Ejemplo n.º 1
0
void BitsetSaver::save(
    const std::vector<bool> &bits)
{
    char byte = 0;
    for (size_t i = 0; i < bits.size(); ++ i)
    {
        const unsigned shift = i % 8;
        const char positionHasNeighbors = bits[i];
        byte |= positionHasNeighbors << shift;
        if (7 == shift)
        {
            if (!os_.write(&byte, sizeof(byte)))
            {
                const boost::format message = boost::format("Failed to write bits into %s: %s") % filePath_.string() % strerror(errno);
                BOOST_THROW_EXCEPTION(common::IoException(errno, message.str()));
            }
            byte = 0;
        }
    }

    if (!os_.write(&byte, sizeof(byte)))
    {
        const boost::format message = boost::format("Failed to write final bits byte into %s: %s") % filePath_.string() % strerror(errno);
        BOOST_THROW_EXCEPTION(common::IoException(errno, message.str()));
    }
}
Ejemplo n.º 2
0
static std::vector<std::string > expandUseBasesMask (
    const std::vector<unsigned int> &readLengths,
    const std::string &useBasesMask,
    const boost::filesystem::path &baseCallsDirectory)
{
    std::vector<std::string > result;
    std::string::const_iterator parseIt(useBasesMask.begin());
    const std::string::const_iterator parseEnd(useBasesMask.end());
    UseBasesMaskGrammar<std::string::const_iterator> parser(readLengths);
    if (!boost::spirit::qi::parse(parseIt, parseEnd, parser, result) ||
        parseEnd != parseIt)
    {
        const boost::format message = boost::format("\n   *** Could not parse the use-bases-mask '%s' for '%s' at: %s ***\n") %
                useBasesMask % baseCallsDirectory.string() % useBasesMask.substr(parseIt - useBasesMask.begin());
        BOOST_THROW_EXCEPTION(common::InvalidOptionException(message.str()));
    }

    ISAAC_THREAD_CERR << "use bases mask: " << boost::algorithm::join(result, ",") << "\n";
    ISAAC_THREAD_CERR << "reads parsed: " << parser.currentRead_ << "\n";

    if (result.size() != readLengths.size())
    {
        const boost::format message = boost::format("\n   *** use-bases-mask '%s' is incompatible with number of reads (%d) in %s ***\n") %
                useBasesMask % readLengths.size() % baseCallsDirectory.string();
        BOOST_THROW_EXCEPTION(common::InvalidOptionException(message.str()));
    }

    return result;
}
Ejemplo n.º 3
0
void ExtractNeighborsWorkflow::scanMaskFile(
    const reference::SortedReferenceMetadata::MaskFile &maskFile,
    const std::vector<uint64_t> &contigOffsets,
    const std::vector<unsigned> &karyotypes,
    std::vector<bool> &neighbors,
    std::vector<bool> &highRepeats)
{
    if (!exists(maskFile.path))
    {
        const boost::format message = boost::format("Mask file %s does not exist: %s") % maskFile.path;
        BOOST_THROW_EXCEPTION(common::IoException(ENOENT, message.str()));
    }

    std::ifstream maskInput(maskFile.path.c_str());
    if (!maskInput)
    {
        const boost::format message = boost::format("Failed to open mask file %s for reading: %s") % maskFile.path % strerror(errno);
        BOOST_THROW_EXCEPTION(common::IoException(errno, message.str()));
    }

    std::size_t scannedKmers = 0, maskNeighbors = 0, maskNonHighRepeats = 0;
    while(maskInput)
    {
        reference::ReferenceKmer<KmerT> referenceKmer;
        if (maskInput.read(reinterpret_cast<char *>(&referenceKmer), sizeof(referenceKmer)))
        {
            ++scannedKmers;
            const reference::ReferencePosition pos = referenceKmer.getReferencePosition();
            if (!pos.isTooManyMatch())
            {
                const reference::ReferencePosition translatedPos = pos.translateContig(karyotypes);
                if (translatedPos.hasNeighbors())
                {
                    neighbors.at(contigOffsets.at(translatedPos.getContigId()) + translatedPos.getPosition()) = true;
                    ++maskNeighbors;
                }

                if (!highRepeats.empty())
                {
                    highRepeats.at(contigOffsets.at(translatedPos.getContigId()) + translatedPos.getPosition()) = false;
                }
                ++maskNonHighRepeats;
            }
        }
    }
    if (!maskInput.eof())
    {
        const boost::format message = boost::format("Failed to scan %s to the end") % maskFile.path % strerror(errno);
        BOOST_THROW_EXCEPTION(common::IoException(errno, message.str()));
    }
    else
    {
        ISAAC_THREAD_CERR << "Scanning " << maskFile.path << " found " << scannedKmers << " kmers of which " <<
            maskNeighbors << " neighbors and " << (scannedKmers - maskNonHighRepeats) << " high repeats" << std::endl;
    }
}
Ejemplo n.º 4
0
void vfeSession::AppendStatusMessage (const boost::format& fmt, int RecommendedPause)
{
  boost::mutex::scoped_lock lock(m_MessageMutex);

  m_StatusQueue.push (StatusMessage (*this, fmt.str(), RecommendedPause));
  m_StatusLineMessage = fmt.str();
  if (m_MaxStatusMessages != -1)
    while (m_StatusQueue.size() > m_MaxStatusMessages)
      m_StatusQueue.pop();
  NotifyEvent(stStatusMessage);
}
Ejemplo n.º 5
0
void FastaDumperOptions::postProcess(bpo::variables_map &vm)
{
    eagle::common::OptionsHelper check(vm);

    if (fastaFiles.empty())
    {
        throw bpo::validation_error(bpo::validation_error::at_least_one_value_required, "", "positional");
    }

    check.addPathOptions(fastaFiles,"positional");
    check.inputPathsExist();

    if ( 1 == fastaFiles.size() && bfs::is_directory(fastaFiles[0]) )
    {
        mode = WHOLE_DIR;
    } else {
        for (unsigned int i = 0; i < fastaFiles.size(); i++)
        {
            if (bfs::is_directory(fastaFiles[i]))
            {
                const boost::format message = boost::format("\n   *** FASTA file #%d has an invalid value: ***"
                                                            "\n   ***       It should point to a file, but a directory already exists with name %s ***\n")
                                                            % i % fastaFiles[i];
                BOOST_THROW_EXCEPTION(eagle::common::InvalidOptionException(message.str()));
            }
        }
        mode = SAFE_MODE;
    }

    check.inRange<unsigned long>(std::make_pair(size,"size"),1);  // 1 <= size < inf
                                                                  // (size == 0) not allowed, so internally used to represent 'until the end'
}
Ejemplo n.º 6
0
	hpgl_exception::hpgl_exception(
		const std::string & a_where, 
		const boost::format & what)
			:m_where(a_where), m_what(what.str())
		{
			m_message = m_where + ": " + m_what;
			//std::cerr << m_message << std::endl;
		}
Ejemplo n.º 7
0
 error::error(
     bool          _status,
     long long     _code,
     boost::format _msg,
     std::string   _file,
     int           _line,
     std::string   _fcn ) :
     error::error( _status, _code, _msg.str(), _file, _line, _fcn ) {}
Ejemplo n.º 8
0
void Logger::log(
    const Level& level,
    const boost::format& message,
    const std::string& filename,
    const int& lineNumber
)
{
    log( level, message.str(), filename, lineNumber );
}
Ejemplo n.º 9
0
  bs_exception::bs_exception (const std::string &who, const boost::format &message)
  : who_ (who),
  what_ (who_ + ": " + message.str ()),
  m_err_ (user_defined)
  {
#ifdef BS_EXCEPTION_COLLECT_BACKTRACE
    what_ += detail::collect_backtrace ();
#endif
  }
Ejemplo n.º 10
0
void Log::Debug( boost::format &fmt )
{
	int ConsoleLogLevel = sConfig.GetIntDefault("Log.ConsoleLogLevel",LOGLEVEL_INFO);
	int FileLogLevel = sConfig.GetIntDefault("Log.FileLogLevel",LOGLEVEL_WARNING);

	if (ConsoleLogLevel >= LOGLEVEL_DEBUG || FileLogLevel >= LOGLEVEL_DEBUG)
	{
		Debug(fmt.str());
	}
}
Ejemplo n.º 11
0
void Trace::send(const boost::format& str, TraceLevelOptions level)
{
    if (not Trace::Pimpl::mTrace) {
        Trace::init();
    }

    boost::mutex::scoped_lock lock(Trace::Pimpl::mTrace->getMutex());

    Pimpl::mTrace->send(str.str(), level);
}
Ejemplo n.º 12
0
void chronometer_t::event_dumb(boost::format const& params) {
    if (is_dumb) {
        if (!log_ptr) {
            log_ptr = logger::instance();
        }
        if (log_ptr) {
            log_ptr->debug("raw/begin/" + name, params.str());
        }
    }
}
Ejemplo n.º 13
0
void Log::Critical( boost::format &fmt )
{
	int ConsoleLogLevel = sConfig.GetIntDefault("Log.ConsoleLogLevel",LOGLEVEL_INFO);
	int FileLogLevel = sConfig.GetIntDefault("Log.FileLogLevel",LOGLEVEL_WARNING);

	if (ConsoleLogLevel >= LOGLEVEL_CRITICAL || FileLogLevel >= LOGLEVEL_CRITICAL)
	{
		Critical(fmt.str());
	}
}
Ejemplo n.º 14
0
void Log::Error( boost::format &fmt )
{
	int ConsoleLogLevel = sConfig.GetIntDefault("Log.ConsoleLogLevel",LOGLEVEL_INFO);
	int FileLogLevel = sConfig.GetIntDefault("Log.FileLogLevel",LOGLEVEL_WARNING);

	if (ConsoleLogLevel >= LOGLEVEL_ERROR || FileLogLevel >= LOGLEVEL_ERROR)
	{
		Error(fmt.str());
	}
}
Ejemplo n.º 15
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BitsetSaver::BitsetSaver(const boost::filesystem::path filePath) :
    filePath_(filePath),
    os_(filePath.c_str())
{
    if (!os_)
    {
        const boost::format message = boost::format("Failed to open file %s for writing: %s") % filePath_ % strerror(errno);
        BOOST_THROW_EXCEPTION(common::IoException(errno, message.str()));
    }
}
Ejemplo n.º 16
0
flowcell::Layout FastqFlowcell::createFilteredFlowcell(
    const std::string &tilesFilter,
    const boost::filesystem::path &baseCallsDirectory,
    const bool compressed,
    const unsigned laneNumberMax,
    const unsigned readNameLength,
    std::string useBasesMask,
    const bool allowVariableFastqLength,
    const char fastqQ0,
    const std::string &seedDescriptor,
    const unsigned seedLength,
    const reference::ReferenceMetadataList &referenceMetadataList,
    unsigned &firstPassSeeds)
{

    FastqPathPairList flowcellFilePaths = findFastqPathPairs(compressed, laneNumberMax, baseCallsDirectory);
    if (flowcellFilePaths.empty())
    {
        const boost::format message = boost::format("\n   *** Could not find any fastq lanes in: %s ***\n") %
            baseCallsDirectory;
        BOOST_THROW_EXCEPTION(common::InvalidOptionException(message.str()));
    }

    FastqFlowcellInfo flowcellInfo = parseFastqFlowcellInfo(flowcellFilePaths, allowVariableFastqLength, fastqQ0, readNameLength);

    std::vector<unsigned int> readLengths;
    if (flowcellInfo.readLengths_.first)
    {
        readLengths.push_back(flowcellInfo.readLengths_.first);
    }
    if (flowcellInfo.readLengths_.second)
    {
        readLengths.push_back(flowcellInfo.readLengths_.second);
    }

    if ("default" == useBasesMask)
    {
        if (readLengths.size() == 1)
        {
            useBasesMask = "y*n";
        }
        else if (readLengths.size() == 2)
        {
            useBasesMask = "y*n,y*n";
        }
        else
        {
            const boost::format message =
                boost::format("\n   *** Could not guess the use-bases-mask for '%s', please supply the explicit value ***\n") %
                baseCallsDirectory.string();
            BOOST_THROW_EXCEPTION(common::InvalidOptionException(message.str()));
        }
    }

    std::vector<unsigned int> readFirstCycles;

    ParsedUseBasesMask parsedUseBasesMask;
    alignment::SeedMetadataList seedMetadataList;
    if (!readLengths.empty())
    {
        parsedUseBasesMask = parseUseBasesMask(readFirstCycles, readLengths, seedLength, useBasesMask, baseCallsDirectory);
        seedMetadataList = parseSeedDescriptor(parsedUseBasesMask.dataReads_, seedDescriptor, seedLength, firstPassSeeds);
    }

    flowcell::Layout fc(baseCallsDirectory,
                        flowcell::Layout::Fastq,
                        flowcell::FastqFlowcellData(compressed, fastqQ0),
                        laneNumberMax,
                        flowcellInfo.readNameLength_,
                        std::vector<unsigned>(),
                        parsedUseBasesMask.dataReads_,
                        seedMetadataList, flowcellInfo.flowcellId_);

    std::string regexString(tilesFilter);
    std::replace(regexString.begin(), regexString.end(), ',', '|');
    boost::regex re(regexString);
    BOOST_FOREACH(const unsigned int lane, flowcellInfo.getLanes())
    {
        std::string laneString((boost::format("s_%d") % lane).str());
        if (boost::regex_search(laneString, re))
        {
            fc.addTile(lane, 1);
        }
    }

    return fc;
}
Ejemplo n.º 17
0
 code_generation_error(std::string const& generator_name, boost::format const& format) noexcept
     : code_generation_error(generator_name, format.str())
 {}
Ejemplo n.º 18
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// error processing
void ObjectManager::error(boost::format err) {
	cout << err.str() << endl;
	assert(false);
}
Ejemplo n.º 19
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 std::string String() const { return format.str(); }  
Ejemplo n.º 20
0
 void NextArg()
 {
   if (output) output(format.str());
 }
Ejemplo n.º 21
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 void debug(const boost::format &msg) { category.debug(msg.str()); }
Ejemplo n.º 22
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 void notice(const boost::format &msg) { category.notice(msg.str()); }
Ejemplo n.º 23
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 bs_kernel_exception::bs_kernel_exception (const std::string &who, error_code ec, const boost::format &message)
 : bs_exception (who, message.str () + ". BlueSky error: " + bs_error_message (ec))
 {
   m_err_ = ec;
 }
Ejemplo n.º 24
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 LoadException(const boost::format &msg)
     : Exception(msg.str()) { }
Ejemplo n.º 25
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 bs_dynamic_lib_exception::bs_dynamic_lib_exception (const boost::format &who)
 : bs_exception (who.str (), "System error: " + dynamic_lib_error_message ())
 {
   m_err_ = user_defined;
 }
Ejemplo n.º 26
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 CUException(const boost::format &format) : Exception(format.str()) { }
Ejemplo n.º 27
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 inline LogManagerItem(Level level, Time time, const std::string &sender, const boost::format &format) :
     m_level(level), m_time(time), m_sender(sender), m_content(format.str()) { }
Ejemplo n.º 28
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 void info(const boost::format &msg) { category.info(msg.str()); }
Ejemplo n.º 29
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 bs_system_exception::bs_system_exception (const std::string &who, error_code ec, const boost::format &message)
 : bs_exception (who, message.str () + ". System error: " + system_message (ec))
 {
   m_err_ = ec;
 }
Ejemplo n.º 30
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 Exception(const boost::format &msg)
     : m_msg(msg.str()) { }