X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=makefile;h=cca54bebacefe9630accd2c7039b356d0dea07c4;hp=e789a1ee5e117bd1e4e50045b4b6f467679bb567;hb=237bbdf363c9e42ee24e2fd63106dccf20d9bf2f;hpb=a95154919f950f86de9104b2b9dcf1f0c7e83387

diff --git a/makefile b/makefile
index e789a1e..cca54be 100644
--- 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)
@@ -12,7 +11,7 @@ build-sam :
 
 Transcript.h : utils.h
 
-Transcripts.h : Transcript.h
+Transcripts.h : my_assert.h Transcript.h
 
 rsem-extract-reference-transcripts : utils.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
 	$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
@@ -48,13 +47,13 @@ PairedEndHit.h : SingleHit.h
 HitContainer.h : GroupInfo.h
 
 
-SamParser.h : sam/sam.h sam/bam.h utils.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h
+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
 
 
 rsem-parse-alignments : parseIt.o sam/libbam.a
 	$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz 
 
-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
+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
 	$(CC) $(COFLAGS) parseIt.cpp
 
 
@@ -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
@@ -74,42 +75,61 @@ 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
 
-mersenne.o : mersenne.cpp randomc.h
-	$(CC) $(COFLAGS) mersenne.cpp
+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 $@
 
-simul_mersenne.h : simul.h randomc.h
+rsem-bam2wig : wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
+	$(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -o $@
 
-rsem-simulate-reads : simulation.o mersenne.o
-	$(CC) -o rsem-simulate-reads simulation.o mersenne.o
+rsem-bam2readdepth : wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
+	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -o $@
 
-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
+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
+
+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
 	$(CC) $(COFLAGS) simulation.cpp
 
-rsem-run-gibbs : Gibbs.o mersenne.o
-	$(CC) -o rsem-run-gibbs Gibbs.o mersenne.o 
+rsem-run-gibbs : Gibbs.o
+	$(CC) -o rsem-run-gibbs Gibbs.o -lpthread
 
 #some header files are omitted
-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
+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
+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