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Makefile.am
102 lines (81 loc) · 4 KB
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Makefile.am
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DEPLOIDVERSION = $(shell git show HEAD | head -1 | sed -e "s/commit //g" | cat)
LASSOVERSION = $(shell git submodule status | grep DEploid-Lasso-lib | sed -e "s/ //g" -e "s/DEploid.*//" | cat)
EXTRA_DIST = bootstrap \
$(top_srcdir)/utilities/dataExplore.r \
$(top_srcdir)/utilities/interpretDEploid.r \
docs/_build/man/dEploid.1
COMPILEDATE = $(shell date -u | sed -e "s/ /-/g")
distdir = $(PACKAGE)-$(VERSION)
bin_PROGRAMS = dEploid dEploid_dbg
man1_MANS = docs/_build/man/dEploid.1
TESTS = unit_tests io_unit_tests
check_PROGRAMS = unit_tests dEploid_dbg io_unit_tests current_unit_tests # dEploid_prof
PROG = DEPLOID
common_flags = -std=c++17 -Isrc/ -DDEPLOIDVERSION=\"${DEPLOIDVERSION}\" -DLASSOVERSION=\"${LASSOVERSION}\" -DCOMPILEDATE=\"${COMPILEDATE}\" -Wall -Wextra
common_LDADD = -lz
common_src = src/random/fastfunc.cpp \
src/random/random_generator.cpp \
src/random/mersenne_twister.cpp \
src/chooseK.cpp \
src/ibd.cpp \
src/mcmc.cpp \
src/panel.cpp \
src/utility.cpp \
src/dEploidIO.cpp \
src/dEploidIO-operation.cpp \
src/dEploidIO-workflow.cpp \
src/updateHap.cpp \
src/txtReader.cpp \
src/vcfReader.cpp \
src/variantIndex.cpp \
src/gzstream/gzstream.cpp \
src/export/dEploidIOExport.cpp \
src/export/dEploidIOExportPosteriorProb.cpp \
src/export/writeMcmcRelated.cpp \
src/lasso/src/lasso.cpp \
src/lasso/src/dEploidLasso.cpp
debug_src = src/debug/mcmcDebug.cpp src/debug/vcfReaderDebug.cpp \
src/lasso/src/lassoDBG.cpp
dEploid_SOURCES = src/dEploid.cpp $(common_src)
dEploid_dbg_SOURCES = $(debug_src) $(dEploid_SOURCES)
dEploid_prof_SOURCES = $(dEploid_SOURCES)
dEploid_CXXFLAGS = $(common_flags) -DNDEBUG -O3
dEploid_dbg_CXXFLAGS = -g $(common_flags) -O3
dEploid_prof_CXXFLAGS = $(common_flags) -DNDEBUG -fno-omit-frame-pointer -pg -O1
dEploid_LDADD = $(common_LDADD)
dEploid_dbg_LDADD = $(common_LDADD)
dEploid_prof_LDADD = $(common_LDADD)
unit_tests_SOURCES = $(common_src) \
tests/unittest/test_runner.cpp \
tests/unittest/test_ibd.cpp \
tests/unittest/test_updateSingleHap.cpp \
tests/unittest/test_utilities.cpp \
tests/unittest/test_panel.cpp \
tests/unittest/test_mcmc.cpp \
tests/unittest/test_updatePairHap.cpp \
tests/unittest/test_workflow.cpp
unit_tests_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
unit_tests_LDADD = -lcppunit -ldl $(common_LDADD)
io_unit_tests_SOURCES = $(common_src) \
tests/unittest/test_runner.cpp \
tests/unittest/test_dEploidIO.cpp \
tests/unittest/test_txtReader.cpp \
tests/unittest/test_vcfReader.cpp
io_unit_tests_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
io_unit_tests_LDADD = -lcppunit -ldl $(common_LDADD)
current_unit_tests_SOURCES = $(common_src) \
tests/unittest/test_runner.cpp \
tests/unittest/test_workflow.cpp
current_unit_tests_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
current_unit_tests_LDADD = -lcppunit -ldl $(common_LDADD)
clean-local: clean-local-check
.PHONY: clean-local-check utilities
clean-local-check:
-rm -rf src/*.gc* tests/unittest/*.gc* src/*.gcov
utilities: utilities/dataExplore.r utilities/interpretDEploid.r
sed -i'.bak' -e '/#!\/usr\/bin\/env Rscript/d' -e '/rm(list=ls())/d' utilities/dataExplore.r ; echo "#!/usr/bin/env Rscript" > tmpTxt; echo "rm(list=ls()); dEploidRootDir=\"$(PWD)\"" >> tmpTxt ; cat utilities/dataExplore.r >> tmpTxt ; mv tmpTxt utilities/dataExplore.r; chmod a+x utilities/dataExplore.r;
sed -i'.bak' -e '/#!\/usr\/bin\/env Rscript/d' -e '/rm(list=ls())/d' utilities/interpretDEploid.r; echo "#!/usr/bin/env Rscript" > tmpTxt; echo "rm(list=ls()); dEploidRootDir=\"$(PWD)\"" >> tmpTxt ; cat utilities/interpretDEploid.r >> tmpTxt ; mv tmpTxt utilities/interpretDEploid.r; chmod a+x utilities/interpretDEploid.r
if ENABLE_BASH_COMPLETION
bashcompletiondir = $(BASH_COMPLETION_DIR)
dist_bashcompletion_DATA = src/dEploid_completion.sh
endif