Var2Vcf.hpp

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// Copyright 2011 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 CGA_TOOLS_COMMAND_VAR2VCF_HPP_
#define CGA_TOOLS_COMMAND_VAR2VCF_HPP_ 1


#include "cgatools/core.hpp"
#include "cgatools/command/Command.hpp"
#include "cgatools/reference/CrrFile.hpp"
#include "cgatools/variants/VariantFileIterator.hpp"
#include "cgatools/variants/SuperlocusIterator.hpp"

namespace cgatools { namespace command {

    class LocusVcfConverter;

    class Var2Vcf : public Command
    {
    public:
        Var2Vcf(const std::string& name);

    protected:
        int run(po::variables_map& vm);
        
    private:
        void writeHeader(
            std::ostream& out,
            LocusVcfConverter& conv) const;
        void writeRecord(
            std::ostream& out,
            LocusVcfConverter& conv) const;
        void writeNoCallRecord(
            std::ostream& out,
            LocusVcfConverter& conv) const;
        void splitForVcf(
            const cgatools::variants::Superlocus& sl,
            std::vector<cgatools::reference::Range>& ranges) const;
        void addVariantRanges(
            std::vector<cgatools::reference::Range>& ranges,
            const std::pair<std::deque<cgatools::variants::Locus>::const_iterator,
                            std::deque<cgatools::variants::Locus>::const_iterator>& loci) const;
        void addNoCallSplits(
            std::vector<uint32_t>& ncSplits,
            const std::pair<std::deque<cgatools::variants::Locus>::const_iterator,
            std::deque<cgatools::variants::Locus>::const_iterator>& loci) const;
        void splitAndAddRange(
            std::vector<cgatools::reference::Range>& ranges,
            const cgatools::reference::Range& range,
            const std::vector<uint32_t>& ncSplits) const;
        void phaseHaplotypes(
            const cgatools::variants::Superlocus& sl,
            std::vector<cgatools::variants::PhasedHypothesis>& hyp) const;
        int scoreHypothesis(
            const cgatools::variants::PhasedHypothesis& hyp,
            const std::set<std::string>& popAlleles) const;
        void addPopAlleles(
            const cgatools::variants::PhasedHypothesis& hyp,
            std::set<std::string>& popAlleles) const;
        std::string getVcfChromosomeName(
            size_t chromosomeId) const;
        std::string getReferenceBuild() const;
        void transferSource(
            std::ostream& out) const;
        void transferMetadataHeader(
            std::ostream& out,
            const std::string& key,
            bool mustExist,
            bool mustBeUnique) const;

        std::string referenceFileName_;
        std::string outputFileName_;
        std::vector<std::string> variantFileNames_;
        bool includeNoCalls_;

        cgatools::reference::CrrFile crr_;
        std::vector< boost::shared_ptr<cgatools::variants::VariantFileIterator> > var_;
    };

} } // cgatools::command

#endif // CGA_TOOLS_COMMAND_VAR2VCF_HPP_

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