Added support for allele-specific expression estimation

[rsem.git] / makefile

diff --git a/makefile b/makefile
index c95fd14467cb0263ac6122d321cd7af4f8e0b9bb..aec4b2ddb6b9aeb37222e7cfeea23c5a6b7a27bb 100644 (file)
--- a/makefile
+++ b/makefile
@@ -15,7 +15,7 @@ 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
 
-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
@@ -82,10 +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
@@ -107,14 +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
@@ -123,7 +125,7 @@ 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