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) -Wall -O2 -c -I. parseIt.cpp
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 : 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 -o $@
+ $(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 -o $@
+ $(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
$(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 -o $@
+ $(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 -o $@
+ $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
+
+.PHONY: ebseq
+
+ebseq :
+ cd EBSeq ; ${MAKE} all
clean :
rm -f *.o *~ $(PROGRAMS)