Added bedpeToBam Makefile

src/bedpeToBam/Makefile

+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
+           -I$(UTILITIES_DIR)/version/ \
+           -I$(UTILITIES_DIR)/gzstream/ \
+           -I$(UTILITIES_DIR)/genomeFile/ \
+           -I$(UTILITIES_DIR)/lineFileUtilities/ \
+           -I$(UTILITIES_DIR)/fileType/ \
+           -I$(UTILITIES_DIR)/BamTools/include \
+		   -I$(UTILITIES_DIR)/BamTools-Ancillary
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= bedToBam.cpp
+OBJECTS= $(SOURCES:.cpp=.o)
+_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= bedToBam
+
+
+all: $(PROGRAM)
+
+.PHONY: all
+
+
+$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
+	@echo "  * linking $(PROGRAM)"
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools $(LIBS)
+
+$(BUILT_OBJECTS): $(SOURCES)
+	@echo "  * compiling" $(*F).cpp
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+$(EXT_OBJECTS):
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/	
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
+				
+clean:
+	@echo "Cleaning up."
+	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+.PHONY: clean