| 1 |
|
# Directories to search for header files |
| 2 |
< |
SEQAN = ./SeqAn-1.2 |
| 3 |
< |
SEARCHDIRS := -I. -I${SEQAN} -I/opt/geo/include |
| 2 |
> |
SEQAN = ./SeqAn-1.3 |
| 3 |
> |
SEARCHDIRS := -I. -I${SEQAN} -I.. -I/opt/geo/include |
| 4 |
|
|
| 5 |
|
SYSTYPE := $(shell uname) |
| 6 |
|
|
| 10 |
|
ifeq ($(MACHTYPE), i686) |
| 11 |
|
MARCH = -march=i686 |
| 12 |
|
else |
| 13 |
< |
MARCH = |
| 14 |
< |
endif |
| 13 |
> |
MARCH = -march=core2 |
| 14 |
> |
endif |
| 15 |
|
|
| 16 |
|
CC := g++ |
| 17 |
< |
BASEFLAGS = -Wall ${SEARCHDIRS} $(MARCH) -DHAVE_CONFIG_H \ |
| 17 |
> |
BASEFLAGS = -Wall -pthread ${SEARCHDIRS} $(MARCH) -DHAVE_CONFIG_H \ |
| 18 |
|
-fno-strict-aliasing -D_REENTRANT |
| 19 |
|
|
| 20 |
|
|
| 21 |
< |
ifeq ($(findstring debug,$(MAKECMDGOALS)),) |
| 22 |
< |
CFLAGS = -O2 -DNDEBUG $(BASEFLAGS) |
| 23 |
< |
LDFLAGS = -L/opt/geo/lib |
| 24 |
< |
else |
| 21 |
> |
ifeq ($(findstring nodebug,$(MAKECMDGOALS)),) |
| 22 |
|
CFLAGS = -g -DMEM_DEBUG -DDEBUG $(BASEFLAGS) |
| 23 |
|
LDFLAGS = -g -L/opt/geo/lib |
| 24 |
+ |
else |
| 25 |
+ |
CFLAGS = -O3 -msse2 -DNDEBUG $(BASEFLAGS) |
| 26 |
+ |
LDFLAGS = -L/opt/geo/lib |
| 27 |
|
endif |
| 28 |
|
|
| 29 |
|
%.o : %.c |
| 44 |
|
# C/C++ linker |
| 45 |
|
|
| 46 |
|
LINKER := g++ |
| 47 |
< |
LIBS = -lz -lbam |
| 47 |
> |
LIBS = -lz -lbam |
| 48 |
> |
BLIBS = ${LIBS} -lpthread -lboost_thread |
| 49 |
|
|
| 50 |
< |
COM_OBJS = common.o reads.o tokenize.o |
| 50 |
> |
COM_OBJS = common.o reads.o tokenize.o utils.o |
| 51 |
|
PREP_OBJS = ${COM_OBJS} qual.o |
| 52 |
|
GFF_OBJS = GBase.o GStr.o codons.o gdna.o GFaSeqGet.o gff.o |
| 53 |
< |
SEG_OBJS = ${COM_OBJS} bwt_map.o junctions.o |
| 54 |
< |
LONGSR_OBJS = ${COM_OBJS} bwt_map.o junctions.o |
| 53 |
> |
SEG_OBJS = ${COM_OBJS} bwt_map.o junctions.o insertions.o coverage.o \ |
| 54 |
> |
fragments.o align_status.o deletions.o fusions.o |
| 55 |
|
|
| 56 |
< |
ALL_EXE = fix_map_ordering bam_merge bam2fastx prep_reads extract_reads long_spanning_reads segment_juncs tophat_reports |
| 56 |
> |
ALL_EXE = fix_map_ordering map2gtf gtf_to_fasta bam_merge bam2fastx \ |
| 57 |
> |
prep_reads extract_reads juncs_db long_spanning_reads gtf_juncs segment_juncs \ |
| 58 |
> |
tophat_reports |
| 59 |
|
|
| 60 |
|
.PHONY : all |
| 61 |
< |
# all: prep_reads |
| 62 |
< |
# all_exe: prep_reads extract_reads segment_juncs long_spanning_reads |
| 63 |
< |
all: bam_merge |
| 64 |
< |
debug: bam_merge |
| 61 |
> |
#all: fix_map_ordering |
| 62 |
> |
all: prep_reads |
| 63 |
> |
#.PHONY : nodebug |
| 64 |
> |
nodebug : all |
| 65 |
> |
#all: prep_reads |
| 66 |
> |
#debug: prep_reads |
| 67 |
> |
|
| 68 |
> |
all_exe: $(ALL_EXE) |
| 69 |
> |
#all: $(ALL_EXE) |
| 70 |
> |
#debug: $(ALL_EXE) |
| 71 |
> |
#all: segment_juncs |
| 72 |
> |
#debug: segment_juncs |
| 73 |
|
#all: bam_dump |
| 74 |
|
#all: sam2bam |
| 75 |
|
#debug: sam2bam |
| 88 |
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 89 |
|
bam2fastx: ./bam2fastx.o |
| 90 |
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 91 |
< |
bam_merge: ./bam_merge.o ./GBase.o |
| 91 |
> |
bam_merge: ./common.o ./tokenize.o ./bam_merge.o |
| 92 |
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 93 |
|
bwt_map.o: bwt_map.h |
| 94 |
< |
fix_map_ordering: ${COM_OBJS} bwt_map.o ./fix_map_ordering.o |
| 94 |
> |
fix_map_ordering: ${COM_OBJS} bwt_map.o fix_map_ordering.o |
| 95 |
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 96 |
< |
long_spanning_reads: ${SEG_OBJS} ./long_spanning_reads.o |
| 96 |
> |
long_spanning_reads: ${SEG_OBJS} fusions.o long_spanning_reads.o |
| 97 |
> |
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${BLIBS} |
| 98 |
> |
prep_reads: ${PREP_OBJS} prep_reads.o |
| 99 |
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 100 |
< |
prep_reads: ${PREP_OBJS} ./prep_reads.o |
| 100 |
> |
extract_reads: ${COM_OBJS} extract_reads.o |
| 101 |
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 102 |
< |
extract_reads: ${COM_OBJS} ./extract_reads.o |
| 102 |
> |
gtf_to_fasta: ${COM_OBJS} bwt_map.o ${GFF_OBJS} FastaTools.o GTFToFasta.o |
| 103 |
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 104 |
< |
gtf_juncs: ${COM_OBJS} bwt_map.o ${GFF_OBJS} ./gtf_juncs.o |
| 104 |
> |
map2gtf: ${COM_OBJS} bwt_map.o ${GFF_OBJS} map2gtf.o |
| 105 |
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 106 |
< |
segment_juncs: ${SEG_OBJS} ./segment_juncs.o |
| 106 |
> |
gtf_juncs: ${COM_OBJS} bwt_map.o ${GFF_OBJS} gtf_juncs.o |
| 107 |
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 108 |
< |
tophat_reports: ${SEG_OBJS} bwt_map.o deletions.o insertions.o inserts.o fragments.o align_status.o tophat_reports.o |
| 108 |
> |
segment_juncs: ${SEG_OBJS} segment_juncs.o |
| 109 |
> |
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${BLIBS} |
| 110 |
> |
juncs_db: ${SEG_OBJS} juncs_db.o |
| 111 |
|
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} |
| 112 |
+ |
tophat_reports: ${SEG_OBJS} inserts.o tophat_reports.o |
| 113 |
+ |
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${BLIBS} |
| 114 |
+ |
tophat_reports.o prep_reads.o fix_map_ordering.o map2gtf.o bam_merge.o bam2fastx.o bwt_map.o common.o: common.h |
| 115 |
+ |
bwt_map.o: common.h bwt_map.h |
| 116 |
|
|
| 117 |
|
# target for removing all object files |
| 118 |
|
|
| 119 |
|
.PHONY : clean |
| 120 |
< |
clean:: |
| 121 |
< |
${RM} *.o sam2bam core core.* ${ALL_EXE} *.o* |
| 120 |
> |
clean:: |
| 121 |
> |
${RM} *.o sam2bam core core.* ${ALL_EXE} |
| 122 |
|
|
| 123 |
|
|
