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1 UTILITIES_DIR = ../utils/
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2 OBJ_DIR = ../../obj/
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3 BIN_DIR = ../../bin/
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4
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5 # -------------------
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6 # define our includes
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7 # -------------------
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8 INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
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9 -I$(UTILITIES_DIR)/version/ \
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10 -I$(UTILITIES_DIR)/gzstream/ \
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11 -I$(UTILITIES_DIR)/genomeFile/ \
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12 -I$(UTILITIES_DIR)/lineFileUtilities/ \
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13 -I$(UTILITIES_DIR)/sequenceUtilities/ \
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14 -I$(UTILITIES_DIR)/fileType/ \
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15 -I$(UTILITIES_DIR)/Fasta/ \
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16
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17 # ----------------------------------
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18 # define our source and object files
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19 # ----------------------------------
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20 SOURCES= fastaFromBedMain.cpp fastaFromBed.cpp
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21 OBJECTS= $(SOURCES:.cpp=.o)
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22 _EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o Fasta.o split.o
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23 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
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24 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
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25 PROGRAM= fastaFromBed
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26
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27
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28 all: $(PROGRAM)
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29
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30 .PHONY: all
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31
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32 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
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33 @echo " * linking $(PROGRAM)"
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34 @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
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35
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36 $(BUILT_OBJECTS): $(SOURCES)
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37 @echo " * compiling" $(*F).cpp
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38 @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
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39
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40 $(EXT_OBJECTS):
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41 @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
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42 @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
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43 @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
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44 @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
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45 @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
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46 @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/Fasta/
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47
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48 clean:
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49 @echo "Cleaning up."
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50 @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
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51
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52 .PHONY: clean |
