--- a/BEDTools-Version-2.14.3/src/utils/BamTools/Makefile	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-# -------------------
-# define our includes
-# -------------------
-OBJ_DIR = ../../../obj/
-INCLUDES = -Isrc/ -Iinclude/
-
-# ----------------------------------
-# define our source and object files
-# ----------------------------------
-
-SOURCES= src/api/BamAlignment.cpp \
-         src/api/BamMultiReader.cpp \
-         src/api/BamReader.cpp \
-         src/api/BamWriter.cpp \
-         src/api/SamHeader.cpp \
-         src/api/SamProgram.cpp \
-         src/api/SamProgramChain.cpp \
-         src/api/SamReadGroup.cpp \
-         src/api/SamReadGroupDictionary.cpp \
-         src/api/SamSequence.cpp \
-         src/api/SamSequenceDictionary.cpp \
-		 src/api/internal/BamHeader_p.cpp \
-		 src/api/internal/BamIndexFactory_p.cpp \
-		 src/api/internal/BamMultiReader_p.cpp \
-		 src/api/internal/BamRandomAccessController_p.cpp \
-		 src/api/internal/BamReader_p.cpp \
-		 src/api/internal/BamStandardIndex_p.cpp \
-		 src/api/internal/BamToolsIndex_p.cpp \
-		 src/api/internal/BamWriter_p.cpp \
-		 src/api/internal/BgzfStream_p.cpp \
-		 src/api/internal/SamFormatParser_p.cpp \
-		 src/api/internal/SamFormatPrinter_p.cpp \
-		 src/api/internal/SamHeaderValidator_p.cpp
-
-# ----------------------------------
-# define our source and object files
-# ----------------------------------
-OBJECTS= $(SOURCES:.cpp=.o)
-LIBRARY=libbamtools.a
-
-all: $(LIBRARY)
-    
-.PHONY: all
-
-$(LIBRARY): $(OBJECTS)
-	[ -d lib ] || mkdir -p lib
-	[ -d include ] || mkdir -p include
-	[ -d include/api ] || mkdir -p include/api
-	[ -d include/shared ] || mkdir -p include/shared
-	
-	@cp src/api/*.h include/api
-	@cp src/shared/*.h include/shared
-	
-		
-	@echo "  * linking $(LIBRARY)"
-	ar cr lib/$@  $^
-		
-$(OBJECTS): $(SOURCES)
-	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
-	
\ No newline at end of file