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Makefile.am
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Makefile.am
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ACLOCAL_AMFLAGS= -I ./make/m4
SUBDIRS=method_lib
EXTRA_DIST=doc/manual.odt \
doc/MPI_API.odt \
process/ExampleModule.h \
process/ExampleModule.cpp \
CREATED \
CHANGELOG \
README.txt
CLEANFILES=doc/manual.odt \
doc/MPI_API.odt \
process/ExampleModule.h \
process/ExampleModule.cpp \
CREATED \
CHANGELOG \
README.txt
dist-hook:
chmod u+w $(distdir)/CREATED
echo "Distribution date: `date`" > CREATED
# This is here to prevent installation of LOKI during a distcheck
DISTCHECK_CONFIGURE_FLAGS=--disable-loki
AM_CPPFLAGS=$(BOOST_CPPFLAGS) $(GSL_CFLAGS) -I$(top_srcdir)/method_lib
AM_LDFLAGS=$(BOOST_LDFLAGS)
bin_PROGRAMS=plato
plato_SOURCES= Process.cpp \
Process.h \
main.cpp \
main.h \
ProcessFactory.cpp \
ProcessFactory.h \
MPIProcess.h \
MPIProcess.cpp \
MPIProcessFactory.h \
MPIProcessFactory.cpp \
process/InputProcess.cpp \
process/InputProcess.h \
process/BatchProcess.cpp \
process/BatchProcess.h \
process/OutputPED.cpp \
process/OutputPED.h \
process/OutputBED.cpp \
process/OutputBED.h \
process/OutputTPED.cpp \
process/OutputTPED.h \
process/TraitLoader.h \
process/TraitLoader.cpp \
process/LogisticRegression.h \
process/LogisticRegression.cpp \
process/LinearRegression.h \
process/LinearRegression.cpp \
process/SampleMissingFilter.h \
process/SampleMissingFilter.cpp \
process/MarkerMissingFilter.h \
process/MarkerMissingFilter.cpp \
process/AlleleFreqFilter.h \
process/AlleleFreqFilter.cpp \
process/TraitMissingFilter.h \
process/TraitMissingFilter.cpp \
process/ConcordanceProcess.h \
process/ConcordanceProcess.cpp \
process/OutputEigenstrat.h \
process/OutputEigenstrat.cpp \
process/OutputBeagle.h \
process/OutputBeagle.cpp \
process/RecodeAlleles.h \
process/RecodeAlleles.cpp \
process/AutoRegression.h \
process/AutoRegression.cpp \
process/CategoricalLoader.h \
process/CategoricalLoader.cpp
plato_LDADD=method_lib/libmethods.la $(BOOST_THREAD_LIB) \
$(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_FILESYSTEM_LIB) $(BOOST_REGEX_LIB) \
$(BOOST_SERIALIZATION_LIB)
############################################################################
# Everything below this line is from Plato 1.x, before the rewrite
############################################################################
orig_plato_src = cdflib.h \
dcdflib.cpp \
ipmpar.c \
Finalize.cc \
Finalize.h \
process/PercentByFamily.cc \
process/PercentByFamily.h \
process/ProcessAlleleFrequency.cc \
process/ProcessAlleleFrequency.h \
process/ProcessBEAGLEOutput.cc \
process/ProcessBEAGLEOutput.h \
process/ProcessBINOutput.cc \
process/ProcessBINOutput.h \
process/ProcessCaConChisq.cc \
process/ProcessCaConChisq.h \
Process.cc \
process/ProcessClusterMissing.cc \
process/ProcessClusterMissing.h \
process/ProcessCMH.cc \
process/ProcessCMH.h \
process/ProcessConcordance.cc \
process/ProcessConcordance.h \
process/ProcessDeletions.cc \
process/ProcessDeletions.h \
process/ProcessEigenstratOutput.cc \
process/ProcessEigenstratOutput.h \
process/ProcessEpistasis.cc \
process/ProcessEpistasis.h \
process/ProcessFBATOutput.cc \
process/ProcessFBATOutput.h \
process/ProcessFilterProcess.cc \
process/ProcessFilterProcess.h \
process/ProcessFst.cc \
process/ProcessFst.h \
process/ProcessGenderCheck.cc \
process/ProcessGenderCheck.h \
process/ProcessGRROutput.cc \
process/ProcessGRROutput.h \
Process.h \
process/ProcessHomozygous.cc \
process/ProcessHomozygous.h \
process/ProcessHWEquilibrium.cc \
process/ProcessHWEquilibrium.h \
process/ProcessIBS.cc \
process/ProcessIBS.h \
process/ProcessImputeOutput.cc \
process/ProcessImputeOutput.h \
process/ProcessKinship.cc \
process/ProcessKinship.h \
process/ProcessLAPISOutput.cc \
process/ProcessLAPISOutput.h \
process/ProcessLD.cc \
process/ProcessLD.h \
process/ProcessLinearReg.cc \
process/ProcessLinearReg.h \
process/ProcessLogReg.cc \
process/ProcessLogReg.h \
process/ProcessMarkerGenoEff.cc \
process/ProcessMarkerGenoEff.h \
process/ProcessMDR.cc \
process/ProcessMDR.h \
process/ProcessMDROutput.cc \
process/ProcessMDROutput.h \
process/ProcessMDRPDT.cc \
process/ProcessMDRPDT.h \
process/ProcessMendelianErrors.cc \
process/ProcessMendelianErrors.h \
process/ProcessMitoCheck.cc \
process/ProcessMitoCheck.h \
process/ProcessPDT2Output.cc \
process/ProcessPDT2Output.h \
process/ProcessPEDOutput.cc \
process/ProcessPEDOutput.h \
process/ProcessPHASEOutput.cc \
process/ProcessPHASEOutput.h \
process/ProcessPowerMarkerOutput.cc \
process/ProcessPowerMarkerOutput.h \
process/ProcessQTDTOutput.cc \
process/ProcessQTDTOutput.h \
process/ProcessRunTDT.cc \
process/ProcessRunTDT.h \
process/ProcessSampleGenoEff.cc \
process/ProcessSampleGenoEff.h \
process/ProcessSTRUCTOutput.cc \
process/ProcessSTRUCTOutput.h \
process/ProcessSuperlinkOutput.cc \
process/ProcessSuperlinkOutput.h \
process/ProcessTPEDOutput.cc \
process/ProcessTPEDOutput.h \
wasp.cc \
wasp.h \
process/ProcessInteraction.h \
process/ProcessInteraction.cpp \
ProcessFactory.cpp \
ProcessFactory.h