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1 #-- Imported variables from top level makefile
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2 # BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
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3
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4 ifndef BIN_DIR
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5 BIN_DIR := $(CURDIR)
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6 endif
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7 ifndef AUX_BIN_DIR
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8 AUX_BIN_DIR := $(CURDIR)
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9 endif
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10
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11 OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@
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12 BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
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13 chmod 755 $(BIN_DIR)/$@
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14 AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
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15 chmod 755 $(AUX_BIN_DIR)/$@
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16 VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
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17
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18 ALL := annotate combineMUMs delta-filter gaps mgaps \
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19 postnuc postpro prenuc prepro repeat-match \
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20 show-aligns show-coords show-tiling show-snps \
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21 show-diff
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22
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23
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24 #-- PHONY rules --#
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25 .PHONY: all clean
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26
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27
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28 all: $(ALL)
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29
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30
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31 clean:
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32 rm -f *.o *~
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33 cd $(BIN_DIR); rm -f $(ALL)
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34 cd $(AUX_BIN_DIR); rm -f $(ALL)
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35
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36
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37
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38
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39 #-- not so PHONY rules --#
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40 delta.o: delta.cc delta.hh
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41 $(OBJ_RULE)
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42
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43 tigrinc.o: tigrinc.cc tigrinc.hh
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44 $(OBJ_RULE)
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45
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46 sw_align.o: sw_align.cc sw_align.hh tigrinc.hh
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47 $(OBJ_RULE)
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48
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49 translate.o: translate.cc translate.hh
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50 $(OBJ_RULE)
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51
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52
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53 annotate: annotate.cc tigrinc.o
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54 $(BIN_RULE)
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55
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56 combineMUMs: combineMUMs.cc tigrinc.o
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57 $(BIN_RULE)
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58
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59 delta-filter: delta-filter.cc tigrinc.o delta.o
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60 $(BIN_RULE)
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61
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62 gaps: gaps.cc tigrinc.o
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63 $(BIN_RULE)
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64
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65 mgaps: mgaps.cc tigrinc.o
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66 $(BIN_RULE)
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67
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68 postnuc: postnuc.cc tigrinc.o sw_align.o
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69 $(AUX_BIN_RULE)
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70
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71 postpro: postpro.cc tigrinc.o sw_align.o translate.o
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72 $(AUX_BIN_RULE)
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73
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74 prenuc: prenuc.cc tigrinc.o
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75 $(AUX_BIN_RULE)
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76
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77 prepro: prepro.cc tigrinc.o translate.o
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78 $(AUX_BIN_RULE)
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79
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80 repeat-match: repeat-match.cc tigrinc.o
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81 $(BIN_RULE)
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82
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83 show-aligns: show-aligns.cc tigrinc.o translate.o delta.o
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84 $(BIN_RULE)
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85
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86 show-coords: show-coords.cc tigrinc.o delta.o
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87 $(BIN_RULE)
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88
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89 show-tiling: show-tiling.cc tigrinc.o delta.o
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90 $(BIN_RULE)
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91
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92 show-snps: show-snps.cc tigrinc.o translate.o delta.o
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93 $(BIN_RULE)
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94
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95 show-diff: show-diff.cc tigrinc.o delta.o
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96 $(BIN_RULE)
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