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
6 .PHONY : all ebseq clean
13 Transcript.h : utils.h
15 Transcripts.h : my_assert.h Transcript.h
17 rsem-extract-reference-transcripts : utils.h my_assert.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 my_assert.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 my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h
54 rsem-parse-alignments : parseIt.o sam/libbam.a
55 $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
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 Transcripts.h sam/sam.h sam/bam.h parseIt.cpp
58 $(CC) -Wall -O2 -c -I. parseIt.cpp
61 rsem-build-read-index : utils.h buildReadIndex.cpp
62 $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
65 simul.h : boost/random.hpp
67 ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
69 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
71 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
73 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
75 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
77 HitWrapper.h : HitContainer.h
79 sam_rsem_aux.h : sam/bam.h
81 sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
83 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
85 sampling.h : boost/random.hpp
87 WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h
89 rsem-run-em : EM.o sam/libbam.a
90 $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
92 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 WriteResults.h EM.cpp
93 $(CC) $(COFLAGS) EM.cpp
97 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
99 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
100 $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
102 rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
103 $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
105 rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
106 $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
108 wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
109 $(CC) $(COFLAGS) wiggle.cpp
111 rsem-simulate-reads : simulation.o
112 $(CC) -o rsem-simulate-reads simulation.o
114 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 WriteResults.h simulation.cpp
115 $(CC) $(COFLAGS) simulation.cpp
117 rsem-run-gibbs : Gibbs.o
118 $(CC) -o rsem-run-gibbs Gibbs.o -lpthread
120 #some header files are omitted
121 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 WriteResults.h Gibbs.cpp
122 $(CC) $(COFLAGS) Gibbs.cpp
124 Buffer.h : my_assert.h
126 rsem-calculate-credibility-intervals : calcCI.o
127 $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
129 #some header files are omitted
130 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 WriteResults.h Buffer.h calcCI.cpp
131 $(CC) $(COFLAGS) calcCI.cpp
133 rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
134 $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
136 rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
137 $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
139 rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
140 $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
143 cd EBSeq ; ${MAKE} all
146 rm -f *.o *~ $(PROGRAMS)
147 cd sam ; ${MAKE} clean
148 cd EBSeq ; ${MAKE} clean