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Commit fcb85d47 authored by Damien Leroux's avatar Damien Leroux
Browse files

various small fixes

parent 2d5d90de
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CMakeLists.txt
View file @ fcb85d47
......@@ -23,15 +23,15 @@ project(spell_qtl)
find_package(Boost 1.56.0 REQUIRED)
#set(CMAKE_CONFIGURATION_TYPES Debug Release CACHE INTERNAL FORCE)
FIND_PACKAGE(PythonInterp 3)
FIND_PACKAGE(PythonLibs 3)
if (${PYTHON_VERSION_MAJOR} EQUAL 3)
FIND_PACKAGE(Boost COMPONENTS python3)
SET(Boost_PYTHON_LIBRARY boost_python-py35)
else()
FIND_PACKAGE(Boost COMPONENTS python)
endif()
include_directories(AFTER ${PYTHON_INCLUDE_DIR})
# FIND_PACKAGE(PythonInterp 3)
# FIND_PACKAGE(PythonLibs 3)
# if (${PYTHON_VERSION_MAJOR} EQUAL 3)
# FIND_PACKAGE(Boost COMPONENTS python3)
# SET(Boost_PYTHON_LIBRARY boost_python-py35)
# else()
# FIND_PACKAGE(Boost COMPONENTS python)
# endif()
# include_directories(AFTER ${PYTHON_INCLUDE_DIR})
set(CMAKE_VERBOSE_MAKEFILE ON)
......@@ -68,7 +68,7 @@ set(CMAKE_CXX_STANDARD 14)
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wextra -Wall -Wno-unused-parameter -pthread -fPIC")
SET(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS} -O2 -DNDEBUG -DEIGEN_NO_DEBUG")
SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS} -Og -ggdb")
SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS} -O0 -ggdb")
add_definitions(-DEIGEN_NO_DEPRECATED_WARNING -DVERSION_MAJOR=\"${VERSION_MAJOR}\" -DVERSION_MINOR=\"${VERSION_MINOR}\" -DVERSION_PATCH=\"${VERSION_PATCH}\")
......@@ -86,11 +86,11 @@ include_directories(AFTER ${CMAKE_SOURCE_DIR}/include/ ${CMAKE_SOURCE_DIR}/inclu
include_directories(SYSTEM /usr/include ${Boost_INCLUDE_DIRS} ${EXPAT_INCLUDE_DIR})
include_directories(AFTER /usr/include ${Boost_INCLUDE_DIRS} ${EXPAT_INCLUDE_DIR})
if(${BUILD_FOR_DEPLOYMENT})
set(libstdcpp ${CMAKE_BINARY_DIR}/libstdc++.a)
else(${BUILD_FOR_DEPLOYMENT})
#if(${BUILD_FOR_DEPLOYMENT})
#set(libstdcpp ${CMAKE_BINARY_DIR}/libstdc++.a)
#else(${BUILD_FOR_DEPLOYMENT})
set(libstdcpp "")
endif(${BUILD_FOR_DEPLOYMENT})
#endif(${BUILD_FOR_DEPLOYMENT})
MESSAGE(STATUS "libstdcpp = ${libstdcpp}")
......@@ -157,9 +157,7 @@ if (${BUILD_FOR_DEPLOYMENT})
add_dependencies(spell-marker glibc.h pouet)
add_dependencies(spell-qtl glibc.h)
MESSAGE(STATUS " PROUT ${libstdcpp}")
set(CMAKE_EXE_LINKER_FLAGS "-include ${CMAKE_BINARY_DIR}/glibc.h -rdynamic -static-libgcc")
set(CMAKE_EXE_LINKER_FLAGS "-include ${CMAKE_BINARY_DIR}/glibc.h -rdynamic -static-libgcc -static-libstdc++")
target_link_libraries(spell-marker ${libstdcpp} ${CMAKE_BINARY_DIR}/libgmp.a)
target_link_libraries(spell-qtl ${libstdcpp})
......@@ -171,12 +169,14 @@ else()
SET_SOURCE_FILES_PROPERTIES(${SPELL_PEDIGREE_SRC} ${SPELL_MARKER_SRC} ${SPELL_QTL_SRC}
PROPERTIES
COMPILE_FLAGS "-Wno-int-in-bool-context -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=0 ${SANITIZER_OPT}")
target_compile_definitions(spell-qtl PUBLIC SPELL_USE_XLNT)
set(CMAKE_EXE_LINKER_FLAGS "-rdynamic ${SANITIZER_OPT}")
endif()
target_compile_definitions(spell-qtl PUBLIC SPELL_USE_XLNT)
target_link_libraries(spell-marker dl gmp)
target_link_libraries(spell-qtl ${Boost_PYTHON_LIBRARY} ${PYTHON_LIBRARY} xlnt dl rt)
# target_link_libraries(spell-qtl ${Boost_PYTHON_LIBRARY} ${PYTHON_LIBRARY} xlnt dl rt)
target_link_libraries(spell-qtl xlnt dl rt)
SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
......
include/bayes/cli.h
View file @ fcb85d47
......@@ -157,6 +157,13 @@ struct bn_settings_t {
*/
/*const_cast<pedigree_type&>(pedigree).load(pedigree_filename, false);*/
pedigree.load(pedigree_filename, false);
for (const auto& pg: pedigree.generations) {
if (pg) {
MSG_DEBUG("Generation " << pg->name << " has " << pg->labels);
} else {
MSG_DEBUG("NULL pg");
}
}
}
};
......
include/bayes/output.h
View file @ fcb85d47
......@@ -378,7 +378,7 @@ void write_vector(ofile& ofs, const std::vector<V>& vec, WRITE_ELEM_FUNC write_e
inline
label_type read_label(ifile& ifs)
{
char f, s;
char f = 0, s = 0;
ifs >> f >> s;
return {f, s};
}
......@@ -427,6 +427,7 @@ void read_geno_matrix(ifile& ifs, geno_matrix& mat)
read_matrix(ifs, mat.collect);
read_matrix(ifs, mat.dispatch);
/* also skip symmetries for now. */
MSG_DEBUG("read geno_matrix " << MATRIX_SIZE(mat.inf_mat) << " labels " << mat.labels);
}
......
include/cache2.h
View file @ fcb85d47
......@@ -120,8 +120,7 @@ template <typename Ret, typename... Args>
*/
std::string func_name = get_func_name(func);
chrono_trace _(func_name);
/*
if (0) {
if (1) {
// msg_handler_t::cout() << "INVOKING " << func_name << "(…)" << std::endl;
std::stringstream ss;
ss << "INVOKING " << func_name << "(" << std::endl;
......@@ -130,13 +129,14 @@ template <typename Ret, typename... Args>
for (size_t i = 0; i < avec.size() - 1; ++i) {
ss << avec[i] << ", ";
}
msg_handler_t::cout() << ss.str() << ')';
ss << ')' << std::endl;
msg_handler_t::cout() << ss.str();
}
// std::thread::id this_id = std::this_thread::get_id();
// active_settings->thread_stacks[this_id].push_back(func_name);
// MSG_DEBUG("[" << this_id << ',' << (this_id == active_settings->main_thread) << "] ENTER " << func_name);
msg_handler_t::run_hooks();
*/
// msg_handler_t::run_hooks();
auto ret = func(*args...);
// active_settings->thread_stacks[this_id].pop_back();
// msg_handler_t::run_hooks();
......@@ -196,24 +196,23 @@ template <typename Ret, typename... Args>
*/
std::string func_name = get_func_name(func);
chrono_trace _(func_name);
/*
if (0) {
// msg_handler_t::cout() << "INVOKING " << func_name << "(" << std::endl;
if (1) {
// msg_handler_t::cout() << "INVOKING " << func_name << "(…)" << std::endl;
std::stringstream ss;
ss << "INVOKING " << func_name << "(…)" << std::endl;
ss << "INVOKING " << func_name << "(" << std::endl;
std::vector<std::string> avec;
do_with_arg_pack(avec.push_back(MESSAGE(args)));
for (size_t i = 0; i < avec.size() - 1; ++i) {
ss << avec[i] << ", ";
}
msg_handler_t::cout() << ss.str() << ')';
ss << ')' << std::endl;
msg_handler_t::cout() << ss.str();
}
// std::thread::id this_id = std::this_thread::get_id();
// active_settings->thread_stacks[this_id].push_back(func_name);
// MSG_DEBUG("[" << this_id << ',' << (this_id == active_settings->main_thread) << "] p ENTER " << func_name);
// msg_handler_t::run_hooks();
// m_promise.set_value(proxy(*args...));
*/
// mutex.lock();
auto ret = proxy(*args...);
// mutex.unlock();
......
include/computations/report_output.h
View file @ fcb85d47
......@@ -359,6 +359,9 @@ struct report_stream_text : public report_stream_filesystem {
void matrix_impl(std::string title, const mws_result& mat) override
{
header(title);
for (const auto& sec: mat.m_column_sections) {
MSG_DEBUG("[matrix_impl keys] " << sec.field_labels());
}
m_file << mat << std::endl;
}
void matrix_impl(std::string title, const mws_result_by_block& mat) override
......@@ -480,7 +483,7 @@ make_full_map_item_list(const point_of_interest_type& poi, const region_of_inter
auto ri = R.begin(), rj = R.end();
auto pi = P.begin(), pj = P.end();
auto li = chrom.raw.marker_locus.begin(), lj = chrom.raw.marker_locus.end();
auto ni = chrom.raw.marker_name.begin(), nj = chrom.raw.marker_name.end();
auto ni = chrom.raw.marker_name.begin()/*, nj = chrom.raw.marker_name.end()*/;
for (; li != lj; ++li, ++ni) {
double l = *li;
while (pi != pj && pi->first < l) {
......
include/data/genoprob_computer2.h
View file @ fcb85d47
......@@ -100,7 +100,22 @@ struct geno_prob_computer {
{
auto it = tr_cache.find(dist);
if (it == tr_cache.end()) {
return tr_cache[dist] = this_gen->exp(dist);
auto& TR = tr_cache[dist] = this_gen->exp(dist);
// if ((TR.array() > 1.).any() || (TR.array() < -1.e-13).any()) {
// double max = TR.array().abs().maxCoeff();
// double min = TR.minCoeff();
// MSG_DEBUG("BAD TR @" << dist << "cM min=" << min << " max=" << max << std::endl << TR);
// abort();
// }
double min = TR.minCoeff();
if (min < 0) {
TR.array() += min;
// double max = TR.array().abs().maxCoeff();
// MSG_DEBUG("BAD TR @" << dist << "cM min=" << min << " max=" << max << std::endl << TR);
// abort();
}
normalize_by_col(TR);
return tr_cache[dist];
}
return it->second;
}
......@@ -193,11 +208,19 @@ struct geno_prob_computer {
/*MSG_DEBUG("0 " << lstring[0]);*/
/*MSG_DEBUG(left[0]);*/
for(++l; l <= r; ++l) {
MatrixXd old_kernel = kernel;
kernel = LV->col(l).asDiagonal() * TR[l - 1] * kernel;
double s = kernel.sum();
if (s == 0) {
return false;
}
if (s != s) {
MSG_ERROR("#" << l << " LEFT KERNEL IS NaN", "");
MSG_DEBUG("LV->col(" << l << ") =" << std::endl << LV->col(l).transpose());
MSG_DEBUG("TR[" << (l - 1) << "] =" << std::endl << TR[l - 1]);
MSG_DEBUG("old kernel =" << std::endl << old_kernel);
abort();
}
kernel /= s;
left[l] = kernel;
std::stringstream ss;
......@@ -213,11 +236,19 @@ struct geno_prob_computer {
right[r-1] = right[r] = kernel = (this_gen->stat_dist.array() * LV->col(r).array()).matrix(); //LV->col(r) / LV->col(r).sum();
{ std::stringstream s; s << ".LV" << r; rstring[r-1] = rstring[r] = s.str(); }
for (--r; r > 0; --r) {
MatrixXd old_kernel = kernel;
kernel = LV->col(r).asDiagonal() * TR[r] * kernel;
double s = kernel.sum();
if (s == 0) {
return false;
}
if (s != s) {
MSG_ERROR("#" << r << " RIGHT KERNEL IS NaN", "");
MSG_DEBUG("LV->col(" << l << ") =" << std::endl << LV->col(l).transpose());
MSG_DEBUG("TR[" << (l - 1) << "] =" << std::endl << TR[l - 1]);
MSG_DEBUG("old kernel =" << std::endl << old_kernel);
abort();
}
kernel /= s;
right[r-1] = kernel;
std::stringstream ss;
......@@ -272,11 +303,16 @@ struct geno_prob_computer {
MSG_DEBUG(L);
MSG_DEBUG(MATRIX_SIZE(R));
MSG_DEBUG(R);
MSG_DEBUG(MATRIX_SIZE(this_gen->get_redux()));
MSG_DEBUG(this_gen->get_redux());
MSG_DEBUG(MATRIX_SIZE(redux));
MSG_DEBUG(redux);
#endif
VectorXd vv = redux * (L * R * inv_stat_dist.array()).matrix();
double s = vv.sum();
if (s != s) {
MSG_ERROR("geno_prob_computer spotted a nan!", "");
MSG_DEBUG(vv);
abort();
}
if (s == 0) {
return vv;
}
......@@ -287,7 +323,7 @@ struct geno_prob_computer {
fast_compute_over_segment_raw(const std::vector<double>& steps)
{
MatrixXd ret(unique_labels.size(), steps.size());
/*MSG_DEBUG(MATRIX_SIZE(ret));*/
MSG_DEBUG(MATRIX_SIZE(ret));
size_t l = 0, last = steps.size() - 1, r = !!(LV->outerSize() - 1);
for (size_t i = 0; i < steps.size(); ++i) {
/* FIXME: optimize the CORRECT initialization of l & r */
......@@ -300,7 +336,7 @@ struct geno_prob_computer {
}
if ((ret.col(i).array() < 0).any()) {
MSG_DEBUG("Bad value at column #" << i << std::endl << ret.col(i).transpose());
MSG_DEBUG((*this_gen));
// MSG_DEBUG((*this_gen));
#if 0
MSG_DEBUG("steps: " << steps);
MSG_DEBUG("LV:" << std::endl << (*LV));
......@@ -329,7 +365,7 @@ struct geno_prob_computer {
/*r += i < last;*/
}
}
/*MSG_DEBUG("STATE PROBABILITIES" << std::endl << ret);*/
// MSG_DEBUG("STATE PROBABILITIES" << std::endl << ret);
return ret;
}
......
include/lumping2.h
View file @ fcb85d47
......@@ -222,7 +222,7 @@ struct lumper {
/*const subset& C = *stack.front();*/
/*std::cout << "** " << C << std::endl;*/
/*std::cout << '.' << std::flush;*/
/*MSG_DEBUG("TACKLING " << C);*/
MSG_DEBUG("TACKLING " << C);
stack.pop_back();
/*stack.pop_front();*/
if (C.size() <= 1) {
......@@ -233,20 +233,19 @@ struct lumper {
/*continue;*/
/*}*/
key_map subsets = compute_keys(C, B);
/*MSG_DEBUG("KEYS: " << subsets);*/
/*MSG_DEBUG("KEYS " << labels[subsets.begin()->second.front()] << ": " << subsets);*/
// MSG_DEBUG("KEYS: " << subsets);
/*size_t size = 0;*/
/*while (size != subsets.size()) {*/
/*size = subsets.size();*/
/*}*/
/* MARK */
if (subsets.size() > 1) {
/*MSG_DEBUG("KEYS " << labels[subsets.begin()->second.front()] << ": " << subsets);*/
MSG_DEBUG("WE HAVE A SPLIT " << labels[C.front()] << '/' << labels[B.front()] << ": " << subsets);
P.erase(C);
for (auto& s: subsets) {
auto io = P.insert(s.second);
if (!io.second) {
/*MSG_DEBUG("PROUT SUBSET ALREADY IN P " << (*io.first));*/
MSG_DEBUG("PROUT SUBSET ALREADY IN P " << (*io.first));
}
if (io.first->size() > 1) {
stack.push_back(&*io.first);
......
include/model/model.h
View file @ fcb85d47
......@@ -916,7 +916,9 @@ struct model {
: m_Y(), m_blocks(), m_X(), m_rank(), m_rss(), m_coefficients(), m_solver_type(), m_computed(false)
, m_with_constraints(false), m_ghost_constraint(), m_all_pops(), m_ancestor_names(), m_max_order(1)
, m_threshold(0), m_rank_fixer()
{}
{
MSG_DEBUG("[NEW MODEL] " << keys());
}
model(const value<MatrixXd>& y, double threshold, const collection<const qtl_pop_type*>& pops, const std::map<char, std::string>& anam, size_t mo=1, SolverType st=SolverType::QR)
: m_Y(y)
......@@ -932,7 +934,9 @@ struct model {
, m_threshold(threshold)
, m_rank_fixer()
/*{ MSG_DEBUG("new model " << __LINE__ << " with Y(" << y.innerSize() << ',' << y.outerSize() << ')'); }*/
{}
{
MSG_DEBUG("[NEW MODEL] " << keys());
}
model(const value<MatrixXd>& y, double threshold, const collection<const qtl_pop_type*>& pops, size_t mo=1, SolverType st=SolverType::QR)
: m_Y(y)
......@@ -948,7 +952,9 @@ struct model {
, m_threshold(threshold)
, m_rank_fixer()
/*{ MSG_DEBUG("new model " << __LINE__ << " with Y(" << y.innerSize() << ',' << y.outerSize() << ')'); }*/
{}
{
MSG_DEBUG("[NEW MODEL] " << keys());
}
model(const model& mo)
: m_Y(mo.m_Y)
......@@ -970,6 +976,7 @@ struct model {
model_block_key mbk = std::make_shared<model_block_key_struc>(*kv.first);
m_blocks.emplace(mbk, kv.second);
}
MSG_DEBUG("[NEW MODEL] " << keys());
}
model(const value<MatrixXd>& y, const model& mo)
......@@ -992,6 +999,7 @@ struct model {
model_block_key mbk = std::make_shared<model_block_key_struc>(*kv.first);
m_blocks.emplace(mbk, kv.second);
}
MSG_DEBUG("[NEW MODEL] " << keys());
}
model&
......@@ -1011,6 +1019,7 @@ struct model {
m_ancestor_names = mo.m_ancestor_names;
m_max_order = mo.m_max_order;
m_threshold = mo.m_threshold;
MSG_DEBUG("[ASSIGN MODEL] " << keys());
return *this;
}
......@@ -1031,6 +1040,7 @@ struct model {
m_ancestor_names.swap(mo.m_ancestor_names);
m_max_order = mo.m_max_order;
m_threshold = mo.m_threshold;
MSG_DEBUG("[ASSIGN MODEL] " << keys());
return *this;
}
......@@ -2022,11 +2032,13 @@ public:
{
for (const auto& kv: m_blocks) {
if (kv.first->type == mbk_CI) {
std::vector<std::vector<char>> labels;
for (const auto& kp: m_all_pops) {
const auto& qgn = (*kp)->qtl_generation_name;
labels.emplace_back(qgn.begin(), qgn.end());
}
// std::vector<std::vector<char>> labels;
// for (const auto& kp: m_all_pops) {
// const auto& qgn = (*kp)->qtl_generation_name;
// labels.emplace_back(qgn.begin(), qgn.end());
// }
const std::vector<std::vector<char>>& labels = kv.second->column_labels;
MSG_DEBUG("mbk_CI to print… Labels are " << labels);
mws.add_column_section(MESSAGE("" << kv.first), labels);
} else {
mws.add_column_section(MESSAGE("" << kv.first), labels_to_ancestor_names(*kv.second));
......@@ -2039,11 +2051,12 @@ public:
{
for (const auto& kv: m_blocks) {
if (kv.first->type == mbk_CI) {
std::vector<std::vector<char>> labels;
for (const auto& kp: m_all_pops) {
const auto& qgn = (*kp)->qtl_generation_name;
labels.emplace_back(qgn.begin(), qgn.end());
}
const std::vector<std::vector<char>>& labels = kv.second->column_labels;
MSG_DEBUG("mbk_CI to print… Labels are " << labels);
// for (const auto& kp: m_all_pops) {
// const auto& qgn = (*kp)->qtl_generation_name;
// labels.emplace_back(qgn.begin(), qgn.end());
// }
mws.add_column_section(kv.first, labels);
mws.add_row_section(kv.first, labels);
} else {
......@@ -2123,14 +2136,30 @@ public:
std::ostream& output_keys(std::ostream& os) const
{
auto output_key = [&] (model_block_key k, value<model_block_type> b) {
os << k;
os << '{';
bool first = true;
for (const auto& label: b->column_labels) {
if (first) {
first = false;
} else {
os << ',' << ' ';
}
os << std::string{label.begin(), label.end()};
}
os << "} (" << b->data.rows() << ',' << b->data.cols() << ')';
};
auto i = m_blocks.begin();
auto j = m_blocks.end();
if (i == j) {
return os << "[empty]";
}
os << i->first;
output_key(i->first, i->second);
for (++i; i != j; ++i) {
os << ", " << i->first;
os << ", ";
output_key(i->first, i->second);
}
return os;
}
......
include/python.h 0 → 100644
View file @ fcb85d47
This diff is collapsed.
include/settings.h
View file @ fcb85d47
......@@ -608,6 +608,13 @@ settings_t::finalize()
MSG_DEBUG("COVAR struct " << covar_per_pop.back());
pop_data->extract_subpops(populations, gt.second, observed_traits, linked_pops, covar_per_pop.back());
}
for (const auto& n_p: linked_pops) {
for (const auto& vp: n_p.second) {
for (const auto& p: vp) {
MSG_DEBUG("trait " << n_p.first << " pop " << p->name << ' ' << MATRIX_SIZE(p->gen->inf_mat) << " labels " << p->gen->labels);
}
}
}
for (const auto& pleio: pleiotropic_traits_descr) {
auto& pops = linked_pops[pleio.name];
MatrixXd xtx = MatrixXd::Zero(pleio.traits.size(), pleio.traits.size());
......
src/bayes/jobs.cc
View file @ fcb85d47
......@@ -135,6 +135,12 @@ job_registry = {
[](bn_settings_t* settings) { return settings->count_markers(); },
[](bn_settings_t* settings, size_t mark)
{
std::string filename = settings->job_filename("compute-alleles-per-marker", mark);
if (check_file(filename, false, true, false)) {
return true;
}
/*const std::string& marker_name = settings->marker_names[mark];*/
auto get_obs
= [&] (const std::string& gen, size_t i)
......@@ -148,7 +154,7 @@ job_registry = {
return ret;
};
ofile dump(settings->job_filename("compute-alleles-per-marker", mark));
ofile dump(filename);
std::set<char> used_alleles;
for (const auto& kv: settings->observed_mark) {
......@@ -181,6 +187,10 @@ job_registry = {
ifile unafs(settings->job_filename("unique_n_alleles", 0));
rw_base()(unafs, unique_n_alleles);
}
std::string filename = settings->job_filename("factor-graph", unique_n_alleles[n]);
if (check_file(filename, false, true, false)) {
return true;
}
/*MSG_DEBUG("Pedigree" << std::endl << settings->pedigree);*/
/*MSG_DEBUG("COMPUTING FACTOR GRAPH FOR " << unique_n_alleles[n] << " ALLELES.");*/
/*factor_graph fg(settings->pedigree, unique_n_alleles[n], settings->noise);*/
......@@ -191,7 +201,7 @@ job_registry = {
/*fg->dump();*/
//fg->to_image(MESSAGE("factor-graph-" << unique_n_alleles[n]), "png");
auto I = instance(fg);
ofile of(settings->job_filename("factor-graph", unique_n_alleles[n]));
ofile of(filename);
I->file_io(of);
rw_comb<int, bn_label_type>()(of, fg->domains);
return true;
......@@ -201,6 +211,11 @@ job_registry = {
[](bn_settings_t* settings) { return settings->count_markers(); },
[](bn_settings_t* settings, size_t mark)
{
std::string filename = settings->job_filename("compute-LV", mark);
if (check_file(filename, false, true, false)) {
return true;
}
const std::string& marker_name = settings->marker_names[mark];
std::set<char> used_alleles;
std::map<char, char> allele_obs_to_idx;
......@@ -377,7 +392,7 @@ job_registry = {
MSG_DEBUG(" * " << kv.first << ' ' << kv.second);
}
ofile ofs(settings->job_filename("compute-LV", mark));
ofile ofs(filename);
rw_base()(ofs, output_prob);
}
return true;
......@@ -581,7 +596,7 @@ job_registry = {
pop_data.marker_observation_filenames[om.first] = om.second.filename;
}
settings->load_full_pedigree_data();
// settings->load_full_pedigree_data();
/*pop_data.genetic_map_filename = settings->map_filename;*/
pop_data.pedigree_filename = settings->pedigree_filename;
......
src/computations/frontends.cc
View file @ fcb85d47
......@@ -312,7 +312,7 @@ model_manager&
qtl_detect_iqtlm(model_manager& mm)
{
report_algo_phase("QTL detection: iQTLm");
MSG_INFO("iQTLm starts with: " << mm.get_selection());
// MSG_INFO("iQTLm starts with: " << mm.get_selection());
std::set<std::map<chromosome_value, locus_key>> history;
std::map<chromosome_value, locus_key> last_sel, new_sel;
new_sel = mm.get_selection();
......
src/computations/model.cc
View file @ fcb85d47
......@@ -190,10 +190,13 @@ model_block_type
cross_indicator(const std::string& trait)
{
const auto& pops = active_settings->linked_pops[trait];
// MSG_DEBUG("[Building Cross Indicator] Have " << pops.size() << " distinct pops");
int n_cols = pops.size();
int n_rows = 0;
for (const auto& pop_vec: pops) {
// MSG_DEBUG("[Building Cross Indicator] Pop has " << pop_vec.size() << " subpops");
for (const auto& pop: pop_vec) {
// MSG_DEBUG("[Building Cross Indicator] Subpop has " << pop->size() << " individuals");
n_rows += pop->size();
}
}
......@@ -217,9 +220,9 @@ cross_indicator(const std::string& trait)
val.column_labels.clear();
val.column_labels.reserve(val.data.outerSize());
for (const auto& pop_vec: pops) {
for (const auto& pop: pop_vec) {
val.column_labels.emplace_back(pop->qtl_generation_name.begin(), pop->qtl_generation_name.end());
}
// for (const auto& pop: pop_vec) {
val.column_labels.emplace_back(pop_vec.front()->qtl_generation_name.begin(), pop_vec.front()->qtl_generation_name.end());
// }
}
/*for (const auto& pop: pops) {*/
......@@ -230,7 +233,7 @@ cross_indicator(const std::string& trait)
/*n_rows += sz;*/
/*++p;*/
/*}*/
/*MSG_DEBUG("cross indicator " << MATRIX_SIZE(val) << std::endl << val);*/
// MSG_DEBUG("[Building Cross Indicator] cross indicator " << MATRIX_SIZE(val) << std::endl << val);
/*MSG_QUEUE_FLUSH();*/
return val;
}
......@@ -492,7 +495,9 @@ init_model(const value<MatrixXd>& Y, const value<model_block_type>& indicator, c
// const char* decomp_method = getenv("DECOMP_METHOD"); /* FIXME get rid of this sh\bt. */
// std::string s(decomp_method ? decomp_method : "");
M.m_max_order = 1;
MSG_DEBUG("[NEW MODEL] indicator labels: " << indicator->column_labels);
M.add_block(model_block_key_struc::cross_indicator(), indicator);
MSG_DEBUG("[NEW MODEL] init_model with CI " << M.keys());
// MSG_DEBUG("covariables " << active_settings->with_covariables << " covars.cols=" << covars->data.cols());
if (covars && covars->data.cols() > 0) {
M.add_block(model_block_key_struc::covariables(), covars);
......
src/computations/report.cc
View file @ fcb85d47
......@@ -311,9 +311,12 @@ analysis_report::report_algo_selection(model& Mbase, std::string chrom, double s
{
init_selection_report();
Mbase.compute();
mm.vMcurrent->compute();
MSG_DEBUG("[report_algo_selection] keys: " << mm.vMcurrent->keys());
++m_selection_index;
m_stream.mode(ReportMode::AlgoSel);
select_book("algo_trace").select_sheet("Computations");