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root/gclib/tophat_cpp/Makefile

#	Line 1 | Line 1
1		# Directories to search for header files
2	<	SEQAN = ./SeqAn-1.2
2	>	SEQAN = ./SeqAn-1.3
3		SEARCHDIRS := -I. -I${SEQAN} -I.. -I/opt/geo/include
4
5		SYSTYPE :=     $(shell uname)
#	Line 10 | Line 10
10		ifeq ($(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 -pthread ${SEARCHDIRS} $(MARCH) -DHAVE_CONFIG_H \
#	Line 22 | Line 22
22		CFLAGS = -g -DMEM_DEBUG -DDEBUG $(BASEFLAGS)
23		LDFLAGS = -g -L/opt/geo/lib
24		else
25	<	CFLAGS = -O2 -DNDEBUG $(BASEFLAGS)
25	>	CFLAGS = -O3 -msse2 -DNDEBUG $(BASEFLAGS)
26		LDFLAGS = -L/opt/geo/lib
27		endif
28
#	Line 50 | Line 50
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 map2gtf gtf_to_fasta bam_merge bam2fastx \
57		prep_reads extract_reads juncs_db long_spanning_reads gtf_juncs segment_juncs \
#	Line 59 | Line 59
59
60		.PHONY : all
61		#all: fix_map_ordering
62	<	all: bam_merge
62	>	all: fix_map_ordering
63		#.PHONY : nodebug
64		nodebug : all
65		#all: prep_reads
#	Line 88 | Line 88
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: ./common.o ./GBase.o ./bam_merge.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} fusions.o long_spanning_reads.o
97		${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${BLIBS}
98	<	prep_reads: ${PREP_OBJS} ./prep_reads.o
98	>	prep_reads: ${PREP_OBJS} prep_reads.o
99		${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
100	<	extract_reads: ${COM_OBJS} ./extract_reads.o
100	>	extract_reads: ${COM_OBJS} extract_reads.o
101		${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
102	<	gtf_to_fasta: ${COM_OBJS} bwt_map.o ${GFF_OBJS} ./FastaTools.o ./GTFToFasta.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	<	map2gtf: ${COM_OBJS} bwt_map.o ${GFF_OBJS} ./map2gtf.o
104	>	map2gtf: ${COM_OBJS} bwt_map.o ${GFF_OBJS} map2gtf.o
105		${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
106	<	gtf_juncs: ${COM_OBJS} bwt_map.o ${GFF_OBJS} ./gtf_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	<	segment_juncs: ${SEG_OBJS} fusions.o segment_juncs.o
108	>	segment_juncs: ${SEG_OBJS} segment_juncs.o
109		${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${BLIBS}
110	<	juncs_db: ${SEG_OBJS} fusions.o juncs_db.o
110	>	juncs_db: ${SEG_OBJS} juncs_db.o
111		${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
112	<	tophat_reports: ${SEG_OBJS} deletions.o fusions.o insertions.o inserts.o fragments.o align_status.o tophat_reports.o
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

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