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ACLOCAL_AMFLAGS = -I ../m4
# Declare program name and install it in $(bindir) directory
bin_PROGRAMS = igor
# List all Igor sources
igor_SOURCES = Aligner.cpp Aligner.h Bestscenarioscounter.cpp Bestscenarioscounter.h Counter.cpp Counter.h Coverageerrcounter.cpp Coverageerrcounter.h Deletion.cpp Deletion.h Dinuclmarkov.cpp Dinuclmarkov.h Errorscounter.cpp Errorscounter.h Errorrate.cpp Errorrate.h Genechoice.cpp Genechoice.h GenModel.cpp GenModel.h HypermutationfullNmererrorrate.cpp HypermutationfullNmererrorrate.h Hypermutationglobalerrorrate.cpp Hypermutationglobalerrorrate.h Insertion.cpp Insertion.h IntStr.cpp IntStr.h main.cpp Model_marginals.cpp Model_marginals.h Model_Parms.cpp Model_Parms.h Pgencounter.cpp Pgencounter.h Rec_Event.cpp Rec_Event.h Singleerrorrate.cpp Singleerrorrate.h Utils.cpp Utils.h
# Include GSL subparts and jemalloc without installation
igor_LDADD = -lgsl -lcblas -ljemalloc -lpthread -ldl #Need to link pthread since it is not statically linked with jemalloc (for now)
igor_CXXFLAGS = -I/usr/include/jemalloc -I/usr/include/gsl $(OPENMP_CXXFLAGS) -DIGOR_DATA_DIR=\"$(pkgdatadir)\"
# Pass IGoR data install directory path through the compiler with -DIGOR_DATA_DIR=\"$(pkgdatadir)\"
# and not in config.h (as it is best practice according to: https://stackoverflow.com/questions/5867136/autoconf-how-to-get-installation-paths-into-config-h#11317815)
#igor_AM_CPPFLAGS = -std=c++11 -I$(srcdir)/../libs/gsl_sub
#igor_AM_CXXFLAGS = -I$(srcdir)/../libs/jemalloc/include/jemalloc $(OPENMP_CXXFLAGS)
#igor_AM_CFLAGS = $(OPENMP_CXXFLAGS)
# Compile using c++11 and include headers from $(srcdir)/../libs/gsl_sub to mimick the use of normal GSL and include it using #<gsl/gsl_foo.h>
#-I$(srcdir)/../libs/jemalloc doesn't really need to have the headers #-fopenMP would not work on every compiler, using AC_OPENMP macro instead
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