void ContigsPrinter::run()
{
SortedReferenceMetadata::Contigs originalContigs;
if (!originalSortedReferenceXml_.empty())
{
SortedReferenceMetadata inXml(reference::loadSortedReferenceXml(originalSortedReferenceXml_));
originalContigs = inXml.getContigs();
}
SortedReferenceMetadata::Contigs outputContigs;
std::ifstream is(genomeFile_.string().c_str());
if (!is) {
BOOST_THROW_EXCEPTION(isaac::common::IoException(errno, "Failed to open reference file " + genomeFile_.string()));
}
int64_t lastAcgtCount(0), lastBasesCount(0), lastContigByteStart(0), lineNumber(0), lastContigGenomicStart(0), streamPos(0);
unsigned index = 0;
std::string lastHeader, line;
SortedReferenceMetadata outXml;
isaac::common::MD5Sum md5Sum;
// TODO: use the MultiFastaReader component to ensure consistency (particularly for the index)
while (std::getline(is, line))
{
streamPos = is.tellg();
++lineNumber;
if ('>' == line[0])
{
std::cerr << "header at:" << streamPos << "\n";
if (!lastHeader.empty())
{
const std::string contigName = lastHeader.substr(1, lastHeader.find_first_of(" \t\r") - 1);
SortedReferenceMetadata::Contigs::const_iterator originalContigIt =
std::find_if(originalContigs.begin(), originalContigs.end(), boost::bind(&SortedReferenceMetadata::Contig::name_, _1) == contigName);
outXml.putContig(lastContigGenomicStart,
contigName,
genomeFile_,
lastContigByteStart,
streamPos - lastContigByteStart - (1 + line.length()), //byte length (assuming newline is one byte long)
lastBasesCount, lastAcgtCount, index, index,
(originalContigs.end() == originalContigIt ? "" : originalContigIt->bamSqAs_),
(originalContigs.end() == originalContigIt ? "" : originalContigIt->bamSqUr_),
isaac::common::MD5Sum::toHexString( md5Sum.getDigest().data, 16 ));
++index;
}
// Reset counters
lastAcgtCount = 0;
lastHeader = line;
lastContigByteStart = streamPos;
lastContigGenomicStart += lastBasesCount;
lastBasesCount = 0;
md5Sum.clear();
}
else
{
lastAcgtCount += std::count_if(line.begin(), line.end(), boost::bind(&oligo::getValue, _1) != oligo::INVALID_OLIGO);
// ignore untranslated '\r'
lastBasesCount += std::count_if(line.begin(), line.end(),
[](char c){return c != '\r';});
// boost::bind(&boost::ref<char>, _1) != '\r');
// MD5 with format characters stripped out
std::string lineStd = line;
boost::to_upper(lineStd);
lineStd.erase(std::remove_if(lineStd.begin(), lineStd.end(), &isspace), lineStd.end()); // isspace should remove ' ', '\n', '\r', '\t'
md5Sum.update( lineStd.c_str(), lineStd.size() );
}
}
if (!is.eof()) {
BOOST_THROW_EXCEPTION(
isaac::common::IoException(errno, "Failed while reading sequence."
" Line:" + boost::lexical_cast<std::string>(lineNumber)
+ " Position:" + boost::lexical_cast<std::string>(is.tellg())
+ " Buffer:" + line + "\n"));
}
std::cerr << "end of stream at:" << streamPos << "\n";
if (!lastHeader.empty())
{
const std::string contigName = lastHeader.substr(1, lastHeader.find_first_of(" \t\r") - 1);
SortedReferenceMetadata::Contigs::const_iterator originalContigIt =
std::find_if(originalContigs.begin(), originalContigs.end(), boost::bind(&SortedReferenceMetadata::Contig::name_, _1) == contigName);
outXml.putContig(lastContigGenomicStart,
contigName,
genomeFile_,
lastContigByteStart,
streamPos - lastContigByteStart, //byte length
lastBasesCount, lastAcgtCount, index, index,
(originalContigs.end() == originalContigIt ? "" : originalContigIt->bamSqAs_),
(originalContigs.end() == originalContigIt ? "" : originalContigIt->bamSqUr_),
isaac::common::MD5Sum::toHexString( md5Sum.getDigest().data, 16 ));
++index;
}
saveSortedReferenceXml(std::cout, outXml);
}
//
// This stream buffer does not support seeking.
//
EXPORT_C TStreamPos MStreamBuf::DoSeekL(TMark,TStreamLocation,TInt)
{
Panic(EStreamCannotSeek);
TStreamPos streamPos(-1);
return streamPos;
}
void Plots::changeOrder(QList<std::tuple<int, int> > orderedFilterInfo)
{
if(orderedFilterInfo.empty())
{
qDebug() << "orderedFilterInfo is empty, do not reorder..";
return;
}
qDebug() << "changeOrder: items = " << orderedFilterInfo.count();
auto gridLayout = static_cast<QGridLayout*> (layout());
auto rowsCount = gridLayout->rowCount();
Q_ASSERT(m_plotsCount <= rowsCount);
qDebug() << "plotsCount: " << m_plotsCount;
QList <std::tuple<size_t, size_t, size_t>> currentOrderedPlotsInfo;
QList <std::tuple<size_t, size_t, size_t>> expectedOrderedPlotsInfo;
for(auto row = 0; row < m_plotsCount; ++row)
{
auto plotItem = gridLayout->itemAtPosition(row, 0);
auto legendItem = gridLayout->itemAtPosition(row, 1);
Q_ASSERT(plotItem);
Q_ASSERT(legendItem);
auto plot = qobject_cast<Plot*> (plotItem->widget());
Q_ASSERT(plot);
currentOrderedPlotsInfo.push_back(std::make_tuple(plot->group(), plot->type(), plot->streamPos()));
}
for(auto filterInfo : orderedFilterInfo)
{
for(auto plotInfo : currentOrderedPlotsInfo)
{
if(std::get<0>(plotInfo) == std::get<0>(filterInfo) && std::get<1>(plotInfo) == std::get<1>(filterInfo))
{
expectedOrderedPlotsInfo.push_back(plotInfo);
}
}
}
Q_ASSERT(currentOrderedPlotsInfo.length() == expectedOrderedPlotsInfo.length());
if(currentOrderedPlotsInfo.length() != expectedOrderedPlotsInfo.length())
return;
for(auto i = 0; i < expectedOrderedPlotsInfo.length(); ++i)
{
qDebug() << "cg: " << std::get<0>(currentOrderedPlotsInfo[i])
<< ", "
<< "ct: " << std::get<1>(currentOrderedPlotsInfo[i])
<< ", "
<< "cp: " << std::get<2>(currentOrderedPlotsInfo[i])
<< ", "
<< "eg: " << std::get<0>(expectedOrderedPlotsInfo[i])
<< ", "
<< "et: " << std::get<1>(expectedOrderedPlotsInfo[i])
<< ", "
<< "ep: " << std::get<2>(expectedOrderedPlotsInfo[i]);
}
for(auto i = 0; i < expectedOrderedPlotsInfo.length(); ++i)
{
if(expectedOrderedPlotsInfo[i] != currentOrderedPlotsInfo[i])
{
// search current item which we should put at expected position
for(auto j = 0; j < expectedOrderedPlotsInfo.length(); ++j)
{
if(expectedOrderedPlotsInfo[i] == currentOrderedPlotsInfo[j])
{
qDebug() << "i: " << i << ", j: " << j;
auto plotWidget = gridLayout->itemAtPosition(j, 0)->widget();
auto legendWidget = gridLayout->itemAtPosition(j, 1)->widget();
{
auto plot = qobject_cast<Plot*> (plotWidget);
qDebug() << "jg: " << plot->group() << ", t: " << plot->type() << ", p: " << plot->streamPos() << ", ptr = " << plot;
}
auto swapPlotWidget = gridLayout->itemAtPosition(i, 0)->widget();
auto swapLegendWidget = gridLayout->itemAtPosition(i, 1)->widget();
{
auto plot = qobject_cast<Plot*> (swapPlotWidget);
qDebug() << "ig: " << plot->group() << ", t: " << plot->type() << ", p: " << plot->streamPos() << ", ptr = " << plot;
}
gridLayout->removeWidget(plotWidget);
gridLayout->removeWidget(legendWidget);
gridLayout->removeWidget(swapPlotWidget);
gridLayout->removeWidget(swapLegendWidget);
gridLayout->addWidget(plotWidget, i, 0);
gridLayout->addWidget(legendWidget, i, 1);
gridLayout->addWidget(swapPlotWidget, j, 0);
gridLayout->addWidget(swapLegendWidget, j, 1);
currentOrderedPlotsInfo[j] = currentOrderedPlotsInfo[i];
currentOrderedPlotsInfo[i] = expectedOrderedPlotsInfo[i];
break;
}
}
}
}
Q_ASSERT(rowsCount == gridLayout->rowCount());
for(auto row = 0; row < m_plotsCount; ++row)
{
auto plotItem = gridLayout->itemAtPosition(row, 0);
auto legendItem = gridLayout->itemAtPosition(row, 1);
Q_ASSERT(plotItem);
Q_ASSERT(legendItem);
auto plot = qobject_cast<Plot*> (plotItem->widget());
Q_ASSERT(plot);
Q_ASSERT(plot->group() == std::get<0>(expectedOrderedPlotsInfo[row]) &&
plot->type() == std::get<1>(expectedOrderedPlotsInfo[row]));
}
}
