Added master makefile to compile all programs in the BEDTools project

Makefile

+# ==========================
+# BEDTools Makefile
+# (c) 2009 Aaron Quinlan
+# ==========================
+
+# define our object and binary directories
+export OBJ_DIR = obj
+export BIN_DIR = bin
+export SRC_DIR = src
+
+# define our common source directories
+# export UTILITIES_DIR = CommonSource/Utilities
+
+# define some default flags
+export CFLAGS ?= -Wall -O3
+export CXXFLAGS ?= $(CFLAGS)
+export LDFLAGS ?= -Wl,-s
+export CXX ?= g++
+
+# define our platform
+#export BLD_PLATFORM ?= linux64-core2
+#include includes/$(BLD_PLATFORM).inc
+
+# define our source subdirectories
+SUBDIRS = $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/sortBed
+
+UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/sequenceUtilities
+all:
+
+	@echo "Building BEDTools:"
+	@echo "========================================================="
+	@for dir in $(SUBDIRS); do \
+		echo "- Building in $$dir"; \
+		$(MAKE) --no-print-directory -C $$dir; \
+		echo ""; \
+	done
+
+	@for dir in $(UTIL_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)/*
+
+.PHONY: clean