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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)/fileType/ \
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14 -I$(UTILITIES_DIR)/BamTools/include \
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15 -I$(UTILITIES_DIR)/BamTools-Ancillary
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16 # ----------------------------------
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17 # define our source and object files
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18 # ----------------------------------
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19 SOURCES= coverageMain.cpp coverageBed.cpp
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20 OBJECTS= $(SOURCES:.cpp=.o)
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21 _EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o BamAncillary.o
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22 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
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23 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
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24 PROGRAM= coverageBed
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25
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26
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27 all: $(PROGRAM)
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28
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29 .PHONY: all
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30
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31 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
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32 @echo " * linking $(PROGRAM)"
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33 @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS)
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34
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35 $(BUILT_OBJECTS): $(SOURCES)
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36 @echo " * compiling" $(*F).cpp
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37 @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
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38
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39 $(EXT_OBJECTS):
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40 @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
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41 @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
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42 @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
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43 @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/
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44 @$(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
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47 clean:
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48 @echo "Cleaning up."
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49 @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
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50
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51 .PHONY: clean
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