CompactDnaSequence.hpp

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// 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_REFERENCE_COMPACTDNASEQUENCE_HPP_
#define CGATOOLS_REFERENCE_COMPACTDNASEQUENCE_HPP_ 1


#include "cgatools/core.hpp"
#include "cgatools/util/Streams.hpp"
#include "cgatools/util/Md5.hpp"

#include <vector>
#include <string>

namespace cgatools { namespace reference {

    struct AmbiguousRegion
    {
        AmbiguousRegion()
            : code_('N'),
              offset_(0),
              length_(0)
        {
        }

        AmbiguousRegion(char code, uint32_t pos, uint32_t length)
            : code_(code),
              offset_(pos),
              length_(length)
        {
        }

        char code_;       
        uint32_t offset_; 
        uint32_t length_; 
    };

    class CompactDnaSequence
    {
    public:
        CompactDnaSequence(const std::string& name,
                           bool circular,
                           const void* packedData,
                           const util::Md5Digest& md5,
                           size_t length,
                           const std::vector<AmbiguousRegion> amb);

        std::string getSequence            (int64_t pos, int64_t length) const;

        std::string getUnambiguousSequence(int64_t pos, int64_t length) const;

        void appendSequence            (std::string& seq, int64_t pos, int64_t length) const;

        void appendUnambiguousSequence(std::string& seq, int64_t pos, int64_t length) const;

        char getBase(int64_t pos) const;

        char getUnambiguousBase(int64_t pos) const;

        size_t extendLeftBy3Mers (size_t pos, size_t count) const;

        size_t extendRightBy3Mers(size_t pos, size_t count) const;

        void validate() const;

        const std::string& getName() const
        {
            return name_;
        }

        bool isCircular() const
        {
            return circular_;
        }

        const util::Md5Digest& getMd5Digest() const
        {
            return md5_;
        }

        size_t length() const
        {
            return length_;
        }

        const std::vector<AmbiguousRegion>& getAmbiguousRegions() const
        {
            return amb_;
        }

    private:
        inline int64_t fixCircularPos(int64_t pos) const;
        void applyAmbiguity(char* seq, int64_t pos, int64_t length) const;

        std::string name_;
        bool circular_;
        const uint8_t* packedData_;
        util::Md5Digest md5_;
        int64_t length_;
        std::vector<AmbiguousRegion> amb_;
    };

} } // cgatools::reference

#endif // CGATOOLS_REFERENCE_COMPACTDNASEQUENCE_HPP_

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