Renamed makefile as Makefile

diff --git a/EBSeq/Makefile b/EBSeq/Makefile
new file mode 100644 (file)
index 0000000..78b6d60
--- /dev/null
+++ b/EBSeq/Makefile
@@ -0,0 +1,15 @@
+CC = g++
+PROGRAMS = EBSeq rsem-for-ebseq-calculate-clustering-info
+
+.PHONY : all EBSeq clean
+
+all : $(PROGRAMS)
+
+EBSeq : 
+       ./install
+
+rsem-for-ebseq-calculate-clustering-info : calcClusteringInfo.cpp
+       $(CC) -O3 -Wall calcClusteringInfo.cpp -o $@
+
+clean : 
+       rm -rf blockmodeling $(PROGRAMS) *~ BiocInstaller

diff --git a/EBSeq/makefile b/EBSeq/makefile
deleted file mode 100644 (file)
index 898c8fa..0000000
--- a/EBSeq/makefile
+++ /dev/null
@@ -1,13 +0,0 @@
-CC = g++
-PROGRAMS = EBSeq rsem-for-ebseq-calculate-clustering-info
-
-all : $(PROGRAMS)
-
-EBSeq : 
-       ./install
-
-rsem-for-ebseq-calculate-clustering-info : calcClusteringInfo.cpp
-       $(CC) -O3 -Wall calcClusteringInfo.cpp -o $@
-
-clean : 
-       rm -rf blockmodeling $(PROGRAMS) *~ BiocInstaller

diff --git a/Makefile b/Makefile
new file mode 100644 (file)
index 0000000..a9a705f
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,148 @@
+CC = g++
+CFLAGS = -Wall -c -I.
+COFLAGS = -Wall -O3 -ffast-math -c -I.
+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
+
+.PHONY : all ebseq clean
+
+all : $(PROGRAMS)
+
+sam/libbam.a :
+       cd sam ; ${MAKE} all
+
+Transcript.h : utils.h
+
+Transcripts.h : my_assert.h Transcript.h
+
+rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
+       $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
+
+rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
+       $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
+
+BowtieRefSeqPolicy.h : RefSeqPolicy.h
+
+RefSeq.h : utils.h
+
+Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h
+
+
+rsem-preref : preRef.o
+       $(CC) preRef.o -o rsem-preref
+
+preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
+       $(CC) $(COFLAGS) preRef.cpp
+
+
+SingleRead.h : Read.h
+
+SingleReadQ.h : Read.h
+
+PairedEndRead.h : Read.h SingleRead.h
+
+PairedEndReadQ.h : Read.h SingleReadQ.h
+
+
+PairedEndHit.h : SingleHit.h
+
+HitContainer.h : GroupInfo.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 -lpthread 
+
+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) -Wall -O2 -c -I. parseIt.cpp
+
+
+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 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
+
+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
+
+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 
+
+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
+
+HitWrapper.h : HitContainer.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
+
+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
+
+rsem-run-em : EM.o sam/libbam.a
+       $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
+
+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
+       $(CC) $(COFLAGS) EM.cpp
+
+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 -lpthread -o $@
+
+rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
+       $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
+
+rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
+       $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -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
+
+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
+       $(CC) $(COFLAGS) simulation.cpp
+
+rsem-run-gibbs : Gibbs.o
+       $(CC) -o rsem-run-gibbs Gibbs.o -lpthread
+
+#some header files are omitted
+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 
+       $(CC) $(COFLAGS) Gibbs.cpp
+
+Buffer.h : my_assert.h
+
+rsem-calculate-credibility-intervals : calcCI.o
+       $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
+
+#some header files are omitted
+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
+       $(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 -lpthread -o $@
+
+rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
+       $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
+
+rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
+       $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
+
+ebseq :
+       cd EBSeq ; ${MAKE} all
+
+clean :
+       rm -f *.o *~ $(PROGRAMS)
+       cd sam ; ${MAKE} clean
+       cd EBSeq ; ${MAKE} clean

diff --git a/makefile b/makefile
deleted file mode 100644 (file)
index 76e1ac3..0000000
--- a/makefile
+++ /dev/null
@@ -1,148 +0,0 @@
-CC = g++
-CFLAGS = -Wall -c -I.
-COFLAGS = -Wall -O3 -ffast-math -c -I.
-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
-
-all : $(PROGRAMS)
-
-sam/libbam.a :
-       cd sam ; ${MAKE} all
-
-Transcript.h : utils.h
-
-Transcripts.h : my_assert.h Transcript.h
-
-rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
-       $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
-
-rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
-       $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
-
-BowtieRefSeqPolicy.h : RefSeqPolicy.h
-
-RefSeq.h : utils.h
-
-Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h
-
-
-rsem-preref : preRef.o
-       $(CC) preRef.o -o rsem-preref
-
-preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
-       $(CC) $(COFLAGS) preRef.cpp
-
-
-SingleRead.h : Read.h
-
-SingleReadQ.h : Read.h
-
-PairedEndRead.h : Read.h SingleRead.h
-
-PairedEndReadQ.h : Read.h SingleReadQ.h
-
-
-PairedEndHit.h : SingleHit.h
-
-HitContainer.h : GroupInfo.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 -lpthread 
-
-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) -Wall -O2 -c -I. parseIt.cpp
-
-
-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 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
-
-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
-
-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 
-
-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
-
-HitWrapper.h : HitContainer.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
-
-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
-
-rsem-run-em : EM.o sam/libbam.a
-       $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
-
-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
-       $(CC) $(COFLAGS) EM.cpp
-
-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 -lpthread -o $@
-
-rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
-       $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-
-rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
-       $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -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
-
-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
-       $(CC) $(COFLAGS) simulation.cpp
-
-rsem-run-gibbs : Gibbs.o
-       $(CC) -o rsem-run-gibbs Gibbs.o -lpthread
-
-#some header files are omitted
-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 
-       $(CC) $(COFLAGS) Gibbs.cpp
-
-Buffer.h : my_assert.h
-
-rsem-calculate-credibility-intervals : calcCI.o
-       $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
-
-#some header files are omitted
-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
-       $(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 -lpthread -o $@
-
-rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
-       $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
-
-rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
-       $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
-
-.PHONY: ebseq
-
-ebseq :
-       cd EBSeq ; ${MAKE} all
-
-clean :
-       rm -f *.o *~ $(PROGRAMS)
-       cd sam ; ${MAKE} clean
-       cd EBSeq ; ${MAKE} clean