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1 # ==========================
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2 # BEDTools Makefile
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3 # (c) 2009 Aaron Quinlan
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4 # ==========================
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5
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6 # define our object and binary directories
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7 export OBJ_DIR = obj
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8 export BIN_DIR = bin
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9 export SRC_DIR = src
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10 export CXX = g++
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11 export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
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12 export LIBS = -lz
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13 export BT_ROOT = src/utils/BamTools/
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14
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15
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16 SUBDIRS = $(SRC_DIR)/annotateBed \
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17 $(SRC_DIR)/bamToBed \
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18 $(SRC_DIR)/bedToBam \
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19 $(SRC_DIR)/bedToIgv \
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20 $(SRC_DIR)/bed12ToBed6 \
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21 $(SRC_DIR)/closestBed \
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22 $(SRC_DIR)/complementBed \
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23 $(SRC_DIR)/coverageBed \
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24 $(SRC_DIR)/fastaFromBed \
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25 $(SRC_DIR)/flankBed \
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26 $(SRC_DIR)/genomeCoverageBed \
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27 $(SRC_DIR)/intersectBed \
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28 $(SRC_DIR)/linksBed \
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29 $(SRC_DIR)/maskFastaFromBed \
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30 $(SRC_DIR)/mergeBed \
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31 $(SRC_DIR)/multiBamCov \
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32 $(SRC_DIR)/multiIntersectBed \
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33 $(SRC_DIR)/nucBed \
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34 $(SRC_DIR)/overlap \
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35 $(SRC_DIR)/pairToBed \
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36 $(SRC_DIR)/pairToPair \
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37 $(SRC_DIR)/shuffleBed \
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38 $(SRC_DIR)/slopBed \
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39 $(SRC_DIR)/sortBed \
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40 $(SRC_DIR)/subtractBed \
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41 $(SRC_DIR)/tagBam \
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42 $(SRC_DIR)/unionBedGraphs \
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43 $(SRC_DIR)/windowBed
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44
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45 UTIL_SUBDIRS = $(SRC_DIR)/utils/lineFileUtilities \
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46 $(SRC_DIR)/utils/bedFile \
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47 $(SRC_DIR)/utils/bedGraphFile \
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48 $(SRC_DIR)/utils/chromsweep \
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49 $(SRC_DIR)/utils/gzstream \
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50 $(SRC_DIR)/utils/fileType \
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51 $(SRC_DIR)/utils/bedFilePE \
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52 $(SRC_DIR)/utils/sequenceUtilities \
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53 $(SRC_DIR)/utils/tabFile \
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54 $(SRC_DIR)/utils/BamTools \
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55 $(SRC_DIR)/utils/BamTools-Ancillary \
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56 $(SRC_DIR)/utils/Fasta \
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57 $(SRC_DIR)/utils/genomeFile
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58
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59 all:
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60 [ -d $(OBJ_DIR) ] || mkdir -p $(OBJ_DIR)
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61 [ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
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62
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63 @echo "Building BEDTools:"
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64 @echo "========================================================="
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65
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66 @for dir in $(UTIL_SUBDIRS); do \
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67 echo "- Building in $$dir"; \
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68 $(MAKE) --no-print-directory -C $$dir; \
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69 echo ""; \
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70 done
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71
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72 @for dir in $(SUBDIRS); do \
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73 echo "- Building in $$dir"; \
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74 $(MAKE) --no-print-directory -C $$dir; \
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75 echo ""; \
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76 done
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77
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78
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79 .PHONY: all
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80
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81 clean:
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82 @echo "Cleaning up."
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83 @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
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84 @rm -Rf $(BT_ROOT)/lib
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85 @rm -f $(BT_ROOT)/src/api/*.o
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86 @rm -f $(BT_ROOT)/src/api/internal/*.o
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87 @rm -Rf $(BT_ROOT)/include
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88
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89 .PHONY: clean
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