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 Transcript.h Transcripts.h
+SamParser.h : sam/sam.h sam/bam.h utils.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h RefSeq.h Refs.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 Transcript.h Transcripts.h sam/sam.h sam/bam.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 RefSeq.h Refs.h sam/sam.h sam/bam.h parseIt.cpp
$(CC) $(COFLAGS) parseIt.cpp
$(CC) $(COFLAGS) simulation.cpp
rsem-run-gibbs : Gibbs.o
- $(CC) -o 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
$(CC) -o rsem-calculate-credibility-intervals calcCI.o
#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 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
$(CC) $(COFLAGS) calcCI.cpp
clean: