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QTL
spell-qtl
Commits
f8749dd1
Commit
f8749dd1
authored
Jun 15, 2017
by
Damien Leroux
Browse files
Compiles with clang. executes 10% faster with clang.
parent
143174a8
Changes
32
Show whitespace changes
Inline
Side-by-side
src/computations/frontends.cc
View file @
f8749dd1
...
...
@@ -17,6 +17,7 @@
#include
"computations/frontends4.h"
#include
<unordered_set>
#include
"output_impl.h"
#if 0
MatrixXd
...
...
src/computations/model.cc
View file @
f8749dd1
...
...
@@ -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
View file @
f8749dd1
...
...
@@ -509,3 +509,4 @@ compute_parental_origins(const value<population_value>& pop,
#endif
#include
"output_impl.h"
src/input/ld_matrices.cc
View file @
f8749dd1
...
...
@@ -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
View file @
f8749dd1
...
...
@@ -17,6 +17,7 @@
#include
"input.h"
#include
"input/read_map.h"
#include
"output_impl.h"
namespace
read_data
{
...
...
src/input/read_mark.cc
View file @
f8749dd1
...
...
@@ -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
View file @
f8749dd1
...
...
@@ -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
View file @
f8749dd1
...
...
@@ -18,6 +18,7 @@
#include
"input.h"
#include
"input/read_trait.h"
//#include "error.h"
#include
"output_impl.h"
static
...
...
src/main.cc
View file @
f8749dd1
...
...
@@ -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
View file @
f8749dd1
...
...
@@ -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
View file @
f8749dd1
...
...
@@ -17,6 +17,7 @@
#include
"pedigree.h"
#include
"pedigree_settings.h"
#include
"output_impl.h"
void
print_usage
();
...
...
src/static_data.cc
View file @
f8749dd1
...
...
@@ -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
;
...
...
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