Updated Makefiles for coverageBed and genomeCoverageBed

src/coverageBed/Makefile

 CXX = g++
 CXXFLAGS = -O3  -Wall
-LDFLAGS =
+LDFLAGS = 
+LIBS=	-lz
 
 UTILITIES_DIR = ../utils/
 OBJ_DIR = ../../obj/
@@ -9,14 +10,14 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/
 
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
 SOURCES= coverageMain.cpp coverageBed.cpp
 OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o lineFileUtilities.o
+_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BGZF.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 PROGRAM= coverageBed
@@ -37,6 +38,7 @@ $(BUILT_OBJECTS): $(SOURCES)
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/	
 	
 clean:
 	@echo "Cleaning up."

src/genomeCoverageBed/Makefile

 CXX = g++
 CXXFLAGS = -O3  -Wall
-LDFLAGS =  
+LDFLAGS = 
+LIBS=	-lz
 
 UTILITIES_DIR = ../utils/
 OBJ_DIR = ../../obj/
@@ -9,14 +10,14 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/
 
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
 SOURCES= genomeCoverageMain.cpp genomeCoverageBed.cpp
 OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o lineFileUtilities.o
+_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BGZF.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 PROGRAM= genomeCoverageBed
@@ -37,6 +38,7 @@ $(BUILT_OBJECTS): $(SOURCES)
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/		
 	
 clean:
 	@echo "Cleaning up."

src/intersectBed/intersectBed.h

@@ -70,6 +70,7 @@ private:
 	bool noHit;
 	bool bamInput;
 	bool bamOutput;
+	
 	// instance of a bed file class.
 	BedFile *bedA, *bedB;