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# Directories to search for header files |
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SEQAN = ./SeqAn-1.2 |
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< |
SEARCHDIRS := -I. -I${SEQAN} -I/opt/geo/include |
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> |
SEARCHDIRS := -I. -I${SEQAN} -I.. -I/opt/geo/include |
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SYSTYPE := $(shell uname) |
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SEG_OBJS = ${COM_OBJS} bwt_map.o junctions.o |
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LONGSR_OBJS = ${COM_OBJS} bwt_map.o junctions.o |
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< |
ALL_EXE = fix_map_ordering bam_merge bam2fastx prep_reads extract_reads long_spanning_reads segment_juncs tophat_reports |
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> |
ALL_EXE = fix_map_ordering map2gtf gtf_to_fasta bam_merge bam2fastx \ |
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> |
prep_reads extract_reads long_spanning_reads gtf_juncs segment_juncs \ |
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> |
tophat_reports |
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.PHONY : all |
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< |
# all: prep_reads |
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> |
all: segment_juncs |
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> |
debug: segment_juncs |
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> |
#all: prep_reads |
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> |
#debug: prep_reads |
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> |
|
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# all_exe: prep_reads extract_reads segment_juncs long_spanning_reads |
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< |
all: $(ALL_EXE) |
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< |
debug: $(ALL_EXE) |
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> |
#all: $(ALL_EXE) |
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> |
#debug: $(ALL_EXE) |
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> |
#all: segment_juncs |
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> |
#debug: segment_juncs |
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#all: bam_dump |
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#all: sam2bam |
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#debug: sam2bam |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
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extract_reads: ${COM_OBJS} ./extract_reads.o |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
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+ |
gtf_to_fasta: ${COM_OBJS} bwt_map.o ${GFF_OBJS} ./FastaTools.o ./GTFToFasta.o |
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+ |
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
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+ |
map2gtf: ${COM_OBJS} bwt_map.o ${GFF_OBJS} ./map2gtf.o |
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+ |
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
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gtf_juncs: ${COM_OBJS} bwt_map.o ${GFF_OBJS} ./gtf_juncs.o |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
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segment_juncs: ${SEG_OBJS} ./segment_juncs.o |
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# target for removing all object files |
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.PHONY : clean |
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< |
clean:: |
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< |
${RM} *.o sam2bam core core.* ${ALL_EXE} *.o* |
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> |
clean:: |
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> |
${RM} *.o sam2bam core core.* ${ALL_EXE} |
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