function/genome_region.hpp

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#ifndef GENESIS_POPULATION_FUNCTION_GENOME_REGION_H_
#define GENESIS_POPULATION_FUNCTION_GENOME_REGION_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/genome_locus_set.hpp"
#include "genesis/population/genome_region_list.hpp"
#include "genesis/population/genome_region.hpp"
 
#ifdef GENESIS_HTSLIB
 
#include "genesis/population/format/vcf_record.hpp"
 
#endif // htslib guard
 
#include <iosfwd>
#include <string>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Comparion Operators
// =================================================================================================
 
bool operator ==( GenomeRegion const& a, GenomeRegion const& b );
 
bool operator !=( GenomeRegion const& a, GenomeRegion const& b );
 
// =================================================================================================
//     Parsing & Printing
// =================================================================================================
 
std::string to_string( GenomeRegion const& region );
std::ostream& operator<<( std::ostream& os, GenomeRegion const& region );
 
GenomeRegion parse_genome_region(
    std::string const& region,
    bool zero_based = false,
    bool end_exclusive = false
);
 
GenomeRegionList parse_genome_regions(
    std::string const& regions,
    bool zero_based = false,
    bool end_exclusive = false
);
 
// =================================================================================================
//     Region Coverage
// =================================================================================================
 
// -------------------------------------------------------------------------
//     Explicit chr and pos
// -------------------------------------------------------------------------
 
bool is_covered( GenomeRegion const& region, std::string const& chromosome, size_t position );
 
inline bool is_covered( GenomeRegionList const& regions, std::string const& chromosome, size_t position )
{
    return regions.is_covered( chromosome, position );
}
 
inline bool is_covered( GenomeLocusSet const& loci, std::string const& chromosome, size_t position )
{
    return loci.is_covered( chromosome, position );
}
 
// -------------------------------------------------------------------------
//     Templates for structs
// -------------------------------------------------------------------------
 
template<class T>
bool is_covered( GenomeRegion const& region, T const& locus )
{
    return is_covered( region, locus.chromosome, locus.position );
}
 
template<class T>
bool is_covered( GenomeRegionList const& regions, T const& locus )
{
    return is_covered( regions, locus.chromosome, locus.position );
}
 
template<class T>
bool is_covered( GenomeLocusSet const& loci, T const& locus )
{
    return is_covered( loci, locus.chromosome, locus.position );
}
 
// -------------------------------------------------------------------------
//     VCF versions
// -------------------------------------------------------------------------
 
#ifdef GENESIS_HTSLIB
 
inline bool is_covered( GenomeRegion const& region, VcfRecord const& variant )
{
    return is_covered( region, variant.get_chromosome(), variant.get_position() );
}
 
inline bool is_covered( GenomeRegionList const& regions, VcfRecord const& variant )
{
    return is_covered( regions, variant.get_chromosome(), variant.get_position() );
}
 
inline bool is_covered( GenomeLocusSet const& loci, VcfRecord const& variant )
{
    return is_covered( loci, variant.get_chromosome(), variant.get_position() );
}
 
#endif // htslib guard
 
} // namespace population
} // namespace genesis
 
#endif // include guard