| 1 |
gpertea |
29 |
# 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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SYSTYPE := $(shell uname) |
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# C compiler |
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MACHTYPE := $(shell uname -m) |
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ifeq ($(MACHTYPE), i686) |
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MARCH = -march=i686 |
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else |
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MARCH = |
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endif |
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CC := g++ |
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BASEFLAGS = -Wall ${SEARCHDIRS} $(MARCH) -DHAVE_CONFIG_H \ |
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-fno-strict-aliasing -D_REENTRANT |
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| 21 |
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ifeq ($(findstring debug,$(MAKECMDGOALS)),) |
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CFLAGS = -O2 -DNDEBUG $(BASEFLAGS) |
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LDFLAGS = -L/opt/geo/lib |
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else |
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CFLAGS = -g -DMEM_DEBUG -DDEBUG $(BASEFLAGS) |
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LDFLAGS = -g -L/opt/geo/lib |
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endif |
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| 29 |
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%.o : %.c |
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${CC} ${CFLAGS} -c $< -o $@ |
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%.o : %.cc |
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${CC} ${CFLAGS} -c $< -o $@ |
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%.o : %.C |
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${CC} ${CFLAGS} -c $< -o $@ |
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%.o : %.cpp |
| 39 |
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${CC} ${CFLAGS} -c $< -o $@ |
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| 41 |
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%.o : %.cxx |
| 42 |
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${CC} ${CFLAGS} -c $< -o $@ |
| 43 |
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| 44 |
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# C/C++ linker |
| 45 |
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| 46 |
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LINKER := g++ |
| 47 |
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LIBS = -lz -lbam |
| 48 |
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| 49 |
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COM_OBJS = common.o reads.o tokenize.o |
| 50 |
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PREP_OBJS = ${COM_OBJS} qual.o |
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GFF_OBJS = GBase.o GStr.o codons.o gdna.o GFaSeqGet.o gff.o |
| 52 |
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SEG_OBJS = ${COM_OBJS} bwt_map.o junctions.o |
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LONGSR_OBJS = ${COM_OBJS} bwt_map.o junctions.o |
| 54 |
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| 55 |
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ALL_EXE = fix_map_ordering bam_merge bam2fastx prep_reads extract_reads long_spanning_reads segment_juncs tophat_reports |
| 56 |
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| 57 |
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.PHONY : all |
| 58 |
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# all: prep_reads |
| 59 |
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# all_exe: prep_reads extract_reads segment_juncs long_spanning_reads |
| 60 |
gpertea |
33 |
all: fix_map_ordering |
| 61 |
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debug: fix_map_ordering |
| 62 |
gpertea |
29 |
#all: bam_dump |
| 63 |
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#all: sam2bam |
| 64 |
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#debug: sam2bam |
| 65 |
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#all: prep_reads |
| 66 |
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#debug: prep_reads |
| 67 |
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sam2bam: ./sam2bam.o |
| 68 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 69 |
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bam_dump: ./bam_dump.o |
| 70 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 71 |
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#all: prep_reads |
| 72 |
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#debug: prep_reads |
| 73 |
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all_bin: ${ALL_EXE} |
| 74 |
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bwt2sam: ${COM_OBJS} bwt_map.o bwt2sam.o |
| 75 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 76 |
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bam2bed: ./bam2bed.o |
| 77 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 78 |
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bam2fastx: ./bam2fastx.o |
| 79 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 80 |
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bam_merge: ./bam_merge.o ./GBase.o |
| 81 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 82 |
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bwt_map.o: bwt_map.h |
| 83 |
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fix_map_ordering: ${COM_OBJS} bwt_map.o ./fix_map_ordering.o |
| 84 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 85 |
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long_spanning_reads: ${SEG_OBJS} ./long_spanning_reads.o |
| 86 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 87 |
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prep_reads: ${PREP_OBJS} ./prep_reads.o |
| 88 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 89 |
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extract_reads: ${COM_OBJS} ./extract_reads.o |
| 90 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 91 |
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gtf_juncs: ${COM_OBJS} bwt_map.o ${GFF_OBJS} ./gtf_juncs.o |
| 92 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 93 |
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segment_juncs: ${SEG_OBJS} ./segment_juncs.o |
| 94 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 95 |
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tophat_reports: ${SEG_OBJS} bwt_map.o deletions.o insertions.o inserts.o fragments.o align_status.o tophat_reports.o |
| 96 |
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 97 |
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| 98 |
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# target for removing all object files |
| 99 |
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| 100 |
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.PHONY : clean |
| 101 |
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clean:: |
| 102 |
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${RM} *.o sam2bam core core.* ${ALL_EXE} *.o* |
