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# Make file for vcftools
# Author: Adam Auton
# ($Revision: 230 $)
# Compiler
CPP = g++
# Output executable
EXECUTABLE = vcftools
# Flag used to turn on compilation of PCA routines
ifndef VCFTOOLS_PCA
VCFTOOLS_PCA = 0
endif
# Compiler flags
CPPFLAGS += -O2 -Wall -Wextra
#CPPFLAGS = -g
# Included libraries (zlib)
LIB = -lz
#LIB = -lz -I/opt/local/include/ -L/opt/local/lib/
SOURCES = vcftools.cpp vcf_file.cpp vcf_entry.cpp \
vcf_entry_getters.cpp vcf_entry_setters.cpp \
vcf_file_filters.cpp vcf_file_output.cpp \
vcf_file_format_convert.cpp \
vcf_file_diff.cpp parameters.cpp \
vcf_file_index.cpp \
output_log.cpp
ifeq ($(VCFTOOLS_PCA), 1)
# Define flag for PCA routine compilation
CPPFLAGS += -DVCFTOOLS_PCA
# Add LAPACK library
LIB += -llapack
# Add PCA source code
SOURCES += dgeev.cpp
endif
all: vcftools
vcftools: $(SOURCES)
$(CPP) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $(SOURCES) -o $@ $(LIB)
ifdef BINDIR
cp $(CURDIR)/$@ $(BINDIR)/$@
endif
clean:
@rm -f vcftools
@rm -f $(BINDIR)/vcftools
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