MainWindow::MainWindow(QWidget *parent) :
QMainWindow(parent),
ui(new Ui::MainWindow)
{
ui->setupUi(this);
mainWidget = new QWidget();
mainLayout = new QVBoxLayout();
horizLayout = new QHBoxLayout();
insertButton = new QPushButton("Insert Value");
deleteKeyButton = new QPushButton("Delete Key");
deleteKeyButton->setVisible(false);
sortButton = new QPushButton("Sort Values");
sortButton->setVisible(false);
sortedValues = new QLabel();
sortedValues->setVisible(false);
sortedValues->setAlignment(Qt::AlignBottom | Qt::AlignCenter);
searchButton = new QPushButton("Search!");
searchButton->setVisible(false);
found = false;
foundVal = 0;
valuesSpinBox = new QSpinBox(this);
valuesSpinBox->setMaximum(999);
valuesSpinBox->setMinimum(-999);
valuesSpinBox->setValue(42);
QFont f;
f.setPointSize(17);
f.setBold(true);
titleLabel = new QLabel("Jasper and Samuel David's\n Super-Cool Cartesian Tree Thingy");
titleLabel->setAlignment(Qt::AlignTop | Qt::AlignCenter);
titleLabel->setFont(f);
horizLayout->addWidget(insertButton);
horizLayout->addWidget(valuesSpinBox);
horizLayout->setAlignment(Qt::AlignTop | Qt::AlignCenter);
horizLayout->addWidget(searchButton);
horizLayout->addWidget(deleteKeyButton);
mainLayout->setAlignment(Qt::AlignTop | Qt::AlignCenter);
mainLayout->addWidget(titleLabel);
mainLayout->addLayout(horizLayout);
mainLayout->addWidget(sortButton);
mainWidget->setLayout(mainLayout);
setCentralWidget(mainWidget);
connect(insertButton,SIGNAL(clicked()),this,SLOT(insert()));
connect(deleteKeyButton, SIGNAL(clicked()), this, SLOT(removeKey()));
connect(sortButton, SIGNAL(clicked()), this, SLOT(sortem()));
connect(searchButton, SIGNAL(clicked()), this, SLOT(searchVal()));
treeWidget = new QWidget();
srand (time(NULL));
}
int main()
{
srand(time(0));
for(int n=0;n<25;n++)
{
x[n]=rand()%11;
}
sortem();
find_median();
find_mode();
histogram();
sortem();
cout<<"To see the data scroll, "<<endl;
system("pause");
scroll();
return 0;
}
int main(int argc, char **argv)
{
ScopedMPIComm< BamSortOptions > world(argc, argv);
Cleanup::prepare();
try {
int rank = world.rank(), size = world.size();
BamVector reads;
BamHeaderPtr header;
std::string outputBam = BamSortOptions::getOptions().getOutputBam();
std::string outputBamTmp = outputBam + ".tmp";
OptionsBaseInterface::FileListType inputBams = BamSortOptions::getOptions().getInputBams();
int partitions = BamSortOptions::getOptions().getNumPartitions();
if (partitions > 1) {
if (size != (int) inputBams.size()) {
if (rank == 0)
std::cerr << "The number of files is a mismatch to the job size. When merging partitions, this is necessary." << BamSortOptions::getDesc() << std::endl;
exit(1);
}
if (size % partitions != 0) {
if (rank == 0)
std::cerr << "The partitions " << partitions << " is not a factor of the size " << size << BamSortOptions::getDesc() << std::endl;
exit(1);
}
}
if (world.rank() == 0)
unlink(outputBamTmp.c_str());
world.barrier();
LOG_VERBOSE_GATHER(1, "Reading input files");
if (partitions > 1) {
std::string myInputFile = inputBams[rank];
int color = rank / partitions;
mpi::communicator partitionWorld = world.split(color);
LOG_VERBOSE_GATHER(1, "Input: " << myInputFile << " split color: " << color << " rank: " << partitionWorld.rank() << " of " << partitionWorld.size());
SamUtils::MPIMergeSam mergeSam(partitionWorld, myInputFile, reads);
if (color == 0)
mergeSam.outputMergedHeader(outputBamTmp);
world.barrier();
} else {
header = BamStreamUtils::readBamFile(world, inputBams, reads);
}
bool needsCollapse = false;
bool keepUnmappedPairedRead = BamSortOptions::getOptions().getKeepUnmappedPairedRead();
std::string unmappedReadPairFile = BamSortOptions::getOptions().getUnmappedReadPairs();
std::string unmappedReadsFile = BamSortOptions::getOptions().getUnmappedReads();
BamVector unmappedReadSingles, unmappedReadPairs, unmappedPairedReads;
if (!unmappedReadPairFile.empty() || !unmappedReadsFile.empty()) {
std::string tmpFile(unmappedReadPairFile + ".tmp");
std::string tmpFile2(unmappedReadsFile + ".tmp");
if (world.rank() == 0) {
unlink(tmpFile.c_str());
unlink(tmpFile2.c_str());
}
world.barrier();
SamUtils::splitUnmapped(reads, unmappedReadSingles, unmappedReadPairs, unmappedPairedReads, keepUnmappedPairedRead);
if (!unmappedReadSingles.empty() || !unmappedReadPairs.empty() || (!keepUnmappedPairedRead && !unmappedPairedReads.empty())) {
needsCollapse = true;
}
LOG_VERBOSE(1, "Purging unmapped read pairs: " << unmappedReadPairs.size());
if (!unmappedReadPairFile.empty() && unmappedReadPairFile.compare("/dev/null") != 0) {
LOG_VERBOSE(1, "Writing unmappedReadPairs " << unmappedReadPairs.size() << " to " << unmappedReadPairFile << " (" << tmpFile << ")");
ScopedMPIFile pairedReads(world, tmpFile);
SamUtils::writeFastqGz(world, unmappedReadPairs, pairedReads, true);
world.barrier();
}
assert(unmappedReadPairs.empty());
LOG_VERBOSE(1, "Purging unmapped read singles: " << unmappedPairedReads.size() << " and " << unmappedReadSingles.size());
if (!unmappedReadsFile.empty() && unmappedReadsFile.compare("/dev/null") != 0) {
LOG_VERBOSE(1, "Writing unmappedPairedReads " << unmappedPairedReads.size() << " to " << unmappedReadsFile << " (" << tmpFile2 << ")");
ScopedMPIFile singleReads(world, tmpFile2);
SamUtils::writeFastqGz(world, unmappedPairedReads, singleReads, !keepUnmappedPairedRead);
LOG_VERBOSE(1, "Writing unmappedReadSingles " << unmappedReadSingles.size() << " to " << unmappedReadsFile << " (" << tmpFile2 << ")");
SamUtils::writeFastqGz(world, unmappedReadSingles, singleReads, true);
world.barrier();
}
assert(unmappedReadSingles.empty());
assert(keepUnmappedPairedRead || unmappedPairedReads.empty());
if (world.rank() == 0) {
unlink(unmappedReadsFile.c_str());
unlink(unmappedReadPairFile.c_str());
rename(tmpFile.c_str(), unmappedReadPairFile.c_str());
if (tmpFile.compare(tmpFile2) != 0) {
rename(tmpFile2.c_str(), unmappedReadsFile.c_str());
}
}
}
if (needsCollapse) {
LOG_DEBUG(1, "Collapsing read vector");
long removed = SamUtils::collapseVector(reads);
LOG_DEBUG(1, "Collapsed: " << removed);
}
BamManager::destroyOrRecycleBamVector(unmappedReadSingles);
BamManager::destroyOrRecycleBamVector(unmappedReadPairs);
if (keepUnmappedPairedRead) {
unmappedPairedReads.clear();
} else {
BamManager::destroyOrRecycleBamVector(unmappedPairedReads);
}
{
LOG_VERBOSE_GATHER(1, "Redistributing reads before the sort:" << reads.size());
BamStreamUtils::distributeReadsFinal(world, reads);
LOG_VERBOSE_GATHER(1, "Sorting myreads: " << reads.size());
SamUtils::MPISortBam sortem(world, reads, outputBamTmp, header.get());
world.barrier();
if (world.rank() == 0) {
unlink(outputBam.c_str());
rename(outputBamTmp.c_str(), outputBam.c_str());
}
}
header.reset();
BamManager::clearRecycledReads();
LOG_VERBOSE_GATHER(1, "Finished");
return 0;
} catch (std::exception &e) {
LOG_ERROR(1, "BamSort-P threw an exception! Aborting...\n\t" << e.what());
world.abort(1);
} catch (...) {
LOG_ERROR(1, "BamSort-P threw an error! Aborting...\n");
world.abort(1);
}
}
