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root/gclib/tophat_cpp/Makefile
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# Line 57 | Line 57
57   tophat_reports
58  
59   .PHONY : all
60 < all: segment_juncs
61 < debug: segment_juncs
60 > all: fix_map_ordering
61 > debug: fix_map_ordering
62   #all: prep_reads
63   #debug: prep_reads
64  
65 < # all_exe: prep_reads extract_reads segment_juncs long_spanning_reads
65 > all_exe: $(ALL_EXE)
66   #all: $(ALL_EXE)
67   #debug: $(ALL_EXE)
68   #all: segment_juncs
# Line 85 | Line 85
85          ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
86   bam2fastx: ./bam2fastx.o
87          ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
88 < bam_merge: ./bam_merge.o ./GBase.o
88 > bam_merge: ./common.o ./GBase.o ./bam_merge.o
89          ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
90   bwt_map.o: bwt_map.h
91   fix_map_ordering: ${COM_OBJS} bwt_map.o ./fix_map_ordering.o

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