Commit f8749dd1 authored by Damien Leroux's avatar Damien Leroux
Browse files

Compiles with clang. executes 10% faster with clang.

parent 143174a8
...@@ -17,6 +17,7 @@ ...@@ -17,6 +17,7 @@
#include "computations/frontends4.h" #include "computations/frontends4.h"
#include <unordered_set> #include <unordered_set>
#include "output_impl.h"
#if 0 #if 0
MatrixXd MatrixXd
......
...@@ -1298,7 +1298,7 @@ double qtl_threshold_all_chromosomes_for_model(const std::string& trait_name, do ...@@ -1298,7 +1298,7 @@ double qtl_threshold_all_chromosomes_for_model(const std::string& trait_name, do
tmp.push_back(make_value<Disk | Sync>(test_with_permutations_for_model, tmp.push_back(make_value<Disk | Sync>(test_with_permutations_for_model,
as_value(trait_name), as_value(n_permut), as_value(trait_name), as_value(n_permut),
as_value((*qtl_chr)->chr), as_value(locus_key(new locus_key_struc())), as_value((*qtl_chr)->chr), as_value(locus_key(new locus_key_struc())),
Mtmp, as_value(y_block_size))); as_value(Mtmp), as_value(y_block_size)));
} }
MatrixXd max_per_chrom(n_permut, tmp.size()); MatrixXd max_per_chrom(n_permut, tmp.size());
for (size_t i = 0; i < tmp.size(); ++i) { for (size_t i = 0; i < tmp.size(); ++i) {
...@@ -1369,4 +1369,5 @@ compute_parental_origins_multipop_extension( ...@@ -1369,4 +1369,5 @@ compute_parental_origins_multipop_extension(
#endif #endif
#include "output_impl.h"
...@@ -509,3 +509,4 @@ compute_parental_origins(const value<population_value>& pop, ...@@ -509,3 +509,4 @@ compute_parental_origins(const value<population_value>& pop,
#endif #endif
#include "output_impl.h"
...@@ -19,6 +19,7 @@ ...@@ -19,6 +19,7 @@
#include "data/chromosome.h" #include "data/chromosome.h"
/*#include "generation_rs.h"*/ /*#include "generation_rs.h"*/
#include "settings.h" #include "settings.h"
#include "output_impl.h"
void read_ld(settings_t* settings, const std::string& qtl_gen, const std::string& filename, std::istream& is) void read_ld(settings_t* settings, const std::string& qtl_gen, const std::string& filename, std::istream& is)
{ {
......
...@@ -17,6 +17,7 @@ ...@@ -17,6 +17,7 @@
#include "input.h" #include "input.h"
#include "input/read_map.h" #include "input/read_map.h"
#include "output_impl.h"
namespace read_data { namespace read_data {
......
...@@ -19,6 +19,7 @@ ...@@ -19,6 +19,7 @@
#include "error.h" #include "error.h"
#include <ios> #include <ios>
#include "output_impl.h"
namespace read_data { namespace read_data {
marker_data read_marker(file& is, int first, int last) { marker_data read_marker(file& is, int first, int last) {
......
...@@ -1818,3 +1818,5 @@ std::ostream& operator << (std::ostream& os, const settings_t& s) ...@@ -1818,3 +1818,5 @@ std::ostream& operator << (std::ostream& os, const settings_t& s)
return os; return os;
} }
#include "output_impl.h"
...@@ -18,6 +18,7 @@ ...@@ -18,6 +18,7 @@
#include "input.h" #include "input.h"
#include "input/read_trait.h" #include "input/read_trait.h"
//#include "error.h" //#include "error.h"
#include "output_impl.h"
static static
......
...@@ -20,6 +20,7 @@ ...@@ -20,6 +20,7 @@
#include "geno_matrix.h" #include "geno_matrix.h"
#include "computations.h" #include "computations.h"
#include "chrono.h" #include "chrono.h"
#include "output_impl.h"
double settings_t::get_threshold(const std::string& trait, size_t y_block_size) double settings_t::get_threshold(const std::string& trait, size_t y_block_size)
......
...@@ -159,3 +159,4 @@ ped_settings_t* ped_settings_t::from_args(int argc, const char** argv) ...@@ -159,3 +159,4 @@ ped_settings_t* ped_settings_t::from_args(int argc, const char** argv)
void print_usage() { print_usage_impl(false, arguments); } void print_usage() { print_usage_impl(false, arguments); }
#include "output_impl.h"
...@@ -17,6 +17,7 @@ ...@@ -17,6 +17,7 @@
#include "pedigree.h" #include "pedigree.h"
#include "pedigree_settings.h" #include "pedigree_settings.h"
#include "output_impl.h"
void print_usage(); void print_usage();
......
...@@ -22,6 +22,7 @@ ...@@ -22,6 +22,7 @@
#include "cache2.h" #include "cache2.h"
#include "geno_matrix.h" #include "geno_matrix.h"
#include "file.h" #include "file.h"
#include "output_impl.h"
size_t file::open_count = 3; /* stdin, stdout, stderr */ size_t file::open_count = 3; /* stdin, stdout, stderr */
std::map<std::string, size_t> file::debug_open_files; std::map<std::string, size_t> file::debug_open_files;
......
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