_DEFAULT + verbose->count - quiet->count);
// Set global path variable.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
// Set endianness.
isetmode(little_endian_mode->count == 0 ? IMODE_BIG : IMODE_LITTLE);
// Set up warning policies.
dsetwarnpolicy(warning_policies);
// Set up error handling.
if (dsethalt())
{
errval = derrinfo();
// FIXME: Use bstrings here.
msglen = strlen(derrstr[errval->errid]) + strlen(prepend) + 1;
msg = malloc(msglen);
memset(msg, '\0', msglen);
strcat(msg, prepend);
strcat(msg, derrstr[errval->errid]);
printd(LEVEL_ERROR, msg, errval->errdata);
// Handle the error.
printd(LEVEL_ERROR, "linker: error occurred.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Check to make sure target is correct.
if (target_arg->count == 0)
target = IMAGE_APPLICATION;
else
{
if (strcmp(target_arg->sval[0], "image") == 0)
target = IMAGE_APPLICATION;
else if (strcmp(target_arg->sval[0], "static") == 0)
target = IMAGE_STATIC_LIBRARY;
else if (strcmp(target_arg->sval[0], "kernel") == 0)
target = IMAGE_KERNEL;
else
{
// Invalid option.
dhalt(ERR_INVALID_TARGET_NAME, NULL);
}
}
// Load all passed objects and use linker bin system to
// produce result.
bins_init();
for (i = 0; i < input_files->count; i++)
if (!bins_load(bautofree(bfromcstr(input_files->filename[i])), symbol_file->count > 0, (symbol_file->count > 0 && symbol_ext->count > 0) ? symbol_ext->sval[0] : "dsym16"))
// Failed to load one of the input files.
dhalt(ERR_BIN_LOAD_FAILED, input_files->filename[i]);
bins_associate();
bins_sectionize();
bins_flatten(bautofree(bfromcstr("output")));
if (target == IMAGE_KERNEL)
bins_write_jump();
saved = bins_optimize(
opt_mode->count == 0 ? OPTIMIZE_SIZE : OPTIMIZE_SPEED,
opt_level->count == 0 ? OPTIMIZE_NONE : opt_level->ival[0]);
if (no_short_literals_arg->count == 0 && target != IMAGE_STATIC_LIBRARY)
saved += bins_compress();
else if (no_short_literals_arg->count == 0)
dwarn(WARN_SKIPPING_SHORT_LITERALS_TYPE, NULL);
else
dwarn(WARN_SKIPPING_SHORT_LITERALS_REQUEST, NULL);
bins_resolve(
target == IMAGE_STATIC_LIBRARY,
target == IMAGE_STATIC_LIBRARY);
bins_save(
bautofree(bfromcstr("output")),
bautofree(bfromcstr(output_file->filename[0])),
target,
keep_output_arg->count > 0,
symbol_file->count > 0 ? symbol_file->filename[0] : NULL,
jumplist_file->count > 0 ? jumplist_file->filename[0] : NULL);
bins_free();
if (saved > 0)
printd(LEVEL_DEFAULT, "linker: saved %i words during optimization.\n", saved);
else if (saved < 0)
printd(LEVEL_DEFAULT, "linker: increased by %i words during optimization.\n", -saved);
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 0;
}
int main(int argc, char *argv[]) {
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "Score file");
struct arg_int *page = arg_int0("p", "page", "<int>", "Page ID");
struct arg_file *output = arg_file0("o", "output", "<file>", "Output file");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,page,output,end};
const char* progname = "scoretool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 Score file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2014 Tuomas Virtanen\n");
goto exit_0;
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Get score information
sd_score score;
sd_score_create(&score);
int ret = sd_score_load(&score, file->filename[0]);
if(ret != SD_SUCCESS) {
printf("Score file %s could not be loaded: %s\n",
file->filename[0],
sd_get_error(ret));
goto exit_0;
}
// See if we want to print a single page or all pages
if(page->count > 0) {
int page_id = page->ival[0];
if(page_id < 0 || page_id >= SD_SCORE_PAGES) {
printf("Page must be between 0 and 3.\n");
goto exit_1;
}
// Print only this page
print_page(&score, page_id);
} else {
for(int i = 0; i < SD_SCORE_PAGES; i++) {
print_page(&score, i);
printf("\n");
}
}
// Save if necessary
if(output->count > 0) {
ret = sd_score_save(&score, output->filename[0]);
if(ret != SD_SUCCESS) {
printf("Failed to save scores file to %s: %s\n",
output->filename[0],
sd_get_error(ret));
}
}
exit_1:
sd_score_free(&score);
exit_0:
arg_freetable(argtable, sizeof(argtable)/sizeof(argtable[0]));
return 0;
}