Makefile.am

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 utilities

man1_MANS = docs/_build/man/dEploid.1

TESTS = unit_tests io_unit_tests
check_PROGRAMS = unit_tests dEploid_dbg dEploid_prof io_unit_tests
PROG = DEPLOID

common_flags = -std=c++0x -Isrc/ -DDEPLOIDVERSION=\"${DEPLOIDVERSION}\" -DLASSOVERSION=\"${LASSOVERSION}\" -DCOMPILEDATE=\"${COMPILEDATE}\"
common_LDADD = -lz

common_src = src/random/fastfunc.cpp \
			 src/random/random_generator.cpp \
			 src/random/mersenne_twister.cpp \
			 src/ibd.cpp \
			 src/mcmc.cpp \
			 src/panel.cpp \
			 src/utility.cpp \
			 src/dEploidIO.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/lasso.cpp \
			 src/lasso/dEploidLasso.cpp

debug_src = src/debug/mcmcDebug.cpp src/debug/vcfReaderDebug.cpp \
			src/lasso/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

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)

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