roll back to original version plus fixed a small bug in calcCI.cpp

[rsem.git] / makefile

diff --git a/makefile b/makefile
index 97cba95d1e8aad570e1f40d871f2c80b8a054768..45ab35d11cee55d44654949830bf4c0b43869d66 100644 (file)
--- a/makefile
+++ b/makefile
@@ -1,8 +1,7 @@
 CC = g++
-#LFLAGS = -Wall -O3 -ffast-math
 CFLAGS = -Wall -c -I.
 COFLAGS = -Wall -O3 -ffast-math -c -I.
-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
+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
 
 
 all : build-sam $(PROGRAMS)
@@ -62,6 +61,8 @@ rsem-build-read-index : utils.h buildReadIndex.cpp
        $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
 
 
+simul.h : boost/random.hpp
+
 ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
 
 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
@@ -74,16 +75,35 @@ PairedEndQModel.h : utils.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h
 
 HitWrapper.h : HitContainer.h
 
-BamWriter.h : sam/sam.h sam/bam.h utils.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
+sam_rsem_aux.h : sam/bam.h
+
+sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
+
+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
+
+sampling.h : boost/random.hpp
 
 rsem-run-em : EM.o sam/libbam.a
        $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
 
-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
+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
        $(CC) $(COFLAGS) EM.cpp
 
-rsem-bam2wig : sam/bam.h sam/sam.h sam/libbam.a bam2wig.cpp
-       $(CC) -O3 -Wall bam2wig.cpp sam/libbam.a -lz -o rsem-bam2wig
+bc_aux.h : sam/bam.h
+
+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
+
+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
+       $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -o $@
+
+rsem-bam2wig : wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
+       $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -o $@
+
+rsem-bam2readdepth : wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
+       $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -o $@
+
+wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
+       $(CC) $(COFLAGS) wiggle.cpp
 
 rsem-simulate-reads : simulation.o
        $(CC) -o rsem-simulate-reads simulation.o
@@ -95,16 +115,21 @@ rsem-run-gibbs : Gibbs.o
        $(CC) -o rsem-run-gibbs Gibbs.o -lpthread
 
 #some header files are omitted
-Gibbs.o : utils.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h boost/random.hpp Gibbs.cpp 
+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 
        $(CC) $(COFLAGS) Gibbs.cpp
 
+Buffer.h : my_assert.h
+
 rsem-calculate-credibility-intervals : calcCI.o
-       $(CC) -o rsem-calculate-credibility-intervals calcCI.o
+       $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
 
 #some header files are omitted
-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 boost/random.hpp
+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
        $(CC) $(COFLAGS) calcCI.cpp
 
+rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
+       $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -o $@
+
 clean:
        rm -f *.o *~ $(PROGRAMS)
        cd sam ; ${MAKE} clean