Makefile tweak.

src/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)/lineFileUtilities/ \
-           -I$(UTILITIES_DIR)/fileType/ \
-           -I$(UTILITIES_DIR)/BamTools/include
-
-# ----------------------------------
-# define our source and object files
-# ----------------------------------
-SOURCES= multiCovMain.cpp multiCovBam.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
-BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= multiCovBam
-
-all: $(PROGRAM)
-
-.PHONY: all
-
-$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
-	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
-
-$(BUILT_OBJECTS): $(SOURCES)
-	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
-
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
-	@$(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

src/bedpeToBam/Makefile

@@ -6,6 +6,7 @@ BIN_DIR = ../../bin/
 # define our includes
 # -------------------
 INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
+           -I$(UTILITIES_DIR)/bedFilePE/ \
            -I$(UTILITIES_DIR)/version/ \
            -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/genomeFile/ \
@@ -17,12 +18,12 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= bedToBam.cpp
+SOURCES= bedpeToBam.cpp
 OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
+_EXT_OBJECTS=bedFile.o bedFilePE.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= bedToBam
+PROGRAM= bedpeToBam
 
 
 all: $(PROGRAM)