sample_counts_filter.hpp

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#ifndef GENESIS_POPULATION_FILTER_SAMPLE_COUNTS_FILTER_H_
#define GENESIS_POPULATION_FILTER_SAMPLE_COUNTS_FILTER_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/sample_counts.hpp"
#include "genesis/population/filter/filter_stats.hpp"
#include "genesis/population/filter/filter_status.hpp"
#include "genesis/population/variant.hpp"
 
#include <array>
#include <cassert>
#include <iosfwd>
#include <stdexcept>
#include <string>
#include <type_traits>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     SampleCounts Filter Tag
// =================================================================================================
 
enum class SampleCountsFilterTag : FilterStatus::IntType
{
    kPassed = 0,
 
    // -------------------------------------------
    //     Position
    // -------------------------------------------
 
    kMaskedPosition,
 
    kMaskedRegion,
 
    // -------------------------------------------
    //     Missing and Invalid
    // -------------------------------------------
 
    kMissing,
 
    kNotPassed,
 
    kInvalid,
 
    // -------------------------------------------
    //     Numeric
    // -------------------------------------------
 
    kEmpty,
 
    kBelowMinReadDepth,
 
    kAboveMaxReadDepth,
 
    kAboveDeletionsCountLimit,
 
    kNotSnp,
 
    kNotBiallelicSnp,
 
    // -------------------------------------------
    //     Special
    // -------------------------------------------
 
    kEnd
};
 
// =================================================================================================
//     SampleCounts Filter Tag Categories
// =================================================================================================
 
enum class SampleCountsFilterTagCategory : FilterStatus::IntType
{
    kPassed = 0,
 
    kMasked,
 
    kMissingInvalid,
 
    kNumeric,
 
    kEnd
};
 
// =================================================================================================
//     SampleCounts Filter Policy
// =================================================================================================
 
enum class SampleCountsFilterPolicy
{
    kAll,
    kOnlyPassing
};
 
// =================================================================================================
//     SampleCounts Filter Stats
// =================================================================================================
 
using SampleCountsFilterStats = FilterStats<SampleCountsFilterTag>;
 
using SampleCountsFilterCategoryStats = FilterStats<SampleCountsFilterTagCategory>;
 
SampleCountsFilterTagCategory sample_counts_filter_tag_to_category( SampleCountsFilterTag tag );
 
SampleCountsFilterCategoryStats sample_counts_filter_stats_category_counts(
    SampleCountsFilterStats const& stats
);
 
size_t sample_counts_filter_stats_category_counts(
    SampleCountsFilterStats const& stats, SampleCountsFilterTagCategory category
);
 
// =================================================================================================
//     Filter Functions
// =================================================================================================
 
// --------------------------------------------------------------------------------------
//     Print sample stats
// --------------------------------------------------------------------------------------
 
std::ostream& print_sample_counts_filter_stats(
    std::ostream& os,
    SampleCountsFilterStats const& stats,
    bool verbose = false
);
 
std::string print_sample_counts_filter_stats(
    SampleCountsFilterStats const& stats,
    bool verbose = false
);
 
// --------------------------------------------------------------------------------------
//     Print category stats
// --------------------------------------------------------------------------------------
 
std::ostream& print_sample_counts_filter_category_stats(
    std::ostream& os,
    SampleCountsFilterCategoryStats const& stats,
    bool verbose = false
);
 
std::string print_sample_counts_filter_category_stats(
    SampleCountsFilterCategoryStats const& stats,
    bool verbose = false
);
 
inline std::ostream& print_sample_counts_filter_category_stats(
    std::ostream& os,
    SampleCountsFilterStats const& stats,
    bool verbose = false
) {
    return print_sample_counts_filter_category_stats(
        os, sample_counts_filter_stats_category_counts( stats ), verbose
    );
}
 
inline std::string print_sample_counts_filter_category_stats(
    SampleCountsFilterStats const& stats,
    bool verbose = false
) {
    return print_sample_counts_filter_category_stats(
        sample_counts_filter_stats_category_counts( stats ), verbose
    );
}
 
} // namespace population
} // namespace genesis
 
#endif // include guard