variant_input_stream_sources.hpp

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#ifndef GENESIS_POPULATION_STREAM_VARIANT_INPUT_STREAM_SOURCES_H_
#define GENESIS_POPULATION_STREAM_VARIANT_INPUT_STREAM_SOURCES_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 <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include "genesis/population/format/frequency_table_input_stream.hpp"
#include "genesis/population/format/sam_variant_input_stream.hpp"
#include "genesis/population/format/simple_pileup_input_stream.hpp"
#include "genesis/population/format/sync_input_stream.hpp"
#include "genesis/population/format/sync_reader.hpp"
#include "genesis/population/format/vcf_input_stream.hpp"
#include "genesis/population/sample_counts.hpp"
#include "genesis/population/stream/variant_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 {
 
// =================================================================================================
//     vector
// =================================================================================================
 
VariantInputStream make_variant_input_stream_from_vector(
    std::vector<Variant> const& variants
);
 
// =================================================================================================
//     SAM/BAM/CRAM
// =================================================================================================
 
// Only available if compiled with htslib
#ifdef GENESIS_HTSLIB
 
VariantInputStream make_variant_input_stream_from_sam_file(
    std::string const& filename,
    SamVariantInputStream const& reader = SamVariantInputStream{}
);
 
#endif // GENESIS_HTSLIB
 
// =================================================================================================
//     Pileup
// =================================================================================================
 
VariantInputStream make_variant_input_stream_from_pileup_file(
    std::string const& filename,
    SimplePileupReader const& reader = SimplePileupReader{}
);
 
VariantInputStream make_variant_input_stream_from_pileup_file(
    std::string const& filename,
    std::vector<size_t> const& sample_indices,
    bool inverse_sample_indices = false,
    SimplePileupReader const& reader = SimplePileupReader{}
);
 
VariantInputStream make_variant_input_stream_from_pileup_file(
    std::string const& filename,
    std::vector<bool> const& sample_filter,
    SimplePileupReader const& reader = SimplePileupReader{}
);
 
// =================================================================================================
//     Sync
// =================================================================================================
 
VariantInputStream make_variant_input_stream_from_sync_file(
    std::string const& filename
);
 
VariantInputStream make_variant_input_stream_from_sync_file(
    std::string const& filename,
    std::vector<size_t> const& sample_indices,
    bool inverse_sample_indices = false
);
 
VariantInputStream make_variant_input_stream_from_sync_file(
    std::string const& filename,
    std::vector<bool> const& sample_filter
);
 
// =================================================================================================
//     Frequency Table
// =================================================================================================
 
VariantInputStream make_variant_input_stream_from_frequency_table_file(
    std::string const& filename,
    char separator_char = '\t',
    FrequencyTableInputStream const& reader = FrequencyTableInputStream{}
);
 
VariantInputStream make_variant_input_stream_from_frequency_table_file(
    std::string const& filename,
    std::vector<std::string> const& sample_names_filter,
    bool inverse_sample_names_filter = false,
    char separator_char = '\t',
    FrequencyTableInputStream const& reader = FrequencyTableInputStream{}
);
 
// =================================================================================================
//     VCF
// =================================================================================================
 
// Only available if compiled with htslib
#ifdef GENESIS_HTSLIB
 
struct VariantInputStreamFromVcfParams
{
    // Types of records to use or discard.
    bool only_snps            = false;
    bool only_biallelic_snps  = false;
    bool only_filter_pass     = false;
 
    // Subset the samples.
    std::vector<std::string> sample_names;
    bool inverse_sample_names = false;
};
 
VariantInputStream make_variant_input_stream_from_pool_vcf_file(
    std::string const& filename,
    VariantInputStreamFromVcfParams const& params = VariantInputStreamFromVcfParams{}
);
 
VariantInputStream make_variant_input_stream_from_individual_vcf_file(
    std::string const& filename,
    VariantInputStreamFromVcfParams const& params = VariantInputStreamFromVcfParams{},
    bool use_allelic_depth = false
);
 
#endif // GENESIS_HTSLIB
 
} // namespace population
} // namespace genesis
 
#endif // include guard