vcf_common.hpp

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#ifndef GENESIS_POPULATION_FORMAT_VCF_COMMON_H_
#define GENESIS_POPULATION_FORMAT_VCF_COMMON_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
*/
 
#ifdef GENESIS_HTSLIB
 
#include <cstdint>
#include <string>
#include <vector>
 
#include "genesis/population/genome_locus_set.hpp"
#include "genesis/population/genome_region.hpp"
#include "genesis/population/genome_region_list.hpp"
 
extern "C" {
    // #include <htslib/vcf.h>
    // #include <htslib/hts.h>
}
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
struct Variant;
class VcfRecord;
 
// =================================================================================================
//     Typedefs and Enums
// =================================================================================================
 
enum class VcfHeaderLine : int
{
    kFilter     = 0,
    kInfo       = 1,
    kFormat     = 2,
    kContig     = 3,
    kStructured = 4, // structured header line TAG=<A=..,B=..>
    kGeneric    = 5  // generic header line
};
 
enum class VcfValueType : int
{
    kFlag    = 0,
    kInteger = 1,
    kFloat   = 2,
    kString  = 3
};
 
enum class VcfValueSpecial : int
{
    kFixed = 0,
 
    kVariable = 1,
 
    kAllele = 2,
 
    kGenotype = 3,
 
    kReference = 4,
};
 
struct VcfSpecification
{
    std::string     id;
    VcfValueType    type;
    VcfValueSpecial special;
    int             number;
    std::string     description;
};
 
// =================================================================================================
//     Typedef and Enum Helpers
// =================================================================================================
 
std::string vcf_value_type_to_string( VcfValueType ht_type );
std::string vcf_value_type_to_string( int ht_type );
std::string vcf_value_special_to_string( VcfValueSpecial vl_type_num );
std::string vcf_value_special_to_string( int vl_type_num );
 
std::string vcf_hl_type_to_string( int hl_type );
 
// =================================================================================================
//     Conversion Functions
// =================================================================================================
 
Variant convert_to_variant_as_pool(
    VcfRecord const& record
);
 
Variant convert_to_variant_as_individuals(
    VcfRecord const& record,
    bool use_allelic_depth = false
);
 
GenomeLocusSet genome_locus_set_from_vcf_file( std::string const& file );
 
GenomeRegionList genome_region_list_from_vcf_file( std::string const& file );
 
void genome_region_list_from_vcf_file( std::string const& file, GenomeRegionList& target );
 
// =================================================================================================
//     VCF Genotype Functions
// =================================================================================================
 
// Forward declare.
class VcfGenotype;
 
std::string vcf_genotype_string( std::vector<VcfGenotype> const& genotypes );
 
size_t vcf_genotype_sum( std::vector<VcfGenotype> const& genotypes );
 
// =================================================================================================
//     VCF Genotype
// =================================================================================================
 
class VcfGenotype
{
public:
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    explicit VcfGenotype( int32_t genotype )
        : genotype_(genotype)
    {}
 
    ~VcfGenotype() = default;
 
    VcfGenotype( VcfGenotype const& ) = default;
    VcfGenotype( VcfGenotype&& )      = default;
 
    VcfGenotype& operator= ( VcfGenotype const& ) = default;
    VcfGenotype& operator= ( VcfGenotype&& )      = default;
 
    // -------------------------------------------------------------------------
    //     Access Functions
    // -------------------------------------------------------------------------
 
    int32_t variant_index() const;
 
    bool is_reference() const;
 
    bool is_alternative() const;
 
    bool is_missing() const;
 
    bool is_phased() const;
 
    int32_t data() const;
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    int32_t genotype_;
};
 
} // namespace population
} // namespace genesis
 
#endif // htslib guard
#endif // include guard