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# Make file for vcftools
# Author: Adam Auton
# ($Revision: 230 $)
# Compiler
CC = gcc
CPP = g++
# Output executable
EXECUTABLE = vcftools
# Flag used to turn on compilation of PCA routines
ifndef VCFTOOLS_PCA
VCFTOOLS_PCA = 0
endif
# Compiler flags
CFLAGS += -O2
#CFLAGS = -Wall -O2 -pg -m64
CPPFLAGS += -O2 -D_FILE_OFFSET_BITS=64
#CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64
# Included libraries (zlib)
LIB = -lz
#LIB = -lz -I/opt/local/include/ -L/opt/local/lib/
OBJS = vcftools.o bcf_file.o vcf_file.o variant_file.o \
header.o bcf_entry.o vcf_entry.o entry.o entry_getters.o entry_setters.o \
vcf_entry_setters.o bcf_entry_setters.o entry_filters.o variant_file_filters.o variant_file_output.o parameters.o \
variant_file_format_convert.o variant_file_diff.o output_log.o bgzf.o gamma.o
ifeq ($(VCFTOOLS_PCA), 1)
# Define flag for PCA routine compilation
CPPFLAGS += -DVCFTOOLS_PCA
# Add LAPACK library
LIB += -llapack
# Add PCA source code
OBJS+= dgeev.o
endif
vcftools: $(OBJS)
$(CPP) $(CPPFLAGS) $(OBJS) $(LDFLAGS) -o vcftools $(LIB)
ifdef BINDIR
cp $(CURDIR)/$@ $(BINDIR)/$@
endif
bgzf: bgzf.c
$(CC) -c $(CFLAGS) $(FLAGS) bgzf.c $(LIB) -o bgzf.o
# pull in dependency info for *existing* .o files
-include $(OBJS:.o=.d)
%.o: %.cpp
$(CPP) -c $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $*.cpp -o $*.o
$(CPP) -MM $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $*.cpp > $*.d
# remove compilation products
clean:
@rm -f vcftools *.o *.d
@rm -f $(BINDIR)/vcftools
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