Compiles with clang. executes 10% faster with clang.

src/computations/frontends.cc

@@ -17,6 +17,7 @@
 
 #include "computations/frontends4.h"
 #include <unordered_set>
+#include "output_impl.h"
 
 #if 0
 MatrixXd

src/computations/model.cc

@@ -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,
                                               as_value(trait_name), as_value(n_permut),
                                               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());
     for (size_t i = 0; i < tmp.size(); ++i) {
@@ -1369,4 +1369,5 @@ compute_parental_origins_multipop_extension(
 #endif
 
 
+#include "output_impl.h"
 

src/computations/probabilities.cc

@@ -509,3 +509,4 @@ compute_parental_origins(const value<population_value>& pop,
 #endif
 
 
+#include "output_impl.h"

src/input/ld_matrices.cc

@@ -19,6 +19,7 @@
 #include "data/chromosome.h"
 /*#include "generation_rs.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)
 {

src/input/read_map.cc

@@ -17,6 +17,7 @@
 
 #include "input.h"
 #include "input/read_map.h"
+#include "output_impl.h"
 
 namespace read_data {
 

src/input/read_mark.cc

@@ -19,6 +19,7 @@
 #include "error.h"
 
 #include <ios>
+#include "output_impl.h"
 
 namespace read_data {
 marker_data read_marker(file& is, int first, int last) {

src/input/read_settings.cc

@@ -1818,3 +1818,5 @@ std::ostream& operator << (std::ostream& os, const settings_t& s)
     return os;
 }
 
+
+#include "output_impl.h"

src/input/read_trait.cc

@@ -18,6 +18,7 @@
 #include "input.h"
 #include "input/read_trait.h"
 //#include "error.h"
+#include "output_impl.h"
 
 
 static

src/main.cc

@@ -20,6 +20,7 @@
 #include "geno_matrix.h"
 #include "computations.h"
 #include "chrono.h"
+#include "output_impl.h"
 
 
 double settings_t::get_threshold(const std::string& trait, size_t y_block_size)

src/pedigree/cli.cc

@@ -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); }
 
+#include "output_impl.h"

src/pedigree/main.cc

@@ -17,6 +17,7 @@
 
 #include "pedigree.h"
 #include "pedigree_settings.h"
+#include "output_impl.h"
 
 void print_usage();
 

src/static_data.cc

@@ -22,6 +22,7 @@
 #include "cache2.h"
 #include "geno_matrix.h"
 #include "file.h"
+#include "output_impl.h"
 
 size_t file::open_count = 3;  /* stdin, stdout, stderr */
 std::map<std::string, size_t> file::debug_open_files;