3 COFLAGS = -Wall -O3 -ffast-math -c -I.
4 PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
11 Transcript.h : utils.h
13 Transcripts.h : my_assert.h Transcript.h
15 rsem-extract-reference-transcripts : utils.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
16 $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
18 rsem-synthesis-reference-transcripts : utils.h Transcript.h Transcripts.h synthesisRef.cpp
19 $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
21 BowtieRefSeqPolicy.h : RefSeqPolicy.h
25 Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h
28 rsem-preref : preRef.o
29 $(CC) preRef.o -o rsem-preref
31 preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
32 $(CC) $(COFLAGS) preRef.cpp
37 SingleReadQ.h : Read.h
39 PairedEndRead.h : Read.h SingleRead.h
41 PairedEndReadQ.h : Read.h SingleReadQ.h
44 PairedEndHit.h : SingleHit.h
46 HitContainer.h : GroupInfo.h
49 SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h
52 rsem-parse-alignments : parseIt.o sam/libbam.a
53 $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
55 parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp
56 $(CC) -Wall -O2 -c -I. parseIt.cpp
59 rsem-build-read-index : utils.h buildReadIndex.cpp
60 $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
63 simul.h : boost/random.hpp
65 ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
67 SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h
69 SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h
71 PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h
73 PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h
75 HitWrapper.h : HitContainer.h
77 sam_rsem_aux.h : sam/bam.h
79 sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
81 BamWriter.h : sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
83 sampling.h : boost/random.hpp
85 rsem-run-em : EM.o sam/libbam.a
86 $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
88 EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp EM.cpp
89 $(CC) $(COFLAGS) EM.cpp
93 BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
95 rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a
96 $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
98 rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
99 $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
101 rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
102 $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
104 wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
105 $(CC) $(COFLAGS) wiggle.cpp
107 rsem-simulate-reads : simulation.o
108 $(CC) -o rsem-simulate-reads simulation.o
110 simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp simulation.cpp
111 $(CC) $(COFLAGS) simulation.cpp
113 rsem-run-gibbs : Gibbs.o
114 $(CC) -o rsem-run-gibbs Gibbs.o -lpthread
116 #some header files are omitted
117 Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h Gibbs.cpp
118 $(CC) $(COFLAGS) Gibbs.cpp
120 Buffer.h : my_assert.h
122 rsem-calculate-credibility-intervals : calcCI.o
123 $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
125 #some header files are omitted
126 calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h Buffer.h calcCI.cpp
127 $(CC) $(COFLAGS) calcCI.cpp
129 rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
130 $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
132 rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
133 $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
135 rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
136 $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
141 cd EBSeq ; ${MAKE} all
144 rm -f *.o *~ $(PROGRAMS)
145 cd sam ; ${MAKE} clean
146 cd EBSeq ; ${MAKE} clean