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# ==========================
# BEDTools Makefile
# (c) 2009 Aaron Quinlan
# ==========================

# define our object and binary directories
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export OBJ_DIR  = obj
export BIN_DIR  = bin
export SRC_DIR  = src
export CXX      = g++
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export CXXFLAGS = -Wall -O2
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export LIBS     = -lz
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SUBDIRS = $(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)/genomeCoverageBed $(SRC_DIR)/groupBy $(SRC_DIR)/intersectBed $(SRC_DIR)/linksBed $(SRC_DIR)/maskFastaFromBed $(SRC_DIR)/mergeBed   $(SRC_DIR)/overlap $(SRC_DIR)/pairToBed $(SRC_DIR)/pairToPair $(SRC_DIR)/shuffleBed $(SRC_DIR)/slopBed $(SRC_DIR)/sortBed $(SRC_DIR)/subtractBed $(SRC_DIR)/windowBed    
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UTIL_SUBDIRS =  $(SRC_DIR)/utils/lineFileUtilities $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/tabFile $(SRC_DIR)/utils/genomeFile $(SRC_DIR)/utils/gzstream $(SRC_DIR)/utils/fileType $(SRC_DIR)/utils/bedFilePE $(SRC_DIR)/utils/sequenceUtilities $(SRC_DIR)/utils/BamTools
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all:

	@echo "Building BEDTools:"
	@echo "========================================================="
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	@for dir in $(UTIL_SUBDIRS); do \
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		echo "- Building in $$dir"; \
		$(MAKE) --no-print-directory -C $$dir; \
		echo ""; \
	done

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	@for dir in $(SUBDIRS); do \
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		echo "- Building in $$dir"; \
		$(MAKE) --no-print-directory -C $$dir; \
		echo ""; \
	done

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.PHONY: all

clean:
	@echo "Cleaning up."
	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*

.PHONY: clean