BaseUtil.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_UTIL_BASEUTIL_HPP_
#define CGATOOLS_UTIL_BASEUTIL_HPP_ 1


#include "cgatools/core.hpp"
#include <string>

namespace cgatools { namespace util { namespace baseutil {

    extern char BASE_COMPATIBILITY[256];
    extern char BASE_COMPLEMENT[256];

    bool isValidBase(char base);

    bool isCalledSequence(const std::string& sequence);

    bool isCalledSequence(const std::string& sequence, size_t start, size_t end);

    bool isValidIupacCode(char iupacCode);

    uint32_t pack(char base);

    char unpack(uint32_t packedBase);

    char disambiguate(char iupacCode);

    inline bool isConsistent(char lhs, char rhs)
    {
        return 0 != ( BASE_COMPATIBILITY[uint8_t(lhs)] &
                      BASE_COMPATIBILITY[uint8_t(rhs)] );
    }

    bool isConsistent(const std::string& lhs, const std::string& rhs);

    bool isConsistent(const std::string& lhs, size_t lhsStart, size_t lhsEnd,
                      const std::string& rhs, size_t rhsStart, size_t rhsEnd);

    char complement(char iupacCode);

    std::string reverseComplement(const std::string& sequence);

} } } // cgatools::util::baseutil

#endif // CGATOOLS_UTIL_BASEUTIL_

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