void DmetEngine::defineStates() {
defineOption("", "num-rows", PgOpt::INT_OPT,
"The number of rows on the chip.",
"-1");
defineOption("", "num-cols", PgOpt::INT_OPT,
"The number of cols on the chip.",
"-1");
defineOption("", "probe-count", PgOpt::INT_OPT,
"The number of probes on the chip.",
"-1");
}
/**
* @brief Define the options used by the log2 ratio engine.
*/
void CNReferenceEngine::defineOptions()
{
defineOptionSection("Input Options");
defineOption("","expr-summary-file", PgOpt::STRING_OPT,
"Expression Summary Table file.",
"");
defineOption("","genotype-calls-file", PgOpt::STRING_OPT,
"Genotype Calls Table file.",
"");
defineOption("","genotype-confidences-file", PgOpt::STRING_OPT,
"Genotype Confidences Table file.",
"");
defineOption("","genotype-report-file", PgOpt::STRING_OPT,
"Genotype Report Table file.",
"");
// defOptMult("", "genotype-chp-file", PgOpt::STRING_OPT, "Genotype CHP file.", "");
// defineOption("","chrRefId", PgOpt::INT_OPT,
// "Reference Chromosome",
// "2");
defineOption("","reference-file", PgOpt::STRING_OPT, "Copy Number Reference file.", "");
defineOptionSection("Output Options");
defineOption("","reference-text-output", PgOpt::BOOL_OPT,
"Output the reference-file in acii text format.",
"false");
defineOptionSection("Analysis Options");
defineOption("", "log2-input", PgOpt::BOOL_OPT, "Input Allele Summaries are in log2.", "false");
defineOption("", "adapter-type-normalization", PgOpt::BOOL_OPT,
"Adapter Type Normalization option. true = perform adapter type normalization.",
"true");
defineOptionSection("Advanced Options");
defineOption("", "set-analysis-name", PgOpt::STRING_OPT, "Analysis name to use as prefix for output files.", "");
defineOptionSection("Execution Control Options");
defineOption("", "mem-usage", PgOpt::INT_OPT,
"How many MB of memory to use for this run.",
"0");
defineSharedOptions();
}
int main(int argc, char *argv[])
{
QApplication a(argc, argv);
SQArgDescMap optionDesc;
QMap<QString, QVariant> option;
if (argc < 2)
{
std::cerr << "Too few arguments, syntax is : -sub subfile videofile" << std::endl;
return 1;
}
sq_add_gsttoyunda_plugin_path(qApp->applicationDirPath());
try {
QGst::init(&argc, &argv);
} catch (QGlib::Error qgerr)
{
std::cerr << "Can't init gstreamer" << std::endl;
return 1;
}
qInstallMessageHandler(myMessageOutput);
defineOption(optionDesc);
QStringList arg = a.arguments();
arg.removeFirst();
bool vopt = SQArg::fillWithDesc(option, arg, optionDesc);
if (vopt == false)
return 1;
VideoPlayer w("");
qDebug() << option["base_image_path"].toString();
if (!option["base_image_path"].toString().isEmpty())
w.setToyundaImagePath(option["base_image_path"].toString());
std::cout << "Subtitle file : " << option["subtitle"].toString().constData() << std::endl;
std::cout << "Video File : " << arg[0].constData() << std::endl;
w.setVideoFile(arg[0]);
w.setSubFile(option["subtitle"].toString());
w.show();
w.play();
w.show();
return a.exec();
}
int runMoc(int argc, char **argv)
{
QCoreApplication app(argc, argv);
QCoreApplication::setApplicationVersion(QString::fromLatin1(QT_VERSION_STR));
bool autoInclude = true;
bool defaultInclude = true;
Preprocessor pp;
Moc moc;
pp.macros["Q_MOC_RUN"];
pp.macros["__cplusplus"];
// Don't stumble over GCC extensions
Macro dummyVariadicFunctionMacro;
dummyVariadicFunctionMacro.isFunction = true;
dummyVariadicFunctionMacro.isVariadic = true;
dummyVariadicFunctionMacro.arguments += Symbol(0, PP_IDENTIFIER, "__VA_ARGS__");
pp.macros["__attribute__"] = dummyVariadicFunctionMacro;
pp.macros["__declspec"] = dummyVariadicFunctionMacro;
QString filename;
QString output;
QFile in;
FILE *out = 0;
// Note that moc isn't translated.
// If you use this code as an example for a translated app, make sure to translate the strings.
QCommandLineParser parser;
parser.setApplicationDescription(QStringLiteral("Qt Meta Object Compiler version %1 (Qt %2)")
.arg(mocOutputRevision).arg(QString::fromLatin1(QT_VERSION_STR)));
parser.addHelpOption();
parser.addVersionOption();
QCommandLineOption outputOption(QStringLiteral("o"));
outputOption.setDescription(QStringLiteral("Write output to file rather than stdout."));
outputOption.setValueName(QStringLiteral("file"));
parser.addOption(outputOption);
QCommandLineOption includePathOption(QStringLiteral("I"));
includePathOption.setDescription(QStringLiteral("Add dir to the include path for header files."));
includePathOption.setValueName(QStringLiteral("dir"));
parser.addOption(includePathOption);
QCommandLineOption macFrameworkOption(QStringLiteral("F"));
macFrameworkOption.setDescription(QStringLiteral("Add Mac framework to the include path for header files."));
macFrameworkOption.setValueName(QStringLiteral("framework"));
parser.addOption(macFrameworkOption);
QCommandLineOption preprocessOption(QStringLiteral("E"));
preprocessOption.setDescription(QStringLiteral("Preprocess only; do not generate meta object code."));
parser.addOption(preprocessOption);
QCommandLineOption defineOption(QStringLiteral("D"));
defineOption.setDescription(QStringLiteral("Define macro, with optional definition."));
defineOption.setValueName(QStringLiteral("macro[=def]"));
parser.addOption(defineOption);
QCommandLineOption undefineOption(QStringLiteral("U"));
undefineOption.setDescription(QStringLiteral("Undefine macro."));
undefineOption.setValueName(QStringLiteral("macro"));
parser.addOption(undefineOption);
QCommandLineOption metadataOption(QStringLiteral("M"));
metadataOption.setDescription(QStringLiteral("Add key/value pair to plugin meta data"));
metadataOption.setValueName(QStringLiteral("key=value"));
parser.addOption(metadataOption);
QCommandLineOption noIncludeOption(QStringLiteral("i"));
noIncludeOption.setDescription(QStringLiteral("Do not generate an #include statement."));
parser.addOption(noIncludeOption);
QCommandLineOption pathPrefixOption(QStringLiteral("p"));
pathPrefixOption.setDescription(QStringLiteral("Path prefix for included file."));
pathPrefixOption.setValueName(QStringLiteral("path"));
parser.addOption(pathPrefixOption);
QCommandLineOption forceIncludeOption(QStringLiteral("f"));
forceIncludeOption.setDescription(QStringLiteral("Force #include <file> (overwrite default)."));
forceIncludeOption.setValueName(QStringLiteral("file"));
parser.addOption(forceIncludeOption);
QCommandLineOption prependIncludeOption(QStringLiteral("b"));
prependIncludeOption.setDescription(QStringLiteral("Prepend #include <file> (preserve default include)."));
prependIncludeOption.setValueName(QStringLiteral("file"));
parser.addOption(prependIncludeOption);
QCommandLineOption noNotesWarningsCompatOption(QStringLiteral("n"));
noNotesWarningsCompatOption.setDescription(QStringLiteral("Do not display notes (-nn) or warnings (-nw). Compatibility option."));
noNotesWarningsCompatOption.setValueName(QStringLiteral("which"));
parser.addOption(noNotesWarningsCompatOption);
QCommandLineOption noNotesOption(QStringLiteral("no-notes"));
noNotesOption.setDescription(QStringLiteral("Do not display notes."));
parser.addOption(noNotesOption);
QCommandLineOption noWarningsOption(QStringLiteral("no-warnings"));
noWarningsOption.setDescription(QStringLiteral("Do not display warnings (implies --no-notes)."));
parser.addOption(noWarningsOption);
QCommandLineOption ignoreConflictsOption(QStringLiteral("ignore-option-clashes"));
ignoreConflictsOption.setDescription(QStringLiteral("Ignore all options that conflict with compilers, like -pthread conflicting with moc's -p option."));
parser.addOption(ignoreConflictsOption);
parser.addPositionalArgument(QStringLiteral("[header-file]"),
QStringLiteral("Header file to read from, otherwise stdin."));
parser.addPositionalArgument(QStringLiteral("[@option-file]"),
QStringLiteral("Read additional options from option-file."));
const QStringList arguments = argumentsFromCommandLineAndFile(app.arguments());
parser.process(arguments);
const QStringList files = parser.positionalArguments();
if (files.count() > 1) {
error("Too many input files specified");
parser.showHelp(1);
} else if (!files.isEmpty()) {
filename = files.first();
}
const bool ignoreConflictingOptions = parser.isSet(ignoreConflictsOption);
output = parser.value(outputOption);
pp.preprocessOnly = parser.isSet(preprocessOption);
if (parser.isSet(noIncludeOption)) {
moc.noInclude = true;
autoInclude = false;
}
if (!ignoreConflictingOptions) {
if (parser.isSet(forceIncludeOption)) {
moc.noInclude = false;
autoInclude = false;
foreach (const QString &include, parser.values(forceIncludeOption)) {
moc.includeFiles.append(QFile::encodeName(include));
defaultInclude = false;
}
}
foreach (const QString &include, parser.values(prependIncludeOption))
moc.includeFiles.prepend(QFile::encodeName(include));
if (parser.isSet(pathPrefixOption))
moc.includePath = QFile::encodeName(parser.value(pathPrefixOption));
}
int main(int ac, char *ag[])
{
QToyunda *toyunda;
QApplication *qapp;
SQArgDescMap optionDesc;
QMap<QString, QVariant> option;
QDebugErrorHandler *errorHandler;
errorHandler = new QDebugErrorHandler();
defineOption(optionDesc);
qapp = new QApplication(ac, ag);
// Handle arguments
QStringList arg = qapp->arguments();
arg.removeFirst();
bool vopt = SQArg::fillWithDesc(option, arg, optionDesc);
// Help
if (option["help"].toBool() || vopt == false) {
QTextStream cout(stdout);
cout << "QToyunda\nSynopsis : ";
cout << "./qtoyunda --player playername --renderer renderername --video videofile --subtitle subtitlefile\n\n";
cout.flush();
if (option["help"].toBool()) {
cout << "All option available :\n";
cout.flush();
SQArg::generateLongHelp(optionDesc);
return 0;
}
return 1;
}
// Player and renderer option
QStringList playerOption;
if (!option["playeroption"].toString().isEmpty())
playerOption = option["playeroption"].toString().split(",");
QStringList rendererOption;
if (!option["rendereroption"].toString().isEmpty())
rendererOption = option["rendereroption"].toString().split(",");
rendererOption << "logo=:/main/Toyunda logo.png";
qDebug() << rendererOption;
toyunda = new QToyunda(errorHandler);
toyunda->setPlayerName(option["player"].toString());
toyunda->setRendererName(option["renderer"].toString());
toyunda->setPlayerOption(playerOption);
toyunda->setRendererOption(rendererOption);
QDir pluginPath = qApp->applicationDirPath();
pluginPath.cd("plugins");
toyunda->setPluginDirectory(pluginPath);
toyunda->loadPlugins();
// FIXME playeroptionhelp and roh must not depend and toyunda
if (option["playeroptionhelp"].toBool()) {
toyunda->showPlayerOption();
return 0;
}
if (option["rendereroptionhelp"].toBool()) {
toyunda->showRendererOption();
return 0;
}
qDebug() << "Init toyunda";
if (!toyunda->init())
{
qCritical() << "Can't init qtoyunda, abord";
return 1;
}
qDebug() << "Load files";
toyunda->load(option["video"].toString(), option["subtitle"].toString());
qDebug() << "Play the video";
toyunda->play();
toyunda->showRenderer();
int ret = qapp->exec();
toyunda->dispose();
return ret;
}
void DmetEngine::defineOptions() {
defineOptionSection("Input Options");
defineOption("", "cel-files", PgOpt::STRING_OPT,
"Text file specifying cel files to process, one per line with the first line being 'cel_files'.",
"");
defineOption("c", "cdf-file", PgOpt::STRING_OPT,
"File defining probe sets. Use either --cdf-file or --spf-file. ",
"");
defineOption("", "spf-file", PgOpt::STRING_OPT,
"File defining probe sets in spf (simple probe format) which is like a text cdf file.",
"");
defineOption("", "special-snps",PgOpt::STRING_OPT,
"File containing all snps of unusual copy (chrX,mito,Y)",
"");
defineOption("", "chrX-probes", PgOpt::STRING_OPT,
"File containing probe_id (1-based) of probes on chrX. "
"Used for copy number probe chrX/Y ratio gender calling. ",
"");
defineOption("", "chrY-probes", PgOpt::STRING_OPT,
"File containing probe_id (1-based) of probes on chrY. "
"Used for copy number probe chrX/Y ratio gender calling. ",
"");
defineOption("", "reference-input", PgOpt::STRING_OPT,
"Reference file with cluster prior information. ",
"");
defineOption("s", "probeset-ids", PgOpt::STRING_OPT,
"Tab delimited file with column 'probeset_id' specifying probesets to analyze.",
"");
defineOption("", "probeset-ids-reported", PgOpt::STRING_OPT,
"Tab delimited file with column 'probeset_id' specifying probesets to report. "
"This should be a subset of those specified with --probeset-ids if that option is used.",
"");
defOptMult("", "chip-type", PgOpt::STRING_OPT,
"Chip types to check library and CEL files against. "
"Can be specified multiple times. "
"The first one is propigated as the chip type in the output files. "
"Warning, use of this option will override the usual check between chip types "
"found in the library files and cel files. You should use this option instead "
"of --force when possible. ",
"");
defineOption("", "region-model", PgOpt::STRING_OPT,
"Regions model parameters. ",
"");
defineOption("", "probeset-model", PgOpt::STRING_OPT,
"Probeset model parameters. ",
"");
defineOption("", "cn-region-gt-probeset-file",
PgOpt::STRING_OPT,
"Tab delimited file mapping probeset ids to copynumber regions. ",
"");
defineOptionSection("Output Options");
defineOption("", "cc-chp-output", PgOpt::BOOL_OPT,
"Output resulting calls in directory called 'chp' under out-dir. "
"This makes one AGCC Multi Data CHP file per cel file analyzed.",
"false");
defineOption("", "reference-output", PgOpt::STRING_OPT,
"File to write reference values to. Specifying this option will turn on "
"dynamic clustering. WARNING: Currently the "
"resulting reference file is not really usable as a reference. "
"See the manual for more info. ",
"");
defineOption("", "batch-name", PgOpt::STRING_OPT,
"The name of the batch for the dynamic cluster analysis. ",
"");
defineOptionSection("Analysis Options");
defineOption("", "set-analysis-name", PgOpt::STRING_OPT,
"Explicitly set the analysis name. This affects output file names (ie prefix) and various meta info.",
"dmet");
defineOption("", "ps-analysis", PgOpt::STRING_OPT,
"Explicitly set the ProbesetSummarizeEngine analysis string.",
"");
defineOption("", "gt-analysis", PgOpt::STRING_OPT,
"Explicitly set the ProbesetGenotypeEngine analysis string.",
"");
defineOption("", "gt-qmethod-spec", PgOpt::STRING_OPT,
"Explicitly set the ProbesetGenotypeEngine quant spec.",
"");
defineOption("", "sample-type", PgOpt::STRING_OPT,
"Set the type of samples being processed. eg genomic, plasmid.",
"unknown");
defineOption("", "batch-info", PgOpt::BOOL_OPT,
"Indicates whether or not information about other cel files in the batch "
"should be reported in CHP headers.",
"false");
defineOption("", "null-context", PgOpt::BOOL_OPT,
"Indicates whether or not context info should be populated in the CHP files.",
"true");
defineOption("", "run-cn-engine", PgOpt::BOOL_OPT,
"Indicates if the CN engine should be run or not.",
"true");
defineOption("", "pra-thresh", PgOpt::INT_OPT,
"The threshold for calling PRAs based on the cluster mean strength.",
"3");
defineOption("", "geno-call-thresh", PgOpt::DOUBLE_OPT,
"The confidence threshold for reporting calls in the CHP file.",
"0.1");
defineOptionSection("Gender Options");
defineOption("", "female-thresh", PgOpt::DOUBLE_OPT,
"Threshold for calling females when using cn-probe-chrXY-ratio method.",
"0.17");
defineOption("", "male-thresh", PgOpt::DOUBLE_OPT,
"Threshold for calling females when using cn-probe-chrXY-ratio method.",
"0.68");
defineOptionSection("Advanced Options");
defineOption("", "call-coder-max-alleles", PgOpt::INT_OPT,
"For encoding/decoding calls, the max number of alleles per marker to allow.",
"6");
defineOption("", "call-coder-type", PgOpt::STRING_OPT,
"The data size used to encode the call.",
"UCHAR");
defineOption("", "call-coder-version", PgOpt::STRING_OPT,
"The version of the encoder/decoder to use",
"1.0");
defineOptionSection("Execution Control Options");
defineOption("", "use-disk", PgOpt::BOOL_OPT,
"Store CEL intensities to be analyzed on disk.", "true");
defineOption("", "disk-cache", PgOpt::INT_OPT,
"Size of intensity memory cache in millions of intensities (when --use-disk=true).",
"50");
defineOptionSection("Engine Options (Not used on command line)");
defOptMult("", "cels", PgOpt::STRING_OPT,
"Cel files to process.",
"");
defOptMult("", "report", PgOpt::STRING_OPT,
"Probesets to report. eg consented.",
"");
}
