void DVDWorker::ScanDVDContents() {
XamSetDvdSpindleSpeed(DVD_SPEED_12X);
WIN32_FIND_DATA findFileData;
memset(&findFileData,0,sizeof(WIN32_FIND_DATA));
string searchcmd = "dvd:\\*";
searchcmd = str_replaceallA(searchcmd,"\\\\","\\");
HANDLE hFind = FindFirstFile(searchcmd.c_str(), &findFileData);
if (hFind != INVALID_HANDLE_VALUE)
{
do {
if (findFileData.dwFileAttributes & FILE_ATTRIBUTE_DIRECTORY)
{
if (strcmp(findFileData.cFileName, "$SystemUpdate") != 0)
{
string source = sprintfaA("dvd:\\%s", findFileData.cFileName);
string dest = sprintfaA("%s\\%s", m_CurrentItem->getDestPath().c_str(), findFileData.cFileName);
RecursiveMkdir(dest);
m_CurrentItem->setCurrentFile(source);
m_CurrentItem->requester->UpdateFileCount(m_CurrentItem);
RecursiveScan(source, dest);
} else if (strcmp(findFileData.cFileName, "$SystemUpdate") == 0 && m_CurrentItem->getIncludeUpdate())
{
string source = sprintfaA("dvd:\\%s", findFileData.cFileName);
string dest = sprintfaA("%s\\%s", m_CurrentItem->getDestPath().c_str(), findFileData.cFileName);
RecursiveMkdir(dest);
m_CurrentItem->setCurrentFile(source);
m_CurrentItem->requester->UpdateFileCount(m_CurrentItem);
RecursiveScan(source, dest);
}
} else {
string source = sprintfaA("dvd:\\%s", findFileData.cFileName);
string dest = sprintfaA("%s\\%s", m_CurrentItem->getDestPath().c_str(), findFileData.cFileName);
m_CurrentItem->setCurrentFile(source);
m_CurrentItem->requester->UpdateFileCount(m_CurrentItem);
FileOperationManager::getInstance().AddFileOperation(source, dest, false);
}
} while (FindNextFile(hFind, &findFileData));
}FindClose(hFind);
m_CurrentItem->setScanComplete(true);
m_CurrentItem->requester->UpdateFileCount(m_CurrentItem);
FileOperationManager::getInstance().DoWork();
}
int PDMlib::Write(const std::string& Name, const size_t& ContainerLength, T* Container, T MinMax[8], const int& NumComp, const int& TimeStep, const double& Time)
{
if(!pImpl->Initialized)
{
std::cerr<<"PDMlib::Write() called before Init()"<<std::endl;
return -1;
}
if(!pImpl->wMetaData->FindContainerInfo(Name))
{
std::cerr<<"PDMlib::Write(): "<<Name<<" is not found in MetaDataFile"<<std::endl;
return -2;
}
if(Container == NULL)
{
std::cerr<<"PDMlib::Write(): Null pointer is passed as Container pointer of pointer"<<std::endl;
return -4;
}
if((NumComp != 1) && (NumComp != 3))
{
std::cerr<<"PDMlib::Write(): NumComp must be 1 or 3 ("<<NumComp<<")"<<std::endl;
return -5;
}
if(TimeStep < 0)
{
std::cerr<<"PDMlib::Write(): TimeStep must be positive number ("<<TimeStep<<")"<<std::endl;
return -6;
}
if(pImpl->FirstCall)
{
pImpl->wMetaData->SetReadOnly();
pImpl->wMetaData->Write();
pImpl->FirstCall = false;
// create directory by atomic operation in MPI world
for ( int i=0; i<pImpl->wMetaData->GetNumProc(); i++)
{
MPI_Barrier(pImpl->wMetaData->GetComm());
if(i != pImpl->wMetaData->GetMyRank()) continue;
if(!RecursiveMkdir(pImpl->wMetaData->GetPath()))
{
std::cerr<<"mkdir faild! field data will be output to current directory!"<<std::endl;
pImpl->wMetaData->SetPath("./");
}
}
}
//タイムスライス情報の出力
pImpl->wMetaData->WriteTimeSlice(TimeStep, Time, MinMax, ContainerLength, Name);
std::string filename;
pImpl->wMetaData->GetFileName(&filename, Name, pImpl->wMetaData->GetMyRank(), TimeStep);
//出力するデータサイズが0の時はタイムスライスだけ出力して終了
if(ContainerLength == 0)
{
return 0;
}
//フィールドデータの出力
ContainerInfo container_info;
pImpl->wMetaData->GetContainerInfo(Name, &container_info);
BaseIO::Write* writer = BaseIO::WriteFactory::create(container_info.Compression, enumType2string(container_info.Type), container_info.nComp);
int write_size = writer->write(filename.c_str(), ContainerLength*NumComp*sizeof(T), ContainerLength*NumComp*sizeof(T), (char*)Container);
delete writer;
return write_size;
}
int processAssemblyOptions(int argc, char * argv[], assemblyOptions& opts)
{
int c;
int index;
static struct option assemblyLongOptions [] = {
{"segments", required_argument, NULL, 's'},
{"group", required_argument, NULL, 'g'},
{"logLevel", required_argument, NULL, 'l'},
{"version", no_argument, NULL, 'V'},
{"inDir", required_argument, NULL, 'i'},
{"outDir", required_argument, NULL, 'o'},
{"help", no_argument, NULL, 'h'},
{"pairedEnd", no_argument, NULL, 'p'},
{"insertSize", required_argument, NULL, 'I'},
{"logToScreen", no_argument, NULL, 0},
{"xml",required_argument,NULL,'x'},
{"velvet",no_argument,NULL,0},
{"cap3",no_argument,NULL,0},
{NULL, no_argument, NULL, 0}
};
try
{
while( (c = getopt_long(argc, argv, "g:hi:I:l:o:ps:Vx:", assemblyLongOptions, &index)) != -1 )
{
switch(c)
{
case 'g':
{
from_string<int>(opts.group, optarg, std::dec);
break;
}
case 'h':
{
assemblyUsage();
exit(1);
break;
}
case 'i':
{
// Test to see if the file is ok.
struct stat inputDirStatus;
int iStat = stat(optarg, &inputDirStatus);
// stat failed
switch (iStat)
{
case -1:
{
switch (errno)
{
case ENOENT:
{
throw ( std::runtime_error("Input directory path does not exist, or path is an empty string.") );
break;
}
case ELOOP:
{
throw ( std::runtime_error("Too many symbolic links encountered while traversing the input directory path."));
break;
}
case EACCES:
{
throw ( std::runtime_error("You do not have permission to access the input directory."));
break;
}
case ENOTDIR:
{
throw ( std::runtime_error("Input is not a directory\n"));
break;
}
default:
{
throw (std::runtime_error("An error occured when reading the input directory"));
break;
}
}
break;
}
default:
{
opts.inputDirName = optarg;
break;
}
}
break;
}
case 'I':
{
from_string<int>(opts.insertSize, optarg, std::dec);
break;
}
case 'l':
{
from_string<int>(opts.logLevel, optarg, std::dec);
if(opts.logLevel > CRASS_DEF_MAX_LOGGING)
{
std::cerr<<PACKAGE_NAME<<" [WARNING]: Specified log level higher than max. Changing log level to "<<CRASS_DEF_MAX_LOGGING<<" instead of "<<opts.logLevel<<std::endl;
opts.logLevel = CRASS_DEF_MAX_LOGGING;
}
break;
}
case 'o':
{
// Test to see if the file is ok.
struct stat outputDirStatus;
int oStat = stat(optarg, &outputDirStatus);
switch (oStat)
{
case -1:
{
switch (errno)
{
case ENOENT:
{
RecursiveMkdir(optarg);
break;
}
case ELOOP:
{
throw ( std::runtime_error("Too many symbolic links encountered while traversing the output directory path."));
break;
}
case EACCES:
{
throw ( std::runtime_error("You do not have permission to access the output directory."));
break;
}
case ENOTDIR:
{
throw ( std::runtime_error("Output path is not a directory\n"));
break;
}
default:
{
throw std::runtime_error("An error occurred when accessing the output directory");
break;
}
}
}
default:
{
opts.outputDirName = optarg;
break;
}
}
break;
}
case 'p':
{
opts.pairedEnd = true;
break;
}
case 's':
{
opts.segments = optarg;
break;
}
case 'V':
{
assemblyVersionInfo();
exit(1);
break;
}
case 'x':
{
// Test to see if the file is ok.
struct stat inputDirStatus;
int xStat = stat(optarg, &inputDirStatus);
// stat failed
switch (xStat)
{
case -1:
{
switch (errno)
{
case ENOENT:
{
throw ( std::runtime_error("Path to the XML file does not exist, or path is an empty string.") );
break;
}
case ELOOP:
{
throw ( std::runtime_error("Too many symbolic links encountered while traversing the path to the XML file."));
break;
}
case EACCES:
{
throw ( std::runtime_error("You do not have permission to access the XML file."));
break;
}
default:
{
throw (std::runtime_error("An error occured when reading the XML file"));
break;
}
}
break;
}
default:
{
opts.xmlFileName = optarg;
break;
}
}
break;
}
case 0:
{
if ( strcmp( "logToScreen", assemblyLongOptions[index].name ) == 0 ) opts.logToScreen = true;
if (!strcmp("velvet",assemblyLongOptions[index].name)){
#ifdef HAVE_VELVET
opts.assembler = velvet;
#else
throw std::runtime_error("crass-assembler cannot use velvet. Please re-compile with velvet in you PATH");
#endif
}
if (!strcmp("cap3",assemblyLongOptions[index].name)){
#ifdef HAVE_CAP3
opts.assembler = cap3;
#else
throw std::runtime_error("crass-assembler cannot use cap3. Please re-compile with cap3 in you PATH");
#endif
}
break;
}
default:
{
assemblyUsage();
exit(1);
break;
}
}
}
// make sure that the required flags are set
if (opts.xmlFileName.empty())
{
throw (std::runtime_error("You must specify an xml file with -x"));
}
if (!(opts.group))
{
throw (std::runtime_error("You must specify a group number with -g"));
}
if (opts.segments.empty())
{
throw (std::runtime_error("You must specify a list of contigs with -s"));
}
if (opts.inputDirName.empty())
{
throw (std::runtime_error("You must specify an input directory with -i"));
}
if (opts.outputDirName.empty()) {
opts.outputDirName = ".";
}
}
catch (std::exception& e)
{
std::cerr<<PACKAGE_NAME<<" [ERROR]: "<<e.what()<<std::endl;
exit(1);
}
return optind;
}
int processOptions(int argc, char *argv[], options *opts)
{
int c;
int index;
bool scalling = false;
while( (c = getopt_long(argc, argv, "a:b:c:d:D:ef:gGhHk:K:l:Ln:o:rs:S:Vw:x:y:z", long_options, &index)) != -1 )
{
switch(c)
{
case 'a':
#if RENDERING
if (strcmp(optarg, "dot") && strcmp(optarg, "neato") && strcmp(optarg, "fdp") && strcmp(optarg, "sfdp") && strcmp(optarg, "twopi") && strcmp(optarg, "circo")) {
std::cerr<<PACKAGE_NAME<<" [WARNING]: '"<<optarg<<"' is not a recognised layout algorithm. Please choose from the following:"<<std::endl;
#ifdef HAVE_NEATO
std::cerr<<"\tneato"<<std::endl;
#endif
#ifdef HAVE_DOT
std::cerr<<"\tdot"<<std::endl;
#endif
#ifdef HAVE_FDP
std::cerr<<"\tfdp"<<std::endl;
#endif
#ifdef HAVE_SFDP
std::cerr<<"\tsfdp"<<std::endl;
#endif
#ifdef HAVE_CIRCO
std::cerr<<"\tcirco"<<std::endl;
#endif
#ifdef HAVE_TWOPI
std::cerr<<"\ttwopi"<<std::endl;
#endif
} else {
opts->layoutAlgorithm = optarg;
}
#else
std::cerr<<PACKAGE_NAME<<" [WARNING]: Not compiled with the correct options to allow rendering of graphs.\nEither use the --enable-rendering option during ./configure and make sure that the graphviz layout programs are in your PATH"<<std::endl;
#endif
break;
case 'b':
from_string<int>(opts->coverageBins, optarg, std::dec);
if (opts->coverageBins < 1)
{
std::cerr<<PACKAGE_NAME<<" [ERROR]: The number of bins for coverage cannot be less than 1"<<std::endl;
usage();
exit(1);
}
break;
case 'c':
if (strcmp(optarg, "red-blue") == 0)
{
opts->graphColourType = RED_BLUE;
}
else if(strcmp(optarg, "read-blue-green") == 0)
{
opts->graphColourType = RED_BLUE_GREEN;
}
else if(strcmp(optarg, "blue-red") == 0)
{
opts->graphColourType = BLUE_RED;
}
else if(strcmp(optarg, "green-blue-red") == 0)
{
opts->graphColourType = GREEN_BLUE_RED;
}
else
{
std::cerr<<PACKAGE_NAME<<" [WARNING]: Unknown graph colour type "<<optarg<<" changing to default colour type (red-blue)"<<std::endl;
opts->graphColourType = RED_BLUE;
}
break;
case 'd':
from_string<unsigned int>(opts->lowDRsize, optarg, std::dec);
if (opts->lowDRsize < 8)
{
std::cerr<<PACKAGE_NAME<<" [WARNING]: The lower bound for direct repeat sizes cannot be "<<opts->lowDRsize<<" changing to "<<CRASS_DEF_MIN_DR_SIZE<<std::endl;
opts->lowDRsize = CRASS_DEF_MIN_DR_SIZE;
}
break;
case 'D':
from_string<unsigned int>(opts->highDRsize, optarg, std::dec);
break;
case 'e':
#ifdef DEBUG
opts->noDebugGraph = true;
#endif
break;
case 'f':
from_string<int>(opts->covCutoff, optarg, std::dec);
break;
case 'g':
opts->logToScreen = true;
break;
case 'G':
opts->showSingles= true;
break;
case 'h':
versionInfo();
usage();
exit(1);
break;
case 'H':
opts->removeHomopolymers = true;
break;
case 'k':
from_string<int>(opts->kmer_clust_size, optarg, std::dec);
if (opts->kmer_clust_size < 4)
{
std::cerr<<PACKAGE_NAME<<" [WARNING]: Minimum value for kmer clustering size is: "<<4<<" changing to "<<CRASS_DEF_K_CLUST_MIN<<std::endl;
opts->kmer_clust_size = CRASS_DEF_K_CLUST_MIN;
}
break;
case 'K':
from_string<int>(opts->cNodeKmerLength, optarg, std::dec);
break;
case 'l':
from_string<int>(opts->logLevel, optarg, std::dec);
if(opts->logLevel > CRASS_DEF_MAX_LOGGING)
{
std::cerr<<PACKAGE_NAME<<" [WARNING]: Specified log level higher than max. Changing log level to "<<CRASS_DEF_MAX_LOGGING<<" instead of "<<opts->logLevel<<std::endl;
opts->logLevel = CRASS_DEF_MAX_LOGGING;
}
break;
case 'L':
opts->longDescription = true;
break;
case 'n':
from_string<unsigned int>(opts->minNumRepeats, optarg, std::dec);
if (opts->minNumRepeats < 2)
{
std::cerr<<PACKAGE_NAME<<" [ERROR]: The mininum number of repeats cannot be less than 2"<<std::endl;
usage();
exit(1);
}
break;
case 'o':
opts->output_fastq = optarg;
// just in case the user put '.' or '..' or '~' as the output directory
if (opts->output_fastq[opts->output_fastq.length() - 1] != '/')
{
opts->output_fastq += '/';
}
// check if our output folder exists
struct stat file_stats;
if (0 != stat(opts->output_fastq.c_str(),&file_stats))
{
RecursiveMkdir(opts->output_fastq);
}
// check that the directory is writable
else if(access(optarg, W_OK))
{
std::cerr<<PACKAGE_NAME<<" [ERROR]: You do not have permission to write to "<<optarg<<std::endl;
exit(1);
}
break;
case 'r':
#ifdef RENDERING
opts->noRendering = true;
#endif
break;
case 's':
from_string<unsigned int>(opts->lowSpacerSize, optarg, std::dec);
if (opts->lowSpacerSize < 8)
{
std::cerr<<PACKAGE_NAME<<" [WARNING]: The lower bound for spacer sizes cannot be "<<opts->lowSpacerSize<<" changing to "<<CRASS_DEF_MIN_SPACER_SIZE<<std::endl;
opts->lowSpacerSize = CRASS_DEF_MIN_SPACER_SIZE;
}
break;
case 'S':
from_string<unsigned int>(opts->highSpacerSize, optarg, std::dec);
break;
case 'V':
versionInfo();
exit(1);
break;
case 'w':
from_string<unsigned int>(opts->searchWindowLength, optarg, std::dec);
if ((opts->searchWindowLength < CRASS_DEF_MIN_SEARCH_WINDOW_LENGTH) || (opts->searchWindowLength > CRASS_DEF_MAX_SEARCH_WINDOW_LENGTH))
{
std::cerr<<PACKAGE_NAME<<" [WARNING]: Specified window length higher than max. Changing window length to " << CRASS_DEF_OPTIMAL_SEARCH_WINDOW_LENGTH << " instead of " << opts->searchWindowLength<<std::endl;
// Change window length
opts->searchWindowLength = CRASS_DEF_OPTIMAL_SEARCH_WINDOW_LENGTH;
}
break;
case 'x':
from_string<double>(opts->averageSpacerScalling, optarg, std::dec);
if (isNotDecimal(opts->averageSpacerScalling))
{
std::cerr<<PACKAGE_NAME<<" [WARNING]: The average spacer scalling must be a decimal number. Changing to "<<CRASS_DEF_HOMOPOLYMER_SCALLING<<" instead of "<<opts->averageSpacerScalling<<std::endl;
opts->averageSpacerScalling = CRASS_DEF_HOMOPOLYMER_SCALLING;
}
scalling = true;
break;
case 'y':
from_string<double>(opts->averageDrScalling, optarg, std::dec);
if (isNotDecimal(opts->averageDrScalling))
{
std::cerr<<PACKAGE_NAME<<" [WARNING]: The average spacer scalling must be a decimal number. Changing to "<<CRASS_DEF_HOMOPOLYMER_SCALLING<<" instead of "<<opts->averageDrScalling<<std::endl;
opts->averageDrScalling = CRASS_DEF_HOMOPOLYMER_SCALLING;
}
scalling = true;
break;
case 'z':
opts->dontPerformScalling = true;
break;
case 0:
#ifdef SEARCH_SINGLETON
if (strcmp("searchChecker", long_options[index].name) == 0) opts->searchChecker = optarg;
#endif
break;
default:
versionInfo();
usage();
exit(1);
break;
}
}
// Sanity checks for the high and low dr size
if (opts->lowDRsize >= opts->highDRsize)
{
std::cerr<<PACKAGE_NAME<<" [ERROR]: The lower direct repeat bound is bigger than the higher bound ("<<opts->lowDRsize<<" >= "<<opts->highDRsize<<")"<<std::endl;
usage();
exit(1);
}
// Sanity checks for the high and low spacer size
if (opts->lowSpacerSize >= opts->highSpacerSize)
{
std::cerr<<PACKAGE_NAME<<" [ERROR]: The lower spacer bound is bigger than the higher bound ("<<opts->lowSpacerSize<<" >= "<<opts->highSpacerSize<<")"<<std::endl;
usage();
exit(1);
}
// sanity check so that the user doesn't specify scalling and no scalling simultaneously
if (scalling & opts->dontPerformScalling) {
std::cerr<<PACKAGE_NAME<<" [ERROR]: Cannot use scalling (-x -y) in conjunction with --noScalling"<<std::endl;
usage();
exit(1);
}
// warn them if they try to scale without specifying to remove homopolymers
if (scalling && !opts->removeHomopolymers)
{
std::cerr<<PACKAGE_NAME<<" [ERROR]: scalling (-x -y) can only be used in conjunction with --removeHomopolymers"<<std::endl;
usage();
exit(1);
}
// scale the direct repeat and spacer lengths if we should
if (opts->removeHomopolymers && !opts->dontPerformScalling)
{
opts->lowDRsize *= opts->averageDrScalling;
opts->highDRsize *= opts->averageDrScalling;
opts->lowSpacerSize *= opts->averageSpacerScalling;
opts->highSpacerSize *= opts->averageSpacerScalling;
}
return optind;
}
