assembly_checker.hpp

/**
 * Copyright 2014-2018 EMBL - European Bioinformatics Institute
 *
 * 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 VCF_ASSEMBLY_CHECKER_HPP
#define VCF_ASSEMBLY_CHECKER_HPP

#include <chrono>
#include <fstream>
#include <memory>
#include <set>
#include <vector>

#include <boost/filesystem.hpp>
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/log/trivial.hpp>

#include "assembly_report/assembly_report.hpp"

#include "bioio/bioio.hpp"

#include "fasta/fasta.hpp"
#include "util/file_utils.hpp"
#include "util/logger.hpp"
#include "util/stream_utils.hpp"
#include "util/string_utils.hpp"

#include "vcf/assembly_check_report_writer.hpp"
#include "vcf/compression.hpp"
#include "vcf/file_structure.hpp"
#include "vcf/normalizer.hpp"
#include "vcf/validator.hpp"


namespace ebi
{
  namespace vcf
  {
    namespace assembly_checker
    {

      bool check_vcf_ref(std::istream & vcf_input,
                         const std::string & sourceName,
                         const std::string & fasta,
                         const std::string & assembly_report,
                         std::vector<std::unique_ptr<ebi::vcf::AssemblyCheckReportWriter>> & outputs,
                         bool requireGenbank = false);

    }
  }
}

#endif // VCF_ASSEMBLY_CHECKER_HPP