--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/Makefile	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,89 @@
+# ==========================
+# BEDTools Makefile
+# (c) 2009 Aaron Quinlan
+# ==========================
+
+# define our object and binary directories
+export OBJ_DIR	= obj
+export BIN_DIR	= bin
+export SRC_DIR	= src
+export CXX		= g++
+export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
+export LIBS		= -lz
+export BT_ROOT  = src/utils/BamTools/
+
+
+SUBDIRS = $(SRC_DIR)/annotateBed \
+		  $(SRC_DIR)/bamToBed \
+		  $(SRC_DIR)/bedToBam \
+		  $(SRC_DIR)/bedToIgv \
+		  $(SRC_DIR)/bed12ToBed6 \
+		  $(SRC_DIR)/closestBed \
+		  $(SRC_DIR)/complementBed \
+		  $(SRC_DIR)/coverageBed \
+		  $(SRC_DIR)/fastaFromBed \
+		  $(SRC_DIR)/flankBed \
+		  $(SRC_DIR)/genomeCoverageBed \
+		  $(SRC_DIR)/intersectBed \
+		  $(SRC_DIR)/linksBed \
+		  $(SRC_DIR)/maskFastaFromBed \
+		  $(SRC_DIR)/mergeBed \
+		  $(SRC_DIR)/multiBamCov \
+		  $(SRC_DIR)/multiIntersectBed \
+		  $(SRC_DIR)/nucBed \
+		  $(SRC_DIR)/overlap \
+		  $(SRC_DIR)/pairToBed \
+		  $(SRC_DIR)/pairToPair \
+		  $(SRC_DIR)/shuffleBed \
+		  $(SRC_DIR)/slopBed \
+		  $(SRC_DIR)/sortBed \
+		  $(SRC_DIR)/subtractBed \
+		  $(SRC_DIR)/tagBam \
+		  $(SRC_DIR)/unionBedGraphs \
+		  $(SRC_DIR)/windowBed
+
+UTIL_SUBDIRS =	$(SRC_DIR)/utils/lineFileUtilities \
+				$(SRC_DIR)/utils/bedFile \
+				$(SRC_DIR)/utils/bedGraphFile \
+				$(SRC_DIR)/utils/chromsweep \
+				$(SRC_DIR)/utils/gzstream \
+				$(SRC_DIR)/utils/fileType \
+				$(SRC_DIR)/utils/bedFilePE \
+				$(SRC_DIR)/utils/sequenceUtilities \
+				$(SRC_DIR)/utils/tabFile \
+				$(SRC_DIR)/utils/BamTools \
+				$(SRC_DIR)/utils/BamTools-Ancillary \
+				$(SRC_DIR)/utils/Fasta \
+				$(SRC_DIR)/utils/genomeFile
+
+all:
+	[ -d $(OBJ_DIR) ] || mkdir -p $(OBJ_DIR)
+	[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
+	
+	@echo "Building BEDTools:"
+	@echo "========================================================="
+	
+	@for dir in $(UTIL_SUBDIRS); do \
+		echo "- Building in $$dir"; \
+		$(MAKE) --no-print-directory -C $$dir; \
+		echo ""; \
+	done
+
+	@for dir in $(SUBDIRS); do \
+		echo "- Building in $$dir"; \
+		$(MAKE) --no-print-directory -C $$dir; \
+		echo ""; \
+	done
+
+
+.PHONY: all
+
+clean:
+	@echo "Cleaning up."
+	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -Rf $(BT_ROOT)/lib
+	@rm -f $(BT_ROOT)/src/api/*.o
+	@rm -f $(BT_ROOT)/src/api/internal/*.o
+	@rm -Rf $(BT_ROOT)/include
+
+.PHONY: clean