int main(int argc, char *argv[])
{
char *readBuffer = NULL;
const char * filename = "../data/Ecoli_raw.fasta";
unsigned int readCount = 0;
readCount = processReads(filename, 17, &readBuffer);
printf("readCount = %d\n",readCount);
printf("%s",readBuffer[0]);
}
processMultireads::processMultireads(QWidget *parent) :
QWidget(parent),
progressView(new analysisProgressView(this)),
multireadsView(new processMultireadsView(this))
{
// set a window title
setWindowTitle(tr("Rcount-multireads"));
// initialize all the other widgets
// get and set the minimal sizes
int minWidth = multireadsView->sizeHint().width();
int minHeight = multireadsView->sizeHint().height()+progressView->sizeHint().height()*1.5;
this->setMinimumHeight(minHeight);
this->setMinimumWidth(minWidth);
// layout
QVBoxLayout *layout = new QVBoxLayout;
layout->addWidget(multireadsView);
layout->addWidget(progressView);
setLayout(layout);
// hide the progressView
//! progressView->hide();
// connections
connect(&processor, SIGNAL(processStatus(QString)), progressView, SLOT(updateStatus(QString)));
connect(&processor, SIGNAL(processProgress(int)), progressView, SLOT(updateProgress(int)));
connect(&processor, SIGNAL(errorMessage(QString)), progressView, SLOT(updateStatus(QString)));
//! connect(&processor, SIGNAL(idleAgain()), this, SLOT(hideProgress()));
connect(&processor, SIGNAL(workFinished(QString)), multireadsView, SLOT(removeFromQueue(QString)));
connect(progressView, SIGNAL(analysisCanceled()), &processor, SLOT(cancelProcessing()));
connect(multireadsView, SIGNAL(closeAll()), &processor, SLOT(cancelProcessing()));
connect(multireadsView, SIGNAL(closeAll()), this, SLOT(close()));
connect(multireadsView, SIGNAL(processReads(QString)), this, SLOT(runProcessor(QString)));
}
int run(const Properties& options, const Arguments& arguments) {
int r = 0;
if ((r = checkOptions(options, arguments)) != 0) {
return r;
}
// parameters
LOG4CXX_INFO(logger, "Parameters:");
LOG4CXX_INFO(logger, boost::format("PE Mode: %d") % options.get< int >("pe-mode", 0));
if (options.find("min-length") != options.not_found()) {
LOG4CXX_INFO(logger, boost::format("Min length: %d") % options.get< int >("min-length"));
}
if (options.find("hard-clip") != options.not_found()) {
LOG4CXX_INFO(logger, boost::format("hard clip: %d") % options.get< int >("hard-clip"));
}
if (options.find("quality-trim") != options.not_found()) {
LOG4CXX_INFO(logger, boost::format("Quality Trim: %d") % options.get< int >("quality-trim"));
}
if (options.find("quality-filter") != options.not_found()) {
LOG4CXX_INFO(logger, boost::format("Quality Filter: %d") % options.get< int >("quality-filter"));
}
// input
std::vector< std::string > filelist;
std::copy(arguments.begin(), arguments.end(), std::back_inserter(filelist));
LOG4CXX_INFO(logger, boost::format("input: %s") % boost::algorithm::join(filelist, ":"));
// output
std::ostream* out = &std::cout;
if (options.find("out") != options.not_found()) {
std::string file = options.get< std::string >("out");
out = new std::ofstream(file.c_str());
LOG4CXX_INFO(logger, boost::format("output: %s") % file);
}
// process
if (*out) {
Statistics stats;
if ((r = processReads(options, filelist, *out, stats)) == 0) {
// report statistics
LOG4CXX_INFO(logger, "Preprocess stats:");
LOG4CXX_INFO(logger, boost::format("Reads parsed:\t%d") % stats.numReadsRead);
if (stats.numReadsRead > 0) {
LOG4CXX_INFO(logger, boost::format("Reads kept:\t%d(%f)") % stats.numReadsKept % ((double)stats.numReadsKept / stats.numReadsRead));
LOG4CXX_INFO(logger, boost::format("Reads failed primer screen:\t%d(%e)") % stats.numReadsPrimer % ((double)stats.numReadsPrimer / stats.numReadsRead));
}
LOG4CXX_INFO(logger, boost::format("Bases parsed:\t%d") % stats.numBasesRead);
if (stats.numBasesRead) {
LOG4CXX_INFO(logger, boost::format("Bases kept:\t%d(%f)") % stats.numBasesKept % ((double)stats.numBasesKept / stats.numBasesRead));
}
LOG4CXX_INFO(logger, boost::format("Number of incorrectly paired reads that were discarded: %d") % stats.numInvalidPE);
}
} else {
LOG4CXX_ERROR(logger, "Failed to open output stream");
}
if (out != &std::cout) {
SAFE_DELETE(out);
}
return r;
}
