diff --git a/src/coverageBed/Makefile b/src/coverageBed/Makefile
index 4de568d74ced3c675edd25fea38cfb7d59c8c5e8..e9ac6bcdc6d37d675ccc9d36dee65f511b9774b2 100755
--- a/src/coverageBed/Makefile
+++ b/src/coverageBed/Makefile
@@ -1,6 +1,7 @@
 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."
diff --git a/src/genomeCoverageBed/Makefile b/src/genomeCoverageBed/Makefile
index 59c4a5dfd34e223e29ed94290e58ce3e785d8f52..e22e8fc9feb01d2d0239650661be4bed0bd475cf 100755
--- a/src/genomeCoverageBed/Makefile
+++ b/src/genomeCoverageBed/Makefile
@@ -1,6 +1,7 @@
 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."
diff --git a/src/intersectBed/intersectBed.h b/src/intersectBed/intersectBed.h
index 29d6a9ddaf0e9306d99e4af62ea8cae44f627027..85e135c422eb935a832acac6eef5ba213065725c 100755
--- a/src/intersectBed/intersectBed.h
+++ b/src/intersectBed/intersectBed.h
@@ -70,6 +70,7 @@ private:
 	bool noHit;
 	bool bamInput;
 	bool bamOutput;
+	
 	// instance of a bed file class.
 	BedFile *bedA, *bedB;