X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=makefile;h=76e1ac39350045f1200d5786e45f3ebf323464f5;hp=cca54bebacefe9630accd2c7039b356d0dea07c4;hb=0f8fbc39759d8a8a4fa755903b8bde403b0da6c9;hpb=237bbdf363c9e42ee24e2fd63106dccf20d9bf2f

diff --git a/makefile b/makefile
index cca54be..76e1ac3 100644
--- a/makefile
+++ b/makefile
@@ -1,22 +1,21 @@
 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
+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)
 
-all : build-sam $(PROGRAMS)
-
-build-sam : 
+sam/libbam.a :
 	cd sam ; ${MAKE} all
 
 Transcript.h : utils.h
 
 Transcripts.h : my_assert.h Transcript.h
 
-rsem-extract-reference-transcripts : utils.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
+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 Transcript.h Transcripts.h synthesisRef.cpp
+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
@@ -51,10 +50,10 @@ SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h
 
 
 rsem-parse-alignments : parseIt.o sam/libbam.a
-	$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz 
+	$(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) $(COFLAGS) parseIt.cpp
+	$(CC) -Wall -O2 -c -I. parseIt.cpp
 
 
 rsem-build-read-index : utils.h buildReadIndex.cpp
@@ -65,13 +64,13 @@ 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
+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 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
+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 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 
+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 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
+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
 
@@ -83,10 +82,12 @@ BamWriter.h : sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h SingleHit.h Pair
 
 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 EM.cpp
+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
@@ -94,13 +95,13 @@ 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 $@
+	$(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -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-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 : wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
-	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -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
@@ -108,14 +109,14 @@ wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
 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
+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 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 WriteResults.h Gibbs.cpp 
 	$(CC) $(COFLAGS) Gibbs.cpp
 
 Buffer.h : my_assert.h
@@ -124,13 +125,24 @@ 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 Buffer.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 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 -o $@
+	$(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 $@
 
-clean:
+.PHONY: ebseq
+
+ebseq :
+	cd EBSeq ; ${MAKE} all
+
+clean :
 	rm -f *.o *~ $(PROGRAMS)
 	cd sam ; ${MAKE} clean
-
+	cd EBSeq ; ${MAKE} clean