output.h 52.5 KB
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/* Spell-QTL  Software suite for the QTL analysis of modern datasets.
 * Copyright (C) 2016,2017  Damien Leroux <damien.leroux@inra.fr>, Sylvain Jasson <sylvain.jasson@inra.fr>
 *
 * 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/>.
 */

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#ifndef _SPELL_BAYES_OUTPUT_H_
#define _SPELL_BAYES_OUTPUT_H_

#include <map>
#include <vector>
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#include <map>
#include <set>
#include <unordered_set>
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#include <unordered_map>
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#include <string>
#include <iostream>
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#include "file.h"
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#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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#include "linear_combination.h"
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/** FOURCC **/

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

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

/** SIZE_T **/

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

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

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/** PTRDIFF_T **/

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

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

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/** STRING **/

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

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

/** DOUBLE **/

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void write_double(ofile& ofs, double sz)
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{
    ofs.write((const char*) &sz, sizeof sz);
}

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

/** INT **/

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void write_int(ofile& ofs, int sz)
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{
    ofs.write((const char*) &sz, sizeof sz);
}

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

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/** CHAR **/

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void write_char(ofile& ofs, char sz)
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{
    ofs.write((const char*) &sz, sizeof sz);
}

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

#if 0
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/** FAST_POLYNOM **/

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void write_fast_polynom(ofile& ofs, const fast_polynom& fp)
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{
    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);
    }
}

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fast_polynom read_fast_polynom(ifile& ifs, int& original_key)
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{
    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 **/

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

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inline algebraic_genotype read_algebraic_genotype(ifile& ifs, const std::map<int, fast_polynom>& pt)
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{
    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 **/

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inline void write_genomatrix(ofile& ofs, const GenoMatrix& mat)
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{
    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
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void read_genomatrix(ifile& ifs, GenoMatrix& mat)
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{
    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(ofile& 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);
    }
}

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geno_matrix* read_geno_matrix(ifile& 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>
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void read_matrix(ifile& ifs, Eigen::Matrix<SCALAR, ROW, COL, C, D, E>& mat)
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{
    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>
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void write_matrix(ofile& ofs, const Eigen::Matrix<SCALAR, ROW, COL, C, D, E>& mat)
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{
    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>
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void read_vector(ifile& ifs, std::vector<V>& vec, READ_ELEM_FUNC read_elem)
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{
    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>
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void write_vector(ofile& ofs, const std::vector<V>& vec, WRITE_ELEM_FUNC write_elem)
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{
    write_size(ofs, vec.size());
    for (const auto& e: vec) {
        write_elem(ofs, e);
    }
}


/** LABEL_TYPE **/

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label_type read_label(ifile& ifs)
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{
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    char f = 0, s = 0;
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    ifs >> f >> s;
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    MSG_DEBUG("[read_label] " << int(f) << ':' << int(s));
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    return {f, s};
}

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


/** GENO_MATRIX **/

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void write_geno_matrix(ofile& 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. */
}

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void read_geno_matrix(ifile& ifs, geno_matrix& mat)
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{
    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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    MSG_DEBUG("read geno_matrix " << MATRIX_SIZE(mat.inf_mat) << " labels " << mat.labels);
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}


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void write_geno_matrix(ofile& ofs, const geno_matrix* ptr)
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{
    write_geno_matrix(ofs, *ptr);
}

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geno_matrix* read_geno_matrix(ifile& ifs)
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{
    geno_matrix* ret = new geno_matrix();
    read_geno_matrix(ifs, *ret);
    return ret;
}


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

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

    virtual ~rw_any() {}

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

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    void operator () (ifile& ifs, std::string& s) { s = read_str(ifs); }
    void operator () (ofile& ofs, const std::string& s) { write_str(ofs, s); }
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    void operator () (ifile& ifs, char& i) { i = read_char(ifs); }
    void operator () (ofile& ofs, char i) { write_char(ofs, i); }
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    void operator () (ifile& ifs, int& i) { i = read_int(ifs); }
    void operator () (ofile& ofs, int i) { write_int(ofs, i); }
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    void operator () (ifile& ifs, bool& i) { i = !!read_char(ifs); }
    void operator () (ofile& ofs, bool i) { write_char(ofs, i); }
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    void operator () (ifile& ifs, double& i) { i = read_double(ifs); }
    void operator () (ofile& ofs, double i) { write_double(ofs, i); }
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    void operator () (ifile& ifs, size_t& i) { i = read_size(ifs); }
    void operator () (ofile& ofs, size_t i) { write_size(ofs, i); }
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    void operator () (ifile& ifs, ptrdiff_t& i) { i = read_ptrdiff(ifs); }
    void operator () (ofile& ofs, ptrdiff_t i) { write_ptrdiff(ofs, i); }
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    void operator () (ifile& ifs, label_type& l) { l = {read_char(ifs), read_char(ifs)}; }
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    void operator () (ofile& ofs, label_type& l) { write_char(ofs, l.first()); write_char(ofs, l.second()); }

    template <typename K>
        auto operator () (ifile& fs, K& has_file_io)
        -> decltype(has_file_io.file_io(fs), void())
        {
            has_file_io.file_io(fs);
        }

    template <typename K>
        auto operator () (ofile& fs, K& has_file_io)
        -> decltype(has_file_io.file_io(fs), void())
        {
            has_file_io.file_io(fs);
        }
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    template <typename V>
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        void operator () (ifile& ifs, std::set<V>& vec)
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        {
            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>
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        void operator () (ofile& ofs, std::set<V>& vec)
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        {
            if (fourcc(ofs, "OSET")) { return; }
            write_size(ofs, vec.size());
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            for (auto& e: vec) {
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                ref() (ofs, e);
            }
        }


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

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    void operator () (ifile& ifs, std::vector<bool>::reference i) { i = !!read_char(ifs); }
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    template <typename V, typename A>
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        void operator () (ifile& ifs, std::vector<V, A>& vec)
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        {
            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>
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        void operator () (ofile& ofs, std::vector<V, A>& vec)
        {
            if (fourcc(ofs, "VECT")) { return; }
            write_size(ofs, vec.size());
            for (auto& e: vec) {
                ref() (ofs, e);
            }
        }

        void operator () (ofile& ofs, std::vector<bool>& vec)
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        {
            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>
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        void operator () (ifile& ifs, std::vector<V, A>& vec, RWElem rw_elem)
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        {
            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>
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        void operator () (ofile& ofs, std::vector<V, A>& vec, RWElem rw_elem)
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        {
            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>
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        void operator () (ifile& ifs, std::map<K, V, A, C>& map)
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        {
            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>
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        void operator () (ifile& ifs, std::unordered_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 () (ofile& ofs, std::map<K, V, A, C>& map)
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        {
            if (fourcc(ofs, "MAP ")) { return; }
            write_size(ofs, map.size());
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            for (auto& kv: map) {
                ref() (ofs, const_cast<K&>(kv.first));
                ref() (ofs, kv.second);
            }
        }

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

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    template <typename IO, typename A, typename B>
        void operator () (IO& fs, std::pair<A, B>& p)
        {
            ref() (fs, p.first);
            ref() (fs, p.second);
        }

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    template <typename SCALAR, int ROW, int COL, int C, int D, int E>
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        void operator () (ifile& ifs, Eigen::Matrix<SCALAR, ROW, COL, C, D, E>& mat) { read_matrix(ifs, mat); }
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    template <typename SCALAR, int ROW, int COL, int C, int D, int E>
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        void operator () (ofile& ofs, Eigen::Matrix<SCALAR, ROW, COL, C, D, E>& mat) { write_matrix(ofs, mat); }
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    void operator () (ifile& ifs, geno_matrix& mat) { read_geno_matrix(ifs, mat); }
    void operator () (ofile& ofs, geno_matrix& mat) { write_geno_matrix(ofs, mat); }
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    void operator () (ifile& ifs, std::shared_ptr<geno_matrix>& ptr)
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    {
        ptr.reset();
        ptr = std::make_shared<geno_matrix>();
        ref() (ifs, *ptr);
        if (!ptr->size()) {
            ptr.reset();
        }
    }

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    void operator () (ofile& ofs, std::shared_ptr<geno_matrix>& ptr)
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    {
        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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/** **/

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struct gamete_LV_type {
    bool is_single;
    typedef union _gamete_lv_value_type {
        Eigen::Vector2d unary;
        Eigen::Vector4d binary;
        
        template <typename STREAM_TYPE>
            void
            file_io(STREAM_TYPE& fs)
            {
                rw_base rw;
                rw(fs, binary);
            }
        
        _gamete_lv_value_type() : binary() {}
        _gamete_lv_value_type(const _gamete_lv_value_type& other) : binary(other.binary) {}
        _gamete_lv_value_type(const Eigen::Vector2d& v) { unary = v; }
        _gamete_lv_value_type(const Eigen::Vector4d& v) { binary = v; }
        friend std::ostream& operator << (std::ostream& os, const _gamete_lv_value_type& glv) { return os << glv.binary.transpose(); }
    } gamete_lv_value_type;
    
    std::map<std::string, gamete_lv_value_type> lv;

    friend std::ostream& operator << (std::ostream& os, const gamete_LV_type& glv) { return os << (glv.is_single ? "Unary{" : "Binary{") << glv.lv << '}'; }
    
    void get(const std::string& key, Eigen::Vector2d& value) const
    {
        auto it = lv.find(key);
        if (it == lv.end()) {
            value = Eigen::Vector2d::Zero();
        } else {
            value = it->second.unary;
        }
    }

    void get(const std::string& key, Eigen::Vector4d& value) const
    {
        auto it = lv.find(key);
        if (it == lv.end()) {
            value = Eigen::Vector4d::Zero();
        } else {
            value = it->second.binary;
        }
    }
    
    void add_normalized(const std::string& key, const Eigen::VectorXd& value) { if (value.size() == 2) { lv[key].unary = value; } else { lv[key].binary = value; } }

    template <typename T>
    void add(const std::string& key, const T& value) { add_normalized(key, value); }

    template <typename STREAM_TYPE>
        void
        file_io(STREAM_TYPE& fs)
        {
            rw_base rw;
            if (rw.fourcc(fs, "GLVT")) { return; }
            rw(fs, is_single);
            rw(fs, lv);
        }
};

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struct gamete_LV_database {
    /* IND.ped / MARK => 1 or 2 gametes (.second will be empty when cross type is DH) */
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    std::map<int, gamete_LV_type> data;
    std::map<double, Eigen::Matrix2d> cache2;
    std::map<double, Eigen::Matrix4d> cache4;
    std::vector<Eigen::Matrix2d> tr2;
    std::vector<Eigen::Matrix4d> tr4;
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    gamete_LV_database() : data(), cache2(), cache4() {}
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    Eigen::Matrix2d
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    get_TR_unary(double dist)
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    {
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        auto it = cache2.find(dist);
        if (it == cache2.end()) {
            double s = .5 + exp(-2. * dist) * .5;
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            double r = 1. - s;
            Eigen::Matrix2d ret;
            ret << s, r, r, s;
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            cache2[dist] = ret;
            return ret;
        }
        return it->second;
    }
    
    Eigen::Matrix4d
    get_TR_binary(double dist)
    {
        auto it = cache4.find(dist);
        if (it == cache4.end()) {
            double s = .5 + exp(-2. * dist) * .5;
            double r = 1. - s;
            double rs = r * s;
            double r2 = r * r;
            double s2 = s * s;
            Eigen::Matrix4d ret;
            ret <<
                s2, rs, rs, r2,
                rs, s2, r2, rs,
                rs, r2, s2, rs,
                r2, rs, rs, s2;
            cache4[dist] = ret;
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            return ret;
        }
        return it->second;
    }
    
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    void get_TR(double dist, Eigen::Matrix2d& result) { result = get_TR_unary(dist); }
    void get_TR(double dist, Eigen::Matrix4d& result) { result = get_TR_binary(dist); }

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    void
    add_gametes(const std::string& mark, int ind, const VectorXd& lv, bool dh)
    {
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        auto it = data.find(ind);
        if (it == data.end()) {
            data[ind].is_single = dh;
        } else {
            if (dh != it->second.is_single) {
                MSG_ERROR("Individual #" << ind << " was first declared as " << (it->second.is_single ? "intercross" : "doubled haploid") << " and is now requested to be the other kind.", "");
            }
        }
        data[ind].add(mark, (lv.array() > 0).select(VectorXd::Ones(lv.size()), VectorXd::Zero(lv.size())).matrix());
//         data[ind].add(mark, lv * (lv.array() > 0).cast<double>().sum());
//         data[ind].add(mark, lv);
#if 0
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        Eigen::Vector2d g1, g2;
        MSG_DEBUG("add_gametes mark=" << mark << " ind=" << ind << " lv=" << lv.transpose() << " dh=" << std::boolalpha << dh);
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        if (!dh) {
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            g1(0) = lv(0) + lv(1);
            g1(1) = lv(2) + lv(3);
            g2(0) = lv(0) + lv(2);
            g2(1) = lv(1) + lv(3);
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        } else {
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            g1 = lv;
            g2(0) = g2(1) = 0;
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        }
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        data[ind][mark] = g1;
        data[-ind][mark] = g2;
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#endif
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    }

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    void init_tr(bool is_single, const std::vector<double>& distances)
    {
        if (is_single) {
            if (tr2.size()) {
                return;
            }
            tr2.reserve(distances.size());
            for (double d: distances) {
                tr2.emplace_back();
                get_TR(d, tr2.back());
            }
        } else {
            if (tr4.size()) {
                return;
            }
            tr4.reserve(distances.size());
            for (double d: distances) {
                tr4.emplace_back();
                get_TR(d, tr4.back());
            }
        }
    }
    
    template <typename V, typename M>
    double gamete_likelihood_impl(std::vector<M>& TR, V& accum, const std::vector<std::string>& marker_names, const gamete_LV_type& gam)
    {
        auto name_i = marker_names.begin();
        V tmp;
        gam.get(*name_i++, tmp);
//         accum = tmp / tmp.sum();
// //         accum = tmp / (tmp.array() > 0).template cast<double>().sum();
        accum = tmp * .25;
        for (const auto& t: TR) {
            gam.get(*name_i++, tmp);
            MSG_DEBUG("accum = " << accum.transpose() << " LV = " << tmp.transpose());
            accum = accum.transpose() * t * tmp.asDiagonal();
        }
        MSG_DEBUG("final accum = " << accum.transpose());
        return accum.sum();
    }
    
    double gamete_likelihood(int ind, const gamete_LV_type& gam, const std::vector<std::string>& marker_names, const std::vector<double>& distances)
    {
        init_tr(gam.is_single, distances);
        if (gam.is_single) {
            Eigen::Vector2d accum;
            return gamete_likelihood_impl(tr2, accum, marker_names, gam);
        } else {
            Eigen::Vector4d accum;
            return gamete_likelihood_impl(tr4, accum, marker_names, gam);
        }
    }
    
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    double
    map_likelihood(const std::vector<std::string>& marker_names, const std::vector<double>& distances)
    {
        if (marker_names.size() != distances.size() + 1) {
            MSG_ERROR("Need to have exactly one more marker name than the number of inter-marker distances", "");
            return NAN;
        }
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        double ret = 0;
        for (const auto& kv: data) {
            ret += log(gamete_likelihood(kv.first, kv.second, marker_names, distances));
        }
        return ret;
#if 0
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        // implicitly, we just garanteed there is at least one marker name in the list
        Eigen::Vector2d all_accum;
        all_accum(0) = all_accum(1) = 0;
        std::vector<Eigen::Matrix2d> TR;
        TR.reserve(distances.size());
        for (double d: distances) {
            TR.push_back(get_TR(d));
        }
        double ret = 0;
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        MSG_DEBUG("DATA" << std::endl << data);
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        for (auto& kv: data) {
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//             int ind = kv.first;
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            MSG_DEBUG("ON GAMETE #" << kv.first);
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            auto& LV = kv.second;
            auto name_i = marker_names.begin();
            auto& gam0 = LV[*name_i++];
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            Eigen::Vector2d accum = gam0;
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//             accum << .5, .5;
//             std::vector<double> norms;
//             double norm_accum = 0;
//             norms.reserve(distances.size());
//             norms.push_back(1.);
//             norm_accum -= log(norms.back());
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            for (size_t i = 0; i < TR.size(); ++i, ++name_i) {
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//                 MSG_DEBUG("accum = " << accum.transpose());
//                 MSG_DEBUG("TR[" << i << ']' << std::endl << TR[i]);
                MSG_DEBUG("accum = " << accum.transpose() << " LV[" << (*name_i) << "] = " << LV[*name_i].transpose());
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                accum = accum.transpose() * TR[i] * LV[*name_i].asDiagonal();
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//                 norms.push_back(accum.lpNorm<2>());
//                 if (norms.back() == 0) {
//                     MSG_ERROR("Have a zero vector, aborting.", "");
//                     return NAN;
//                 }
//                 accum.array() /= norms.back();
//                 norm_accum += log(norms.back());
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            }
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            MSG_DEBUG("final accum = " << accum.transpose());
//             ret += norm_accum + log(accum.lpNorm<1>());
            ret += log(accum.lpNorm<1>());
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        }
        return ret;
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#endif
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    }

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

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

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

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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();
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                size_t n_condensed_mark = chr.condensed.marker_name.size();
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                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});
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                /*MSG_DEBUG("[assemble.using.map] #haplo_size=" << chr.haplo_sizes.size());*/
                /*MSG_QUEUE_FLUSH();*/
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                for (size_t ind = 0; ind < n_ind; ++ind) {
                    auto& mat = ind_LVmat[ind];
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                    mat = MatrixXd::Ones(n_states, n_condensed_mark);
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                    size_t m = 0;
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                    int haplo_counter = 0;
                    auto haplo_size_i = chr.haplo_sizes.begin();
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                    for (const auto& mark: chr.raw.marker_name) {
                        const auto& svec = mark_ind_lv.find(mark)->second;
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                        /*MSG_DEBUG("[assemble.using.map] haplo_size=" << (*haplo_size_i) << " column=" << m);*/
                        /*MSG_QUEUE_FLUSH();*/
                        mat.col(m).array() *= svec[ind].array();
                        ++haplo_counter;
                        if (haplo_counter == *haplo_size_i) {
                            ++m;
                            ++haplo_size_i;
                            haplo_counter = 0;
                        }
                    }
                    auto hi = chr.begin();
                    for (int c = 0; c < mat.cols(); ++c, ++hi) {
                        double sum = mat.col(c).sum();
                        if (sum == 0) {
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                            /*std::stringstream ss;*/
                            /*ss << "Detected inconsistent observations! Generation is " << gen << ", chromosome " << chr.name << ", individual #" << (ind + 1) << ", involving markers";*/
                            /*auto haplo = *hi;*/
                            /*for (size_t i = haplo.first; i < haplo.second; ++i) {*/
                                /*ss << ' ' << chr.raw.marker_name[i];*/
                            /*}*/
                            /*MSG_WARNING(ss.str());*/
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                        } else {
                            mat.col(c) /= sum;
                        }
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                    }
                }
            }
        }
    }

    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;
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                auto it = chr_gen_lv_vec.second.find(gen);
                if (it == chr_gen_lv_vec.second.end()) {
                    /* whine */
                    MSG_ERROR("Generation " << gen << " doesn't exist!", "Double-check the generation names given in commandline.");
                    continue;
                }
                const auto& lv_vec = it->second;
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                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)
        {
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            ifile ifs(filename);
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            LV_database ret;
            ret.file_io(ifs);
            return ret;
        }

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

    /*
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    static
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        bool lv_check_fourcc(ifile& ifs, const char* fourcc)
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        {
            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)
        {
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            ifile ifs(filename);
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            return load_from(ifs);
        }

    static
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        LV_database load_from(ifile& ifs)
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        {
            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)
    {
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        ofile ofs(filename);
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        save_to(ofs);
    }

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    void save_to(ofile& ofs)
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    {
        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) {
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                os << "CHROMOSOME " << chr_gen_vec_lv.first << std::endl;
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                for (const auto& gen_vec_lv: chr_gen_vec_lv.second) {
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                    os << "* generation " << gen_vec_lv.first << std::endl;
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                    size_t i = 0;
                    for (const auto& lv: gen_vec_lv.second) {
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                        os << "  #" << i << std::endl;
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                        ++i;
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                        os << lv << std::endl;
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                    }
                }
            }
            return os;
        }
};


/** **/


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template <typename V>
std::vector<V>
filter_vector(const std::vector<V>& vec, const std::vector<size_t>& list)
{
    std::vector<V> ret;
    ret.reserve(list.size());
    for (size_t i: list) {
        ret.push_back(vec[i]);
    }
    return ret;
}


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struct qtl_pop_type {
    std::string name;
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    std::string qtl_generation_name;
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    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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    std::map<char, std::string> ancestor_names;
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    trait covariables;
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    qtl_pop_type()
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        : name(), qtl_generation_name(), indices(), gen(), LV(), observed_traits_filename(), observed_traits(), covariables()
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    {}
    qtl_pop_type(const std::string& n, const std::string& qgn, const std::vector<size_t>& i, std::shared_ptr<geno_matrix> g,
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                 const std::map<std::string, std::vector<MatrixXd>>& lv, const std::string& otf, const std::vector<trait>& ot,
                 const std::map<char, std::string>& anam, const trait& covar)
        : name(n), qtl_generation_name(qgn), indices(i), gen(g), LV(lv), observed_traits_filename(otf), observed_traits(ot), ancestor_names(anam), covariables(covar)
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    {
        /*MSG_DEBUG("new qtl_pop with " << ancestor_names.size() << " ancestor names");*/
        /*for (const auto& kv: ancestor_names) {*/
            /*MSG_DEBUG(" * " << kv.first << ": " << kv.second);*/
        /*}*/
    }
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    std::shared_ptr<qtl_pop_type>
        filter_clone(const trait& this_trait) const
        {
            const std::vector<size_t>& keep = this_trait.good_indices;
            std::shared_ptr<qtl_pop_type> ret = std::make_shared<qtl_pop_type>();
            ret->name = name;
            ret->qtl_generation_name = qtl_generation_name;
            ret->gen = gen;
            ret->observed_traits_filename = observed_traits_filename;
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            for (const auto& t: observed_traits) {
                if (t.name == this_trait.name) {
                    ret->observed_traits.emplace_back(t);
                }
            }
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            ret->ancestor_names = ancestor_names;
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            auto i = indices.begin();
            auto j = indices.end();
            auto filt = keep.begin();
            auto filt_end = keep.end();

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            ret->covariables = covariables % this_trait;

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            /*MSG_DEBUG("Filtering <" << indices << "> with <" << keep << '>');*/
            std::vector<size_t> keep_indices;
            keep_indices.reserve(keep.size());
            while (filt != filt_end && i != j) {
                if (*i == *filt) {
                    keep_indices.push_back(i - indices.begin());
                    ++i;
                    ++filt;
                } else if (*i < *filt) {
                    ++i;
                } else {
                    ++filt;
                }
            }

            ret->indices = filter_vector(indices, keep_indices);
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            /*MSG_DEBUG("Filtered indices " << ret->indices << " (" << ret->indices.size() << ')');*/
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            for (const auto& kv: LV) {
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                /*MSG_DEBUG("Filtering LV on " << kv.first << ", keeping " << keep_indices.size() << " elements");*/
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                ret->LV[kv.first] = filter_vector(kv.second, keep_indices);
            }
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            /*MSG_DEBUG("Resulting LV (" << ret->LV.size() << ')');*/
            /*for (const auto& lv: ret->LV) {*/
                /*MSG_DEBUG("** " << lv.first << " (" << lv.second.size() << ')');*/
                /*auto ri = ret->indices.begin();*/
                /*for (const auto& v: lv.second) {*/
                    /*MSG_DEBUG("* " << (*ri++));*/
                    /*MSG_DEBUG("" << v);*/
                /*}*/
            /*}*/
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            return ret;
        }
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    size_t size() const
    {
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        /*return observed_traits.front().values.size();*/
        return indices.size();
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    }

    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;
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    std::map<char, std::string> ancestor_names;
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    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(const std::string& dir)
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    {
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        std::stringstream filename;
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//        for (char c: name) {
//            if (strchr(forbidden, c)) {
//                filename << '_';
//            } else {
//                filename << c;
//            }
//        }
        filename << dir << '/' << name << ".spell-marker.data";
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        save_to(filename.str());
        return filename.str();
    }

    void save_to(const std::string& filename)
    {
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        ofile ofs(filename);
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        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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            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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        write_fourcc(ofs, "ANAM");
        write_size(ofs, ancestor_names.size());
        for (const auto& kv: ancestor_names) {
            write_char(ofs, kv.first);
            write_str(ofs, kv.second);
        }
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    }

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        bool pop_check_fourcc(ifile& ifs, const char* fourcc)
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        {
            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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        pop_data_type* load_from(const std::string& filename)
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        {
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            ifile ifs(filename);
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            pop_data_type* ret = new pop_data_type();
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            ret->name = read_str(ifs);
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            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);
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            }