output.h 33.6 KB
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#ifndef _SPELL_BAYES_OUTPUT_H_
#define _SPELL_BAYES_OUTPUT_H_

#include <map>
#include <vector>
#include <string>
#include <iostream>
#include <fstream>
#include <cstring>

#include "eigen.h"
#include "error.h"
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#include "data/chromosome.h"
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/*#include "generation_rs_fwd.h"*/
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#include "input/read_trait.h"
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#include "tensor.h"
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/** FOURCC **/

inline
bool check_fourcc(std::ifstream& ifs, const char* fourcc)
{
    char buf[4] = {0, 0, 0, 0};
    ifs.read(buf, 4);
    return strncmp(fourcc, buf, 4);
}

inline
void write_fourcc(std::ofstream& ofs, const char* fourcc)
{
    ofs.write(fourcc, 4);
}

/** SIZE_T **/

inline
void write_size(std::ofstream& ofs, size_t sz)
{
    ofs.write((const char*) &sz, sizeof sz);
}

inline
size_t read_size(std::ifstream& ifs)
{
    size_t ret;
    ifs.read((char*) &ret, sizeof ret);
    return ret;
}

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/** PTRDIFF_T **/

inline
void write_ptrdiff(std::ofstream& ofs, ptrdiff_t sz)
{
    ofs.write((const char*) &sz, sizeof sz);
}

inline
ptrdiff_t read_ptrdiff(std::ifstream& ifs)
{
    ptrdiff_t ret;
    ifs.read((char*) &ret, sizeof ret);
    return ret;
}

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/** STRING **/

inline
std::string read_str(std::ifstream& ifs)
{
    size_t sz = read_size(ifs);
    std::vector<char> tmp(sz);
    ifs.read(&tmp[0], sz);
    return {tmp.begin(), tmp.end()};
}

inline
void write_str(std::ofstream& ofs, const std::string& s)
{
    write_size(ofs, s.size());
    ofs.write(s.c_str(), s.size());
}

/** DOUBLE **/

inline
void write_double(std::ofstream& ofs, double sz)
{
    ofs.write((const char*) &sz, sizeof sz);
}

inline
double read_double(std::ifstream& ifs)
{
    double ret;
    ifs.read((char*) &ret, sizeof ret);
    return ret;
}

/** INT **/

inline
void write_int(std::ofstream& ofs, int sz)
{
    ofs.write((const char*) &sz, sizeof sz);
}

inline
int read_int(std::ifstream& ifs)
{
    int ret;
    ifs.read((char*) &ret, sizeof ret);
    return ret;
}

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/** CHAR **/

inline
void write_char(std::ofstream& ofs, char sz)
{
    ofs.write((const char*) &sz, sizeof sz);
}

inline
char read_char(std::ifstream& ifs)
{
    char ret;
    ifs.read(&ret, sizeof ret);
    return ret;
}

#if 0
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/** FAST_POLYNOM **/

inline
void write_fast_polynom(std::ofstream& ofs, const fast_polynom& fp)
{
    impl::f_polynom f = fp;
    write_int(ofs, fp.value);
    write_int(ofs, f.r_exp);
    write_int(ofs, f.s_exp);
    write_size(ofs, f.P.size());
    for (double c: f.P) {
        write_double(ofs, c);
    }
}

inline
fast_polynom read_fast_polynom(std::ifstream& ifs, int& original_key)
{
    original_key = read_int(ifs);
    impl::f_polynom ret = fast_polynom::zero;
    ret.r_exp = read_int(ifs);
    ret.s_exp = read_int(ifs);
    size_t sz = read_size(ifs);
    ret.P.resize(sz);
    for (size_t i = 0; i < sz; ++i) {
        ret.P[i] = read_double(ifs);
    }
    return ret;
}

/** ALGREBRAIC GENOTYPE **/

inline void write_algebraic_genotype(std::ofstream& ofs, const algebraic_genotype& ag)
{
    ofs.write((const char*) &ag.genotype, sizeof ag.genotype);
    ofs.write((const char*) &ag.type, sizeof ag.type);
    write_int(ofs, ag.poly.value);
}

inline algebraic_genotype read_algebraic_genotype(std::ifstream& ifs, const std::map<int, fast_polynom>& pt)
{
    algebraic_genotype ag;
    ifs.read((char*) &ag.genotype, sizeof ag.genotype);
    ifs.read((char*) &ag.type, sizeof ag.type);
    ag.poly = pt.find(read_int(ifs))->second;
    return ag;
}

/** GENOMATRIX **/

inline void write_genomatrix(std::ofstream& ofs, const GenoMatrix& mat)
{
    write_fourcc(ofs, "SGEM");
    /*std::map<decltype(fast_polynom::value), impl::f_polynom>*/
    std::set<fast_polynom> poly_table;
    for (int j = 0; j < mat.cols(); ++j) {
        for (int i = 0; i < mat.rows(); ++i) {
            poly_table.insert(mat(i, j).poly);
        }
    }
    write_size(ofs, poly_table.size());
    for (const auto& fp: poly_table) {
        write_fast_polynom(ofs, fp);
    }
    write_int(ofs, mat.cols());
    write_int(ofs, mat.rows());
    /*MSG_DEBUG("[write_genomatrix] cols=" << mat.cols() << " rows=" << mat.rows());*/
    for (int j = 0; j < mat.cols(); ++j) {
        for (int i = 0; i < mat.rows(); ++i) {
            /*write_int(ofs, mat(i, j).value);*/
            write_algebraic_genotype(ofs, mat(i, j));
        }
    }
}

inline
void read_genomatrix(std::ifstream& ifs, GenoMatrix& mat)
{
    if (check_fourcc(ifs, "SGEM")) {
        MSG_ERROR("File is not valid or has been corrupted", "");
        return;
    }
    std::map<int, fast_polynom> poly_map;

    size_t table_size = read_size(ifs);
    int key;

    for (size_t i = 0; i < table_size; ++i) {
        auto f = read_fast_polynom(ifs, key);
        poly_map[key] = f;
    }

    int cols = read_int(ifs);
    int rows = read_int(ifs);
    /*MSG_DEBUG("[read_genomatrix] cols=" << cols << " rows=" << rows);*/
    mat.resize(rows, cols);
    for (int j = 0; j < mat.cols(); ++j) {
        for (int i = 0; i < mat.rows(); ++i) {
            mat(i, j) = read_algebraic_genotype(ifs, poly_map);
        }
    }
}

/** GENERATION_RS **/

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inline void write_geno_matrix(std::ofstream& ofs, const geno_matrix* gen)
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{
    write_fourcc(ofs, "SGRS");
    write_str(ofs, gen->name);
    write_size(ofs, gen->P.size());
    for (const auto& p: gen->P) {
        write_double(ofs, p.weight);
        write_genomatrix(ofs, p.G.data);
    }
}

inline
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geno_matrix* read_geno_matrix(std::ifstream& ifs)
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{
    if (check_fourcc(ifs, "SGRS")) {
        MSG_ERROR("File is not valid or has been corrupted", "");
    }
    /*MSG_DEBUG("pouet 1"); MSG_QUEUE_FLUSH();*/
    std::string name = read_str(ifs);
    /*MSG_DEBUG("pouet 2"); MSG_QUEUE_FLUSH();*/
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    geno_matrix* ret = geno_matrix::blank(name);
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    /*MSG_DEBUG("pouet 3"); MSG_QUEUE_FLUSH();*/
    size_t n_p = read_size(ifs);
    /*MSG_DEBUG("Have " << n_p << " processes"); MSG_QUEUE_FLUSH();*/
    ret->P.resize(n_p);
    for (size_t i = 0; i < n_p; ++i) {
        ret->P[i].weight = read_double(ifs);
        GenoMatrix tmp;
        read_genomatrix(ifs, tmp);
        ret->P[i].G = convert(tmp);
        /*MSG_DEBUG("Read process");*/
        /*MSG_DEBUG(ret->P[i]);*/
    }
    ret->precompute();
    return ret;
}
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#endif

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/** MATRIX<SCALAR, R, C> **/

template <typename MATRIX_TYPE>
struct resize_matrix_impl;

template <> struct resize_matrix_impl<VectorXd> { void operator () (VectorXd& v, size_t rows, size_t) { v.resize(rows); } };
template <> struct resize_matrix_impl<MatrixXd> { void operator () (MatrixXd& m, size_t rows, size_t cols) { m.resize(rows, cols); } };

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template <typename SCALAR, int ROW, int COL, int C, int D, int E>
struct resize_matrix_impl<Eigen::Matrix<SCALAR, ROW, COL, C, D, E>> {
    void operator () (Eigen::Matrix<SCALAR, ROW, COL, C, D, E>& m, size_t r, size_t c) { m.resize(r, c); }
};

template <typename SCALAR, int ROW, int C, int D, int E>
struct resize_matrix_impl<Eigen::Matrix<SCALAR, ROW, 1, C, D, E>> {
    void operator () (Eigen::Matrix<SCALAR, ROW, 1, C, D, E>& v, size_t r, size_t) { v.resize(r); }
};

template <typename SCALAR, int COL, int C, int D, int E>
struct resize_matrix_impl<Eigen::Matrix<SCALAR, 1, COL, C, D, E>> {
    void operator () (Eigen::Matrix<SCALAR, 1, COL, C, D, E>& v, size_t, size_t c) { v.resize(c); }
};

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template <typename MATRIX_TYPE>
void resize_matrix(MATRIX_TYPE& m, size_t r, size_t c) { resize_matrix_impl<MATRIX_TYPE>()(m, r, c); }

template <typename SCALAR, int ROW, int COL, int C, int D, int E>
void read_matrix(std::ifstream& ifs, Eigen::Matrix<SCALAR, ROW, COL, C, D, E>& mat)
{
    size_t scalar_sz = read_size(ifs);
    if (scalar_sz != sizeof(SCALAR)) {
        MSG_ERROR("WRONG SIZE OF SCALAR, CAN'T READ FILE", "Make sure spell-marker and spell-qtl are always executed on machines with same word size.");
    }
    size_t n_row = read_size(ifs);
    size_t n_col = read_size(ifs);
    if (ROW != Eigen::Dynamic && ((int) n_row) != ROW) {
        MSG_ERROR("WRONG ROW COUNT. FILE IS NOT A LOCUS VECTOR FILE OR IS CORRUPTED", "You may want to run spell-marker again");
    }
    if (COL != Eigen::Dynamic && ((int) n_col) != COL) {
        MSG_ERROR("WRONG COLUMN COUNT. FILE IS NOT A LOCUS VECTOR FILE OR IS CORRUPTED", "You may want to run spell-marker again");
    }
    resize_matrix(mat, n_row, n_col);
    ifs.read((char*) mat.data(), n_row * n_col * sizeof(SCALAR));
}

template <typename SCALAR, int ROW, int COL, int C, int D, int E>
void write_matrix(std::ofstream& ofs, const Eigen::Matrix<SCALAR, ROW, COL, C, D, E>& mat)
{
    write_size(ofs, sizeof(SCALAR));
    write_size(ofs, mat.rows());
    write_size(ofs, mat.cols());
    ofs.write((const char*) mat.data(), mat.size() * sizeof(SCALAR));
}


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template <typename V, typename READ_ELEM_FUNC>
void read_vector(std::ifstream& ifs, std::vector<V>& vec, READ_ELEM_FUNC read_elem)
{
    size_t sz = read_size(ifs);
    vec.clear();
    vec.reserve(sz);
    for (size_t i = 0; i < sz; ++i) {
        vec.emplace_back(read_elem(ifs));
    }
}


template <typename V, typename WRITE_ELEM_FUNC>
void write_vector(std::ofstream& ofs, const std::vector<V>& vec, WRITE_ELEM_FUNC write_elem)
{
    write_size(ofs, vec.size());
    for (const auto& e: vec) {
        write_elem(ofs, e);
    }
}


/** LABEL_TYPE **/

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inline
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label_type read_label(std::ifstream& ifs)
{
    char f, s;
    ifs >> f >> s;
    return {f, s};
}

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void write_label(std::ofstream& ofs, const label_type& l)
{
    ofs << l.first() << l.second();
}


/** GENO_MATRIX **/

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inline
void write_geno_matrix(std::ofstream& ofs, const geno_matrix& mat)
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{
    write_fourcc(ofs, "SGEM");
    write_str(ofs, mat.name);
    /* skip variant, it's deprecated. Or should be. */
    write_vector(ofs, mat.labels, write_label);
    write_matrix(ofs, mat.inf_mat);
    write_matrix(ofs, mat.p);
    write_matrix(ofs, mat.p_inv);
    write_matrix(ofs, mat.diag);
    write_matrix(ofs, mat.stat_dist);
    write_matrix(ofs, mat.collect);
    write_matrix(ofs, mat.dispatch);
    /* also skip symmetries for now. */
}

inline
void read_geno_matrix(std::ifstream& ifs, geno_matrix& mat)
{
    if (check_fourcc(ifs, "SGEM")) {
        MSG_ERROR("File is not valid or has been corrupted", "");
        return;
    }
    mat.name = read_str(ifs);
    /* skip variant. */
    read_vector(ifs, mat.labels, read_label);
    read_matrix(ifs, mat.inf_mat);
    read_matrix(ifs, mat.p);
    read_matrix(ifs, mat.p_inv);
    read_matrix(ifs, mat.diag);
    read_matrix(ifs, mat.stat_dist);
    read_matrix(ifs, mat.collect);
    read_matrix(ifs, mat.dispatch);
    /* also skip symmetries for now. */
}


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inline
void write_geno_matrix(std::ofstream& ofs, const geno_matrix* ptr)
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{
    write_geno_matrix(ofs, *ptr);
}

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geno_matrix* read_geno_matrix(std::ifstream& ifs)
{
    geno_matrix* ret = new geno_matrix();
    read_geno_matrix(ifs, *ret);
    return ret;
}


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template <class DERIVED>
struct rw_any {
    bool fourcc(std::ifstream& ifs, const char* cc)
    {
        if (check_fourcc(ifs, cc)) {
            MSG_ERROR("File is not valid or has been corrupted (expected " << cc << ')', "");
            return true;
        }
        return false;
    }

    bool fourcc(std::ofstream& ofs, const char* cc)
    {
        write_fourcc(ofs, cc);
        return false;
    }

    virtual ~rw_any() {}

    DERIVED& ref() { return *dynamic_cast<DERIVED*>(this); }

    void operator () (std::ifstream& ifs, std::string& s) { s = read_str(ifs); }
    void operator () (std::ofstream& ofs, const std::string& s) { write_str(ofs, s); }

    void operator () (std::ifstream& ifs, char& i) { i = read_char(ifs); }
    void operator () (std::ofstream& ofs, char i) { write_char(ofs, i); }

    void operator () (std::ifstream& ifs, int& i) { i = read_int(ifs); }
    void operator () (std::ofstream& ofs, int i) { write_int(ofs, i); }

    void operator () (std::ifstream& ifs, bool& i) { i = !!read_char(ifs); }
    void operator () (std::ofstream& ofs, bool i) { write_char(ofs, i); }

    void operator () (std::ifstream& ifs, double& i) { i = read_double(ifs); }
    void operator () (std::ofstream& ofs, double i) { write_double(ofs, i); }

    void operator () (std::ifstream& ifs, size_t& i) { i = read_size(ifs); }
    void operator () (std::ofstream& ofs, size_t i) { write_size(ofs, i); }

    void operator () (std::ifstream& ifs, ptrdiff_t& i) { i = read_ptrdiff(ifs); }
    void operator () (std::ofstream& ofs, ptrdiff_t i) { write_ptrdiff(ofs, i); }

    void operator () (std::ifstream& ifs, label_type& l) { l = {read_char(ifs), read_char(ifs)}; }
    void operator () (std::ofstream& ofs, const label_type& l) { write_char(ofs, l.first()); write_char(ofs, l.second()); }

    template <typename V>
        void operator () (std::ifstream& ifs, std::set<V>& vec)
        {
            if (fourcc(ifs, "OSET")) { return; }
            size_t sz = read_size(ifs);
            vec.clear();
            for (size_t i = 0; i < sz; ++i) {
                V tmp;
                ref() (ifs, tmp);
                vec.emplace(tmp);
            }
        }

    template <typename V>
        void operator () (std::ofstream& ofs, const std::set<V>& vec)
        {
            if (fourcc(ofs, "OSET")) { return; }
            write_size(ofs, vec.size());
            for (const auto& e: vec) {
                ref() (ofs, e);
            }
        }


    template <typename V>
        void operator () (std::ifstream& ifs, std::unordered_set<V>& vec)
        {
            if (fourcc(ifs, "USET")) { return; }
            size_t sz = read_size(ifs);
            vec.clear();
            for (size_t i = 0; i < sz; ++i) {
                V tmp;
                ref() (ifs, tmp);
                vec.emplace(tmp);
            }
        }

    template <typename V>
        void operator () (std::ofstream& ofs, const std::unordered_set<V>& vec)
        {
            if (fourcc(ofs, "USET")) { return; }
            write_size(ofs, vec.size());
            for (const auto& e: vec) {
                ref() (ofs, e);
            }
        }

    void operator () (std::ifstream& ifs, std::vector<bool>::reference i) { i = !!read_char(ifs); }

    template <typename V, typename A>
        void operator () (std::ifstream& ifs, std::vector<V, A>& vec)
        {
            if (fourcc(ifs, "VECT")) { return; }
            size_t sz = read_size(ifs);
            vec.clear();
            vec.reserve(sz);
            for (size_t i = 0; i < sz; ++i) {
                vec.emplace_back();
                ref() (ifs, vec.back());
            }
        }

    template <typename V, typename A>
        void operator () (std::ofstream& ofs, const std::vector<V, A>& vec)
        {
            if (fourcc(ofs, "VECT")) { return; }
            write_size(ofs, vec.size());
            for (const auto& e: vec) {
                ref() (ofs, e);
            }
        }

    template <typename V, typename A, typename RWElem>
        void operator () (std::ifstream& ifs, std::vector<V, A>& vec, RWElem rw_elem)
        {
            if (fourcc(ifs, "VECT")) { return; }
            size_t sz = read_size(ifs);
            vec.clear();
            vec.reserve(sz);
            for (size_t i = 0; i < sz; ++i) {
                vec.emplace_back();
                rw_elem(ifs, vec.back());
            }
        }

    template <typename V, typename A, typename RWElem>
        void operator () (std::ofstream& ofs, std::vector<V, A>& vec, RWElem rw_elem)
        {
            if (fourcc(ofs, "VECT")) { return; }
            write_size(ofs, vec.size());
            for (auto& e: vec) {
                rw_elem(ofs, e);
            }
        }

    template <typename K, typename V, typename A, typename C>
        void operator () (std::ifstream& ifs, std::map<K, V, A, C>& map)
        {
            if (fourcc(ifs, "MAP ")) { return; }
            size_t count = read_size(ifs);
            map.clear();
            for (size_t i = 0; i < count; ++i) {
                K key;
                V value;
                ref() (ifs, key);
                ref() (ifs, value);
                map.emplace(std::move(key), std::move(value));
            }
        }

    template <typename K, typename V, typename A, typename C>
        void operator () (std::ofstream& ofs, const std::map<K, V, A, C>& map)
        {
            if (fourcc(ofs, "MAP ")) { return; }
            write_size(ofs, map.size());
            for (const auto& kv: map) {
                ref() (ofs, kv.first);
                ref() (ofs, kv.second);
            }
        }

    template <typename SCALAR, int ROW, int COL, int C, int D, int E>
        void operator () (std::ifstream& ifs, Eigen::Matrix<SCALAR, ROW, COL, C, D, E>& mat) { read_matrix(ifs, mat); }

    template <typename SCALAR, int ROW, int COL, int C, int D, int E>
        void operator () (std::ofstream& ofs, const Eigen::Matrix<SCALAR, ROW, COL, C, D, E>& mat) { write_matrix(ofs, mat); }

    void operator () (std::ifstream& ifs, geno_matrix& mat) { read_geno_matrix(ifs, mat); }
    void operator () (std::ofstream& ofs, geno_matrix& mat) { write_geno_matrix(ofs, mat); }

    void operator () (std::ifstream& ifs, std::shared_ptr<geno_matrix>& ptr)
    {
        ptr.reset();
        ptr = std::make_shared<geno_matrix>();
        ref() (ifs, *ptr);
        if (!ptr->size()) {
            ptr.reset();
        }
    }

    void operator () (std::ofstream& ofs, const std::shared_ptr<geno_matrix>& ptr)
    {
        if (ptr) {
            ref() (ofs, *ptr.get());
        } else {
            geno_matrix _;
            ref() (ofs, _);
        }
    }
};


struct rw_base : public rw_any<rw_base> {
    virtual ~rw_base() {}
    using rw_any<rw_base>::fourcc;
    using rw_any<rw_base>::ref;
    using rw_any<rw_base>::operator ();
};



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/** **/


struct LV_database {
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    /* GEN / MARK / IND => LV_vec */
    std::map<std::string, std::map<std::string, std::vector<VectorXd>>> data_by_marker;
    /* CHROM / GEN / IND => LV_mat */
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    std::map<std::string, std::map<std::string, std::vector<MatrixXd>>> data;

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    LV_database() : data_by_marker(), data() {}

    void assemble_using_map(const std::vector<chromosome>& map)
    {
        data.clear();
        for (const auto& chr: map) {
            for (const auto& gen_dat: data_by_marker) {
                const auto& gen = gen_dat.first;
                const auto& mark_ind_lv = gen_dat.second;
                size_t n_states = mark_ind_lv.begin()->second.front().size();
                size_t n_mark = chr.raw.marker_name.size();
                size_t n_ind = mark_ind_lv.begin()->second.size();
                auto& ind_LVmat = data[chr.name][gen];
                ind_LVmat.resize(n_ind, {n_states, n_mark});
                size_t m = 0;
                for (const auto& mark: chr.raw.marker_name) {
                    for (size_t ind = 0; ind < n_ind; ++ind) {
                        ind_LVmat[ind].col(m) = mark_ind_lv.find(mark)->second[ind];
                    }
                    ++m;
                }
            }
        }
    }

    MatrixXd operator () (
            std::vector<std::string>::const_iterator begin,
            std::vector<std::string>::const_iterator end,
            const std::string& gen, size_t ind) const
    {
        const auto& milv = data_by_marker.find(gen)->second;
        size_t n_states = milv.find(*begin)->second.front().size();
        MatrixXd LV(n_states, end - begin);
        for (size_t i = 0; i < n_states; ++i) {
            LV.col(i) = milv.find(*begin)->second[ind];
        }
        return LV;
    }

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    MatrixXd& operator () (const std::string& chr, const std::string& gen, size_t ind)
    {
        return data[chr][gen][ind];
    }

    const MatrixXd& operator () (const std::string& chr, const std::string& gen, size_t ind) const
    {
        return data.find(chr)->second.find(gen)->second[ind];
    }

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    std::map<std::string, std::vector<MatrixXd>>
        extract(const std::string& gen, const std::vector<size_t> ind_vec) const
        {
            std::map<std::string, std::vector<MatrixXd>> ret;
            for (const auto& chr_gen_lv_vec: data) {
                const std::string& chr = chr_gen_lv_vec.first;
                const auto& lv_vec = chr_gen_lv_vec.second.find(gen)->second;
                auto& ret_lv_vec = ret[chr];
                ret_lv_vec.reserve(ind_vec.size());
                for (size_t i: ind_vec) {
                    ret_lv_vec.push_back(lv_vec[i]);
                }
            }
            return ret;
        }

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    template <typename STREAM_TYPE>
        void
        file_io(STREAM_TYPE& fs)
        {
            rw_base rw;
            if (rw.fourcc(fs, "SMLV")) { return; }
            rw(fs, data_by_marker);
            rw(fs, data);
        }

    static
        LV_database
        load_from(const std::string& filename)
        {
            std::ifstream ifs(filename);
            LV_database ret;
            ret.file_io(ifs);
            return ret;
        }

    void
        save_to(const std::string& filename)
        {
            std::ofstream ofs(filename);
            file_io(ofs);
        }

    /*
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    static
        bool lv_check_fourcc(std::ifstream& ifs, const char* fourcc)
        {
            if (check_fourcc(ifs, fourcc)) {
                MSG_ERROR("FILE IS NOT A LOCUS VECTOR FILE OR IS CORRUPTED", "You may want to run spell-marker again.");
                return true;
            }
            return false;
        }

    static
        LV_database load_from(const std::string& filename)
        {
            std::ifstream ifs(filename);
            return load_from(ifs);
        }

    static
        LV_database load_from(std::ifstream& ifs)
        {
            LV_database LV;

            if (lv_check_fourcc(ifs, "SMLV")) { return {}; }
            size_t n_chrom = read_size(ifs);
            size_t n_gen = read_size(ifs);
            for (size_t c = 0; c < n_chrom; ++c) {
                if (lv_check_fourcc(ifs, "SCHR")) { return {}; }
                std::string chr_name = read_str(ifs);
                for (size_t g = 0; g < n_gen; ++g) {
                    if (lv_check_fourcc(ifs, "SGEN")) { return {}; }
                    std::string gen_name = read_str(ifs);
                    size_t n_ind = read_size(ifs);
                    LV.data[chr_name][gen_name].resize(n_ind);
                    for (size_t i = 0; i < n_ind; ++i) {
                        if (lv_check_fourcc(ifs, "SLV_")) { return {}; }
                        read_matrix(ifs, LV.data[chr_name][gen_name][i]);
                    }
                }
            }
            return LV;
        }

    void save_to(const std::string& filename)
    {
        std::ofstream ofs(filename);
        save_to(ofs);
    }

    void save_to(std::ofstream& ofs)
    {
        write_fourcc(ofs, "SMLV");
        write_size(ofs, data.size());
        write_size(ofs, data.begin()->second.size());
        for (const auto& chr_gen_vec_lv: data) {
            write_fourcc(ofs, "SCHR");
            write_str(ofs, chr_gen_vec_lv.first);
            for (const auto& gen_vec_lv: chr_gen_vec_lv.second) {
                write_fourcc(ofs, "SGEN");
                write_str(ofs, gen_vec_lv.first);
                write_size(ofs, gen_vec_lv.second.size());
                for (const auto& lv: gen_vec_lv.second) {
                    write_fourcc(ofs, "SLV_");
                    write_matrix(ofs, lv);
                }
            }
        }
    }
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    */
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    friend
        std::ostream& operator << (std::ostream& os, const LV_database& LV)
        {
            for (const auto& chr_gen_vec_lv: LV.data) {
                MSG_DEBUG("CHROMOSOME " << chr_gen_vec_lv.first);
                for (const auto& gen_vec_lv: chr_gen_vec_lv.second) {
                    MSG_DEBUG("* generation " << gen_vec_lv.first);
                    size_t i = 0;
                    for (const auto& lv: gen_vec_lv.second) {
                        MSG_DEBUG("  #" << i);
                        ++i;
                        MSG_DEBUG(lv);
                    }
                }
            }
            return os;
        }
};


/** **/


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struct qtl_pop_type {
    std::string name;
    std::vector<size_t> indices;
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    std::shared_ptr<geno_matrix> gen;
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    std::map<std::string, std::vector<MatrixXd>> LV;
    std::string observed_traits_filename;
    std::vector<trait> observed_traits;
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    /*qtl_pop_type(const std::string& n, const std::vector<size_t>& ind, const geno_matrix* g,*/
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                 /*std::vector<MatrixXd>&& lv, const std::string& otf, std::vector<trait>&& ot)*/
        /*: name(n), indices(ind), gen(g), LV(std::move(lv)), observed_traits_filename(ofs), observed_traits(std::move(ot))*/
    /*{}*/

    size_t size() const
    {
        return observed_traits.front().values.size();
    }

    const MatrixXd& get_LV(const std::string& chr, size_t i) const { return LV.find(chr)->second[i]; }
};


/** **/


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struct pop_data_type {
    std::string name;
    std::map<std::string, std::string> marker_observation_filenames;
    std::string genetic_map_filename;
    std::string pedigree_filename;
    std::string qtl_generation_name;
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    std::vector<std::shared_ptr<geno_matrix>> generations;
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    LV_database LV;
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    std::map<std::string, std::vector<size_t>> families;
    std::map<size_t, std::shared_ptr<geno_matrix>> gen_by_id;

    void
        assemble_chromosomes(const std::vector<chromosome>& map)
        {
            LV.assemble_using_map(map);
        }

    void
        set_qtl_generation(const std::string& name)
        {
            qtl_generation_name = name;
        }
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    std::string save()
    {
        static const char* forbidden = ":?*/\\";
        std::stringstream filename;
        for (char c: name) {
            if (strchr(forbidden, c)) {
                filename << '_';
            } else {
                filename << c;
            }
        }
        filename << ".popdata";
        save_to(filename.str());
        return filename.str();
    }

    void save_to(const std::string& filename)
    {
        std::ofstream ofs(filename);
        write_fourcc(ofs, "SPOP");
        write_str(ofs, name);
        write_size(ofs, marker_observation_filenames.size());
        for (const auto& kv: marker_observation_filenames) {
            write_str(ofs, kv.first);
            write_str(ofs, kv.second);
        }
        write_str(ofs, genetic_map_filename);
        write_str(ofs, pedigree_filename);
        write_str(ofs, qtl_generation_name);
        write_size(ofs, generations.size());
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        for (const auto& g: generations) {
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            write_fourcc(ofs, "SGTE");
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            if (g) {
                write_geno_matrix(ofs, *g);
            } else {
                geno_matrix _;
                write_geno_matrix(ofs, _);
            }
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        }
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        LV.file_io(ofs);
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        write_fourcc(ofs, "SFAM");
        write_size(ofs, families.size());
        for (const auto& kv: families) {
            write_str(ofs, kv.first);
            write_size(ofs, kv.second.size());
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            for (size_t i: kv.second) {
                write_size(ofs, i);
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            }
        }
        write_fourcc(ofs, "SGBI");
        write_size(ofs, gen_by_id.size());
        for (const auto& kv: gen_by_id) {
            write_size(ofs, kv.first);
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            write_size(ofs, std::find(generations.begin(), generations.end(), kv.second) - generations.begin());
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        }
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    }

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    static
        bool pop_check_fourcc(std::ifstream& ifs, const char* fourcc)
        {
            if (check_fourcc(ifs, fourcc)) {
                MSG_ERROR("Could not read FOURCC \"" << fourcc << "\". This is not a valid population data file.", "");
                return true;
            }
            return false;
        }

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    static
        pop_data_type load_from(const std::string& filename)
        {
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#define CHECK_4CC(_fourcc_) if (pop_check_fourcc(ifs, _fourcc_)) { return ret; }
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            std::ifstream ifs(filename);
            pop_data_type ret;
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            CHECK_4CC("SPOP");
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            ret.name = read_str(ifs);
            size_t n_mof = read_size(ifs);
            for (size_t i = 0; i < n_mof; ++i) {
                std::string k = read_str(ifs);
                std::string v = read_str(ifs);
                ret.marker_observation_filenames[k] = v;
            }
            ret.genetic_map_filename = read_str(ifs);
            ret.pedigree_filename = read_str(ifs);
            ret.qtl_generation_name = read_str(ifs);
            size_t n_gen = read_size(ifs);
            for (size_t i = 0; i < n_gen; ++i) {
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                CHECK_4CC("SGTE");
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                ret.generations.emplace_back(std::make_shared<geno_matrix>());
                read_geno_matrix(ifs, *ret.generations.back());
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            }
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            /*ret.LV = LV_database::load_from(ifs);*/
            ret.LV.file_io(ifs);
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            CHECK_4CC("SFAM");
            size_t n_fam = read_size(ifs);
            for (size_t f = 0; f < n_fam; ++f) {
                std::string k = read_str(ifs);
                size_t n_ind = read_size(ifs);
                auto& fam = ret.families[k];
                for (size_t i = 0; i < n_ind; ++i) {
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                    ret.families[k].push_back(read_size(ifs));
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                }
            }
            CHECK_4CC("SGBI");
            size_t n_gbi = read_size(ifs);
            for (size_t g = 0; g < n_gbi; ++g) {
                size_t k = read_size(ifs);
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                ret.gen_by_id[k] = ret.generations[read_size(ifs)];
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            }
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            return ret;
        }

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    size_t size() const { return families.find(qtl_generation_name)->second.size(); }

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    std::shared_ptr<geno_matrix> get_geno_matrix(const std::string& family, size_t ind) const
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    {
        return gen_by_id.find(families.find(family)->second[ind])->second;
    }

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    std::map<std::shared_ptr<geno_matrix>, std::vector<size_t>>
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        all_qtl_geno_matrix() const
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        {
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            std::map<std::shared_ptr<geno_matrix>, std::vector<size_t>> ret;
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            size_t i = 0;
            for (size_t ind: families.find(qtl_generation_name)->second) {
                ret[gen_by_id.find(ind)->second].push_back(i);