CallDiffResult.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_VARIANTS_CALLDIFFRESULT_HPP_
#define CGATOOLS_VARIANTS_CALLDIFFRESULT_HPP_ 1


#include "cgatools/core.hpp"
#include "cgatools/variants/Call.hpp"

namespace cgatools { namespace variants {

    struct CallDiffResult
    {
        enum MatchType
        {
            REF_IDENTICAL   = 0, 
            ALT_IDENTICAL   = 1, 
            REF_CONSISTENT  = 2, 
            ALT_CONSISTENT  = 3, 
            ONLY_A          = 4, 
            ONLY_B          = 5, 
            MISMATCH        = 6, 
            PHASE_MISMATCH  = 7, 
            PLOIDY_MISMATCH = 8, 
            MATCH_TYPE_LAST = 9
        };

        static MatchType mergeMatchTypes(MatchType mtA, MatchType mtB);

        static const char* getMatchTypeString(MatchType mt);

        static std::string getMatchTypeString(const std::vector<MatchType>& mt);

        static std::string getSimpleMatchTypeString(const std::vector<MatchType>& mt);

        size_t lhsOffset_;

        size_t rhsOffset_;

        std::vector<MatchType> matchType_;

        boost::array<std::vector< std::vector< std::pair<MatchType, const Call*> > >, 2> callClass_;

        std::vector<size_t> perm_;
    };

} } // cgatools::variants

#endif // CGATOOLS_VARIANTS_CALLDIFFRESULT_HPP_

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