ReferenceSupportReader.hpp

Go to the documentation of this file.

// Copyright 2010 Complete Genomics, Inc.
//
// Licensed under the Apache License, Version 2.0 (the "License"); you
// may not use this file except in compliance with the License. You
// may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
// implied. See the License for the specific language governing
// permissions and limitations under the License.

#ifndef CGATOOLS_CGDATA_REFERENCESUPPORTREADER_HPP_
#define CGATOOLS_CGDATA_REFERENCESUPPORTREADER_HPP_ 1


#include "cgatools/core.hpp"
#include "cgatools/util/Streams.hpp"
#include "cgatools/util/DelimitedFile.hpp"
#include "cgatools/reference/CrrFile.hpp"
#include "cgatools/cgdata/GenomeMetadata.hpp"

#include <limits>
#include <boost/noncopyable.hpp>
#include <boost/scoped_ptr.hpp>
#include <boost/shared_ptr.hpp>

namespace cgatools { namespace cgdata {

    class ReferenceSupportReader : boost::noncopyable
    {
    public:
        ReferenceSupportReader(const reference::CrrFile& crr,
                               const GenomeMetadata& exp);

        void seek(const reference::Range& r);

        int32_t getMinScore(const reference::Range& r,
                            int32_t noDataValue =
                                std::numeric_limits<int32_t>::min() ) const;

        int32_t getMaxWeightedCoverage(const reference::Range& r,
                                       int32_t noDataValue = 0) const;

    private:
        struct File
        {
            std::string filename_;
            boost::shared_ptr<std::istream> f_;
            util::DelimitedFile parser_;
            bool hasWeightedCoverage_;
            uint32_t offset_;
            int32_t score_;
            int32_t uniqueCoverage_;
            int32_t weightedCoverage_;

            File(const std::string& fn);
        };

        struct DataItem
        {
            bool hasData_;
            int32_t score_;
            int32_t uniqueCoverage_;
            int32_t weightedCoverage_;

            DataItem() : hasData_(false), score_(0) {}
        };

        const reference::CrrFile& crr_;
        const GenomeMetadata& exp_;

        uint16_t chromosome_;
        uint32_t bufferStartOffset_;
        std::vector<DataItem> buffer_;
        boost::scoped_ptr<File> file_;

        void checkRange(const reference::Range& r) const;
    };

} } // cgatools::cgdata

#endif // CGATOOLS_CGDATA_REFERENCESUPPORTREADER_HPP_

---