-rsem-bam2wig : sam/bam.h sam/sam.h sam/libbam.a bam2wig.cpp
- $(CC) -O3 -Wall bam2wig.cpp sam/libbam.a -lz -o rsem-bam2wig
+bc_aux.h : sam/bam.h
+
+BamConverter.h : utils.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 $@
+
+rsem-bam2wig : wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
+ $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -o $@
+
+rsem-bam2readdepth : wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
+ $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -o $@
+
+wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
+ $(CC) $(COFLAGS) wiggle.cpp