StateCounts.hpp

#ifndef SEQUENCE_VARIANTMATRIX_STATECOUNTS_HPP__
#define SEQUENCE_VARIANTMATRIX_STATECOUNTS_HPP__

#include "VariantMatrix.hpp"
#include "VariantMatrixViews.hpp"
#include <limits>
#include <vector>

namespace Sequence
{
    struct StateCounts
    {
        static constexpr VariantMatrix::value_type max_allele
            = std::numeric_limits<VariantMatrix::value_type>::max();
        std::vector<std::int32_t> counts;
        std::size_t max_allele_idx;
        std::uint32_t n;
        std::int8_t refstate;

        StateCounts(const std::int8_t refstate_);
        StateCounts();
        void operator()(ConstRowView &);
        void operator()(const RowView &);
    };

    std::vector<StateCounts>
    process_variable_sites(const VariantMatrix& m,
                           const std::vector<std::int8_t>& refstates);
    std::vector<StateCounts>
    process_variable_sites(const VariantMatrix& m, const std::int8_t refstate);
    std::vector<StateCounts> process_variable_sites(const VariantMatrix& m);
} // namespace Sequence

#endif