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QTL
spell-qtl
Commits
27d6a61a
Commit
27d6a61a
authored
Jul 27, 2018
by
Damien Leroux
Browse files
Reorganization of include files. Added missing license.
parent
679163b5
Changes
201
Hide whitespace changes
Inline
Side-by-side
.idea/misc.xml
View file @
27d6a61a
...
...
@@ -11,6 +11,7 @@
<excludeRoots>
<file
path=
"$PROJECT_DIR$/PAG_XXV"
/>
<file
path=
"$PROJECT_DIR$/attic"
/>
<file
path=
"$PROJECT_DIR$/attic/attic"
/>
<file
path=
"$PROJECT_DIR$/cmake-build-debug/CMakeFiles"
/>
<file
path=
"$PROJECT_DIR$/cmake-build-release/CMakeFiles"
/>
<file
path=
"$PROJECT_DIR$/data"
/>
...
...
@@ -18,7 +19,6 @@
<file
path=
"$PROJECT_DIR$/examples/F3-outbred-pleio/spell"
/>
<file
path=
"$PROJECT_DIR$/examples/small/S.cache"
/>
<file
path=
"$PROJECT_DIR$/examples/three_parents_F2/spell"
/>
<file
path=
"$PROJECT_DIR$/include/attic"
/>
<file
path=
"$PROJECT_DIR$/sample-data"
/>
<file
path=
"$PROJECT_DIR$/sandbox"
/>
<file
path=
"$PROJECT_DIR$/simulation"
/>
...
...
@@ -38,8 +38,12 @@
<file
path=
"$PROJECT_DIR$/src/experiments"
/>
<file
path=
"$PROJECT_DIR$/src/include-graphs"
/>
<file
path=
"$PROJECT_DIR$/src/misc_outputs"
/>
<file
path=
"$PROJECT_DIR$/src/r-glue/package"
/>
<file
path=
"$PROJECT_DIR$/test_ril_ril2"
/>
<file
path=
"$PROJECT_DIR$/tests/TestCodeCoverage"
/>
</excludeRoots>
</component>
<component
name=
"JavaScriptSettings"
>
<option
name=
"languageLevel"
value=
"ES6"
/>
</component>
</project>
\ No newline at end of file
3rd-party/ThreadPool/ThreadPool.h
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27d6a61a
...
...
@@ -14,7 +14,7 @@
#include
<future>
#include
<functional>
#include
<stdexcept>
#include
"error.h"
#include
"
io/
error.h"
class
ThreadPool
{
...
...
CMakeLists.txt
View file @
27d6a61a
...
...
@@ -108,18 +108,18 @@ set(SPELL_MAP_SRC
set
(
SPELL_MARKER_SRC
src/input/read_mark.cc src/input/read_map.cc
# src/input/design.cc src/input/xml/xml_design.cc src/input/xml/xml_format.cc
src/static_data.cc
src/bayes/main.cc src/bayes/dispatch.cc src/bayes/jobs.cc src/bayes/cli.cc
)
# src/input/design.cc src/input/xml/xml_design.cc src/input/xml/xml_format.cc
set
(
SPELL_QTL_SRC
src/input/read_map.cc src/input/read_trait.cc src/input/read_settings.cc src/input/ld_matrices.cc
# src/input/xml/xml_format.cc src/input/xml/xml_settings.cc
src/static_data.cc src/main.cc src/beta_gamma.cc
src/computations/basic_data.cc src/computations/probabilities.cc src/computations/model.cc src/computations/frontends.cc
src/computations/report.cc
)
# src/input/xml/xml_format.cc src/input/xml/xml_settings.cc
MESSAGE
(
STATUS
"spell-pedigree src =
${
SPELL_PEDIGREE_SRC
}
"
)
...
...
include
/all.h
→
attic
/all.h
View file @
27d6a61a
File moved
include/cache
/async.h
→
attic
/async.h
View file @
27d6a61a
...
...
@@ -15,7 +15,9 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef _SPEL_CACHE_ASYNC_H_
#ifdef _SPEL_CACHE_ASYNC_H_
#error "_SPEL_CACHE_ASYNC_H_ already defined!"
#else
#define _SPEL_CACHE_ASYNC_H_
#define DEFAULT_CACHE_DIR "tmp/"
...
...
include
/attic/bool_expr.h
→
attic
/attic/bool_expr.h
View file @
27d6a61a
File moved
src/bayes
/bayes.cc
→
attic
/bayes.cc
View file @
27d6a61a
File moved
include/model
/block.h
→
attic
/block.h
View file @
27d6a61a
...
...
@@ -15,7 +15,9 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef _SPEL_MODEL_BLOCK_H_
#ifdef _SPEL_MODEL_BLOCK_H_
#error "_SPEL_MODEL_BLOCK_H_ already defined!"
#else
#define _SPEL_MODEL_BLOCK_H_
#include
"labelled_matrix.h"
...
...
src/bayes
/bn.cc
→
attic
/bn.cc
View file @
27d6a61a
File moved
include/bayes
/bn.h
→
attic
/bn.h
View file @
27d6a61a
File moved
include
/bracket.h
→
attic
/bracket.h
View file @
27d6a61a
...
...
@@ -15,7 +15,9 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef _SPEL_BRACKET_H_
#ifdef _SPEL_BRACKET_H_
#error "_SPEL_BRACKET_H_ already defined!"
#else
#define _SPEL_BRACKET_H_
#include
"eigen.h"
...
...
include
/bracket2.h
→
attic
/bracket2.h
View file @
27d6a61a
...
...
@@ -15,7 +15,9 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef _SPEL_BRACKET_H_
#ifdef _SPEL_BRACKET_H_
#error "_SPEL_BRACKET_H_ already defined!"
#else
#define _SPEL_BRACKET_H_
#include
"eigen.h"
...
...
include
/cache.h
→
attic
/cache.h
View file @
27d6a61a
File moved
include/cache
/call_tuple.h
→
attic
/call_tuple.h
View file @
27d6a61a
...
...
@@ -15,7 +15,9 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef _SPEL_3RD_PARTY_TUPLE_CALL_CODE_H_
#ifdef _SPEL_3RD_PARTY_TUPLE_CALL_CODE_H_
#error "_SPEL_3RD_PARTY_TUPLE_CALL_CODE_H_ already defined!"
#else
#define _SPEL_3RD_PARTY_TUPLE_CALL_CODE_H_
/* from http://stackoverflow.com/a/10766422 */
...
...
include/cache
/cartesian_product.h
→
attic
/cartesian_product.h
View file @
27d6a61a
...
...
@@ -15,7 +15,9 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef _SPEL_CACHE_CARTESIAN_PRODUCT_H_
#ifdef _SPEL_CACHE_CARTESIAN_PRODUCT_H_
#error "_SPEL_CACHE_CARTESIAN_PRODUCT_H_ already defined!"
#else
#define _SPEL_CACHE_CARTESIAN_PRODUCT_H_
namespace
cache
{
...
...
sr
c/computations.cc
→
atti
c/computations.cc
View file @
27d6a61a
File moved
src/bayes
/convert_to_mapmaker.cc
→
attic
/convert_to_mapmaker.cc
View file @
27d6a61a
File moved
src/bayes
/csv.cc
→
attic
/csv.cc
View file @
27d6a61a
File moved
src/input
/design.cc
→
attic
/design.cc
View file @
27d6a61a
File moved
include/input
/design.h
→
attic
/design.h
View file @
27d6a61a
...
...
@@ -15,7 +15,9 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef _SPEL_DESIGN_H_
#ifdef _SPEL_DESIGN_H_
#error "_SPEL_DESIGN_H_ already defined!"
#else
#define _SPEL_DESIGN_H_
#include
<map>
...
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