Common::String SciEngine::unwrapFilename(const Common::String &name) const {
Common::String prefix = getFilePrefix() + "-";
if (name.hasPrefix(prefix.c_str()))
return Common::String(name.c_str() + prefix.size());
else
return name;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void WriteImages::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setImagePrefix( reader->readString("ImagePrefix", getImagePrefix()) );
setFilePrefix( reader->readValue("FilePrefix", getFilePrefix()) );
setOutputPath( reader->readString("OutputPath", getOutputPath()) );
setColorsArrayPath( reader->readDataArrayPath("ColorsArrayPath", getColorsArrayPath()) );
setImageFormat( reader->readValue("ImageFormat", getImageFormat()) );
setPlane(reader->readValue("Plane", getPlane()));
reader->closeFilterGroup();
}
Common::String SciEngine::wrapFilename(const Common::String &name) const {
return getFilePrefix() + "-" + name;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void WriteImages::setupFilterParameters()
{
FilterParameterVector parameters;
{
ChoiceFilterParameter::Pointer parameter = ChoiceFilterParameter::New();
parameter->setHumanLabel("Image Format");
parameter->setPropertyName("ImageFormat");
QVector<QString> choices;
choices.push_back("tif");
choices.push_back("bmp");
choices.push_back("png");
parameter->setChoices(choices);
parameter->setCategory(FilterParameter::Parameter);
parameters.push_back(parameter);
}
{
ChoiceFilterParameter::Pointer parameter = ChoiceFilterParameter::New();
parameter->setHumanLabel("Plane");
parameter->setPropertyName("Plane");
QVector<QString> choices;
choices.push_back("XY");
choices.push_back("XZ");
choices.push_back("YZ");
parameter->setChoices(choices);
parameter->setCategory(FilterParameter::Parameter);
parameters.push_back(parameter);
}
{
QStringList linkedProps;
linkedProps << "ImagePrefix";
parameters.push_back(LinkedBooleanFilterParameter::New("File Prefix", "FilePrefix", getFilePrefix(), linkedProps, FilterParameter::Parameter));
}
parameters.push_back(OutputPathFilterParameter::New("Output Directory Path", "OutputPath", getOutputPath(), FilterParameter::Parameter));
parameters.push_back(StringFilterParameter::New("Image File Prefix", "ImagePrefix", getImagePrefix(), FilterParameter::Parameter));
parameters.push_back(SeparatorFilterParameter::New("Cell Data", FilterParameter::RequiredArray));
parameters.push_back(DataArraySelectionFilterParameter::New("Color Data", "ColorsArrayPath", getColorsArrayPath(), FilterParameter::RequiredArray));
setFilterParameters(parameters);
}
int main(int argc, char const * argv[])
{
// Additional checks
seqan::ArgumentParser parser = buildParser();
seqan::ArgumentParser::ParseResult res = seqan::parse(parser, argc, argv);
// Check if input was successfully parsed.
if (res != seqan::ArgumentParser::PARSE_OK)
return res == seqan::ArgumentParser::PARSE_ERROR;
// Check if one or two input files (single or paired-end) were given.
int fileCount = getArgumentValueCount(parser, 0);
if (fileCount < 1) {
printShortHelp(parser);
return 1;
}
unsigned int radius = 1;
getOptionValue(radius, parser, "r");
seqan::CharString readsFileName;
getOptionValue(readsFileName, parser, "i");
// Open input file, BamFileIn can read SAM and BAM files.
seqan::BamFileIn bamFileIn(seqan::toCString(readsFileName));
seqan::CharString _filterChromosomes;
seqan::getOptionValue(_filterChromosomes, parser, "fc");
std::string filterChromosomes = seqan::toCString(_filterChromosomes);
OccurenceMap occurenceMap;
Statistics stats;
std::cout << "read bam file... ";
auto t1 = std::chrono::steady_clock::now();
seqan::BamAlignmentRecord record;
seqan::BamHeader header;
readHeader(header, bamFileIn);
const auto chromosomeFilterSet = calculateChromosomeFilter(filterChromosomes, contigNames(context(bamFileIn)));
const auto chromosomes = contigNames(context(bamFileIn));
processBamFile(bamFileIn, chromosomeFilterSet, occurenceMap, stats);
auto t2 = std::chrono::steady_clock::now();
std::cout << std::chrono::duration_cast<std::chrono::duration<float>>(t2 - t1).count() << "s" << std::endl;
std::vector<std::pair<unsigned int, unsigned int>> hits(radius * 2 + 1);
t1 = std::chrono::steady_clock::now();
std::cout << "calculating 5'-ends around peaks... ";
for (unsigned int fileIndex = 0;fileIndex < static_cast<unsigned int>(fileCount); ++fileIndex)
{
seqan::CharString fileName_;
getArgumentValue(fileName_, parser, fileIndex, 0);
const std::string fileName = seqan::toCString(fileName_);
std::ifstream infile(fileName);
std::string chromosome, dummy;
unsigned int start, end;
while (infile >> chromosome >> start >> end >> dummy)
{
int rID = -1;
for (unsigned int i = 0;i < length(chromosomes);++i)
if (chromosomes[i] == chromosome)
{
rID = i;
break;
}
if (rID == -1)
{
std::cout << "invalid chromosome name: " << chromosome << " in file " << fileName << std::endl;
return -1;
}
seqan::BamAlignmentRecord record;
record.beginPos = std::max<int>(start - radius, 0);
record.rID = rID;
record.flag = 0;
unsigned int index = 0;
if (start < radius)
index += radius - start;
while (record.beginPos <= static_cast<__int32>(start + radius))
{
BamRecordKey<NoBarcode> pos(record);
auto el = occurenceMap.find(pos);
if(el != occurenceMap.end())
hits[index].first += el->second;
pos.init(pos.getRID(), pos.get5EndPosition(), true);
el = occurenceMap.find(pos);
if (el != occurenceMap.end())
hits[index].second += el->second;
++record.beginPos;
++index;
}
}
std::string outFilename = getFilePrefix(fileName) + std::string("_5PrimeEnds.tab");
if (seqan::isSet(parser, "o"))
{
seqan::CharString outFileName_;
getOptionValue(outFileName_, parser, "o");
outFilename = seqan::toCString(outFileName_);
}
std::fstream fs;
std::cout << "writing " << outFilename << std::endl;
#ifdef _MSC_VER
fs.open(outFilename, std::fstream::out, _SH_DENYNO);
#else
fs.open(outFilename, std::fstream::out);
#endif
int i = - static_cast<int>(radius);
for (const auto& hit : hits)
fs << i++ << "\t" << hit.first << "\t" << hit.second << std::endl;
fs.close();
}
t2 = std::chrono::steady_clock::now();
std::cout << std::chrono::duration_cast<std::chrono::duration<float>>(t2 - t1).count() << "s" << std::endl;
return 0;
}
