variant_input_iterator.hpp

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#ifndef GENESIS_POPULATION_FORMATS_VARIANT_INPUT_ITERATOR_H_
#define GENESIS_POPULATION_FORMATS_VARIANT_INPUT_ITERATOR_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2022 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/formats/sam_variant_input_iterator.hpp"
#include "genesis/population/formats/simple_pileup_input_iterator.hpp"
#include "genesis/population/formats/sync_input_iterator.hpp"
#include "genesis/population/formats/sync_reader.hpp"
#include "genesis/population/formats/vcf_input_iterator.hpp"
#include "genesis/population/base_counts.hpp"
#include "genesis/population/variant.hpp"
#include "genesis/utils/containers/lambda_iterator.hpp"
 
#include <cassert>
#include <functional>
#include <stdexcept>
#include <string>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
// Cannot include the header, as it itself needs the VariantInputIterator to be defined first.
// We could split this whole file into two, one for the VariantInputIterator definition,
// and one for the functions to create it from sources... Maybe do that in the future.
// As of now, this forward declaration means that the VariantParallelInputIterator header
// needs to be included by the user at some point themselves... which they probably do anyway.
class VariantParallelInputIterator;
 
// =================================================================================================
//     Generic Variant Iterator
// =================================================================================================
 
struct VariantInputIteratorData
{
    std::string file_path;
 
    std::string source_name;
 
    std::vector<std::string> sample_names;
};
 
using VariantInputIterator = utils::LambdaIterator<Variant, VariantInputIteratorData>;
 
// =================================================================================================
//     Input Sources
// =================================================================================================
 
// -------------------------------------------------------------------------
//     SAM/BAM/CRAM
// -------------------------------------------------------------------------
 
// Only available if compiled with htslib
#ifdef GENESIS_HTSLIB
 
VariantInputIterator make_variant_input_iterator_from_sam_file(
    std::string const& filename,
    SamVariantInputIterator const& reader = SamVariantInputIterator{}
);
 
#endif // GENESIS_HTSLIB
 
// -------------------------------------------------------------------------
//     Pileup
// -------------------------------------------------------------------------
 
VariantInputIterator make_variant_input_iterator_from_pileup_file(
    std::string const& filename,
    SimplePileupReader const& reader = SimplePileupReader{}
);
 
VariantInputIterator make_variant_input_iterator_from_pileup_file(
    std::string const& filename,
    std::vector<size_t> const& sample_indices,
    bool inverse_sample_indices = false,
    SimplePileupReader const& reader = SimplePileupReader{}
);
 
VariantInputIterator make_variant_input_iterator_from_pileup_file(
    std::string const& filename,
    std::vector<bool> const& sample_filter,
    SimplePileupReader const& reader = SimplePileupReader{}
);
 
// -------------------------------------------------------------------------
//     Sync
// -------------------------------------------------------------------------
 
VariantInputIterator make_variant_input_iterator_from_sync_file(
    std::string const& filename
);
 
VariantInputIterator make_variant_input_iterator_from_sync_file(
    std::string const& filename,
    std::vector<size_t> const& sample_indices,
    bool inverse_sample_indices = false
);
 
VariantInputIterator make_variant_input_iterator_from_sync_file(
    std::string const& filename,
    std::vector<bool> const& sample_filter
);
 
// -------------------------------------------------------------------------
//     VCF
// -------------------------------------------------------------------------
 
// Only available if compiled with htslib
#ifdef GENESIS_HTSLIB
 
VariantInputIterator make_variant_input_iterator_from_pool_vcf_file(
    std::string const& filename,
    bool only_biallelic = true,
    bool only_filter_pass = true
);
 
VariantInputIterator make_variant_input_iterator_from_pool_vcf_file(
    std::string const& filename,
    std::vector<std::string> const& sample_names,
    bool inverse_sample_names = false,
    bool only_biallelic = true,
    bool only_filter_pass = true
);
 
VariantInputIterator make_variant_input_iterator_from_individual_vcf_file(
    std::string const& filename,
    bool use_allelic_depth = false,
    bool only_biallelic = true,
    bool only_filter_pass = true
);
 
VariantInputIterator make_variant_input_iterator_from_individual_vcf_file(
    std::string const& filename,
    std::vector<std::string> const& sample_names,
    bool inverse_sample_names = false,
    bool use_allelic_depth = false,
    bool only_biallelic = true,
    bool only_filter_pass = true
);
 
#endif // GENESIS_HTSLIB
 
// -------------------------------------------------------------------------
//     Variant Parallel Input Iterator
// -------------------------------------------------------------------------
 
VariantInputIterator make_variant_input_iterator_from_variant_parallel_input_iterator(
    VariantParallelInputIterator const& parallel_input,
    bool allow_ref_base_mismatches = false,
    bool allow_alt_base_mismatches = true,
    std::string const& source_sample_separator = ":"
);
 
} // namespace population
} // namespace genesis
 
#endif // include guard