variant_input_stream_adapters.hpp

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#ifndef GENESIS_POPULATION_STREAM_VARIANT_INPUT_STREAM_ADAPTERS_H_
#define GENESIS_POPULATION_STREAM_VARIANT_INPUT_STREAM_ADAPTERS_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2024 Lucas Czech
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lucas.czech@sund.ku.dk>
    University of Copenhagen, Globe Institute, Section for GeoGenetics
    Oster Voldgade 5-7, 1350 Copenhagen K, Denmark
*/
 
#include "genesis/population/genome_locus_set.hpp"
#include "genesis/population/sample_counts.hpp"
#include "genesis/population/stream/variant_gapless_input_stream.hpp"
#include "genesis/population/stream/variant_input_stream_sources.hpp"
#include "genesis/population/stream/variant_input_stream.hpp"
#include "genesis/population/stream/variant_parallel_input_stream.hpp"
#include "genesis/population/variant.hpp"
#include "genesis/sequence/reference_genome.hpp"
#include "genesis/sequence/sequence_dict.hpp"
#include "genesis/utils/containers/generic_input_stream.hpp"
 
#include <cassert>
#include <functional>
#include <stdexcept>
#include <string>
#include <unordered_map>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Variant Parallel Input Stream
// =================================================================================================
 
VariantInputStream make_variant_input_stream_from_variant_parallel_input_stream(
    VariantParallelInputStream const& parallel_input,
    VariantParallelInputStream::JoinedVariantParams const& joined_variant_params = VariantParallelInputStream::JoinedVariantParams{}
);
 
// =================================================================================================
//     Variant Gapless Input Stream
// =================================================================================================
 
VariantInputStream make_variant_input_stream_from_variant_gapless_input_stream(
    VariantGaplessInputStream const& gapless_input
);
 
inline VariantInputStream make_variant_gapless_input_stream(
    VariantInputStream const& input
) {
    auto gapless_input = VariantGaplessInputStream( input );
    return make_variant_input_stream_from_variant_gapless_input_stream( gapless_input );
}
 
inline VariantInputStream make_variant_gapless_input_stream(
    VariantInputStream const& input,
    std::shared_ptr<::genesis::sequence::ReferenceGenome> ref_genome
) {
    auto gapless_input = VariantGaplessInputStream( input );
    gapless_input.reference_genome( ref_genome );
    return make_variant_input_stream_from_variant_gapless_input_stream( gapless_input );
}
 
inline VariantInputStream make_variant_gapless_input_stream(
    VariantInputStream const& input,
    std::shared_ptr<::genesis::sequence::SequenceDict> seq_dict
) {
    auto gapless_input = VariantGaplessInputStream( input );
    gapless_input.sequence_dict( seq_dict );
    return make_variant_input_stream_from_variant_gapless_input_stream( gapless_input );
}
 
inline VariantInputStream make_variant_gapless_input_stream(
    VariantInputStream const& input,
    std::shared_ptr<GenomeLocusSet> genome_locus_set
) {
    auto gapless_input = VariantGaplessInputStream( input );
    gapless_input.genome_locus_set( genome_locus_set );
    return make_variant_input_stream_from_variant_gapless_input_stream( gapless_input );
}
 
inline VariantInputStream make_variant_gapless_input_stream(
    VariantInputStream const& input,
    std::shared_ptr<::genesis::sequence::ReferenceGenome> ref_genome,
    std::shared_ptr<GenomeLocusSet> genome_locus_set
) {
    auto gapless_input = VariantGaplessInputStream( input );
    gapless_input.reference_genome( ref_genome );
    gapless_input.genome_locus_set( genome_locus_set );
    return make_variant_input_stream_from_variant_gapless_input_stream( gapless_input );
}
 
inline VariantInputStream make_variant_gapless_input_stream(
    VariantInputStream const& input,
    std::shared_ptr<::genesis::sequence::SequenceDict> seq_dict,
    std::shared_ptr<GenomeLocusSet> genome_locus_set
) {
    auto gapless_input = VariantGaplessInputStream( input );
    gapless_input.sequence_dict( seq_dict );
    gapless_input.genome_locus_set( genome_locus_set );
    return make_variant_input_stream_from_variant_gapless_input_stream( gapless_input );
}
 
// =================================================================================================
//     Merging Input Stream
// =================================================================================================
 
VariantInputStream make_variant_merging_input_stream(
    VariantInputStream const& input,
    std::unordered_map<std::string, std::string> const& sample_name_to_group,
    bool allow_ungrouped_samples = false,
    SampleCountsFilterPolicy filter_policy = SampleCountsFilterPolicy::kOnlyPassing
);
 
} // namespace population
} // namespace genesis
 
#endif // include guard