2 #LFLAGS = -Wall -O3 -ffast-math
4 COFLAGS = -Wall -O3 -ffast-math -c -I.
5 PROGRAMS = rsem-bam2wig rsem-build-read-index rsem-run-em rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-parse-alignments rsem-preref rsem-simulate-reads rsem-run-gibbs rsem-calculate-credibility-intervals
8 all : build-sam $(PROGRAMS)
13 Transcript.h : utils.h
15 Transcripts.h : Transcript.h
17 rsem-extract-reference-transcripts : utils.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
18 $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
20 rsem-synthesis-reference-transcripts : utils.h Transcript.h Transcripts.h synthesisRef.cpp
21 $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
23 BowtieRefSeqPolicy.h : RefSeqPolicy.h
27 Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h
30 rsem-preref : preRef.o
31 $(CC) preRef.o -o rsem-preref
33 preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
34 $(CC) $(COFLAGS) preRef.cpp
39 SingleReadQ.h : Read.h
41 PairedEndRead.h : Read.h SingleRead.h
43 PairedEndReadQ.h : Read.h SingleReadQ.h
46 PairedEndHit.h : SingleHit.h
48 HitContainer.h : GroupInfo.h
51 SamParser.h : sam/sam.h sam/bam.h utils.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h
54 rsem-parse-alignments : parseIt.o sam/libbam.a
55 $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz
57 parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h parseIt.cpp
58 $(CC) $(COFLAGS) parseIt.cpp
61 rsem-build-read-index : utils.h buildReadIndex.cpp
62 $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
65 ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
67 SingleModel.h : utils.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 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 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 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 BamWriter.h : sam/sam.h sam/bam.h utils.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
79 rsem-run-em : EM.o sam/libbam.a
80 $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
82 EM.o : utils.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 EM.cpp simul.h
83 $(CC) $(COFLAGS) EM.cpp
85 rsem-bam2wig : sam/bam.h sam/sam.h sam/libbam.a bam2wig.cpp
86 $(CC) -O3 -Wall bam2wig.cpp sam/libbam.a -lz -o rsem-bam2wig
88 mersenne.o : mersenne.cpp randomc.h
89 $(CC) $(COFLAGS) mersenne.cpp
91 simul_mersenne.h : simul.h randomc.h
93 rsem-simulate-reads : simulation.o mersenne.o
94 $(CC) -o rsem-simulate-reads simulation.o mersenne.o
96 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 simul_mersenne.h randomc.h simulation.cpp
97 $(CC) $(COFLAGS) simulation.cpp
99 rsem-run-gibbs : Gibbs.o mersenne.o
100 $(CC) -o rsem-run-gibbs Gibbs.o mersenne.o
102 #some header files are omitted
103 Gibbs.o : randomc.h utils.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h Gibbs.cpp
104 $(CC) $(COFLAGS) Gibbs.cpp
106 rsem-calculate-credibility-intervals : calcCI.o
107 $(CC) -o rsem-calculate-credibility-intervals calcCI.o
109 #some header files are omitted
110 calcCI.o : utils.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h calcCI.cpp
111 $(CC) $(COFLAGS) calcCI.cpp
114 rm -f *.o *~ $(PROGRAMS)
115 cd sam ; ${MAKE} clean