| 1 |
gpertea |
29 |
# Directories to search for header files |
| 2 |
|
|
SEQAN = ./SeqAn-1.2 |
| 3 |
|
|
SEARCHDIRS := -I. -I${SEQAN} -I/opt/geo/include |
| 4 |
|
|
|
| 5 |
|
|
SYSTYPE := $(shell uname) |
| 6 |
|
|
|
| 7 |
|
|
# C compiler |
| 8 |
|
|
|
| 9 |
|
|
MACHTYPE := $(shell uname -m) |
| 10 |
|
|
ifeq ($(MACHTYPE), i686) |
| 11 |
|
|
MARCH = -march=i686 |
| 12 |
|
|
else |
| 13 |
|
|
MARCH = |
| 14 |
|
|
endif |
| 15 |
|
|
|
| 16 |
|
|
CC := g++ |
| 17 |
|
|
BASEFLAGS = -Wall ${SEARCHDIRS} $(MARCH) -DHAVE_CONFIG_H \ |
| 18 |
|
|
-fno-strict-aliasing -D_REENTRANT |
| 19 |
|
|
|
| 20 |
|
|
|
| 21 |
|
|
ifeq ($(findstring debug,$(MAKECMDGOALS)),) |
| 22 |
|
|
CFLAGS = -O2 -DNDEBUG $(BASEFLAGS) |
| 23 |
|
|
LDFLAGS = -L/opt/geo/lib |
| 24 |
|
|
else |
| 25 |
|
|
CFLAGS = -g -DMEM_DEBUG -DDEBUG $(BASEFLAGS) |
| 26 |
|
|
LDFLAGS = -g -L/opt/geo/lib |
| 27 |
|
|
endif |
| 28 |
|
|
|
| 29 |
|
|
%.o : %.c |
| 30 |
|
|
${CC} ${CFLAGS} -c $< -o $@ |
| 31 |
|
|
|
| 32 |
|
|
%.o : %.cc |
| 33 |
|
|
${CC} ${CFLAGS} -c $< -o $@ |
| 34 |
|
|
|
| 35 |
|
|
%.o : %.C |
| 36 |
|
|
${CC} ${CFLAGS} -c $< -o $@ |
| 37 |
|
|
|
| 38 |
|
|
%.o : %.cpp |
| 39 |
|
|
${CC} ${CFLAGS} -c $< -o $@ |
| 40 |
|
|
|
| 41 |
|
|
%.o : %.cxx |
| 42 |
|
|
${CC} ${CFLAGS} -c $< -o $@ |
| 43 |
|
|
|
| 44 |
|
|
# C/C++ linker |
| 45 |
|
|
|
| 46 |
|
|
LINKER := g++ |
| 47 |
|
|
LIBS = -lz -lbam |
| 48 |
|
|
|
| 49 |
|
|
COM_OBJS = common.o reads.o tokenize.o |
| 50 |
|
|
PREP_OBJS = ${COM_OBJS} qual.o |
| 51 |
|
|
GFF_OBJS = GBase.o GStr.o codons.o gdna.o GFaSeqGet.o gff.o |
| 52 |
|
|
SEG_OBJS = ${COM_OBJS} bwt_map.o junctions.o |
| 53 |
|
|
LONGSR_OBJS = ${COM_OBJS} bwt_map.o junctions.o |
| 54 |
|
|
|
| 55 |
|
|
ALL_EXE = fix_map_ordering bam_merge bam2fastx prep_reads extract_reads long_spanning_reads segment_juncs tophat_reports |
| 56 |
|
|
|
| 57 |
|
|
.PHONY : all |
| 58 |
|
|
# all: prep_reads |
| 59 |
|
|
# all_exe: prep_reads extract_reads segment_juncs long_spanning_reads |
| 60 |
gpertea |
67 |
all: $(ALL_EXE) |
| 61 |
|
|
debug: $(ALL_EXE) |
| 62 |
gpertea |
29 |
#all: bam_dump |
| 63 |
|
|
#all: sam2bam |
| 64 |
|
|
#debug: sam2bam |
| 65 |
|
|
#all: prep_reads |
| 66 |
|
|
#debug: prep_reads |
| 67 |
|
|
sam2bam: ./sam2bam.o |
| 68 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 69 |
|
|
bam_dump: ./bam_dump.o |
| 70 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 71 |
|
|
#all: prep_reads |
| 72 |
|
|
#debug: prep_reads |
| 73 |
|
|
all_bin: ${ALL_EXE} |
| 74 |
|
|
bwt2sam: ${COM_OBJS} bwt_map.o bwt2sam.o |
| 75 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 76 |
|
|
bam2bed: ./bam2bed.o |
| 77 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 78 |
|
|
bam2fastx: ./bam2fastx.o |
| 79 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 80 |
|
|
bam_merge: ./bam_merge.o ./GBase.o |
| 81 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 82 |
|
|
bwt_map.o: bwt_map.h |
| 83 |
|
|
fix_map_ordering: ${COM_OBJS} bwt_map.o ./fix_map_ordering.o |
| 84 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 85 |
|
|
long_spanning_reads: ${SEG_OBJS} ./long_spanning_reads.o |
| 86 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 87 |
|
|
prep_reads: ${PREP_OBJS} ./prep_reads.o |
| 88 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 89 |
|
|
extract_reads: ${COM_OBJS} ./extract_reads.o |
| 90 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 91 |
|
|
gtf_juncs: ${COM_OBJS} bwt_map.o ${GFF_OBJS} ./gtf_juncs.o |
| 92 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 93 |
|
|
segment_juncs: ${SEG_OBJS} ./segment_juncs.o |
| 94 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 95 |
|
|
tophat_reports: ${SEG_OBJS} bwt_map.o deletions.o insertions.o inserts.o fragments.o align_status.o tophat_reports.o |
| 96 |
|
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 97 |
|
|
|
| 98 |
|
|
# target for removing all object files |
| 99 |
|
|
|
| 100 |
|
|
.PHONY : clean |
| 101 |
|
|
clean:: |
| 102 |
|
|
${RM} *.o sam2bam core core.* ${ALL_EXE} *.o* |
