Fixed a minor bug which only affects paired-end reads for reporting how many alignmen...

[rsem.git] / makefile

diff --git a/makefile b/makefile
index e2711b532be12b82ff45a01d845597c0ed8d0ff8..d706f55ba04e7cf91ac376310e21c5b1fc5de55e 100644 (file)
--- a/makefile
+++ b/makefile
@@ -3,7 +3,6 @@ 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 rsem-sam-validator rsem-scan-for-paired-end-reads
 
-
 all : $(PROGRAMS)
 
 sam/libbam.a :
@@ -96,10 +95,10 @@ BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem
 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
+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 $@
 
-rsem-bam2readdepth : wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
+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 $@
 
 wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
@@ -136,7 +135,10 @@ rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam
 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 $@
 
-clean:
+ebseq :
+       cd EBSeq ; ${MAKE} all
+
+clean :
        rm -f *.o *~ $(PROGRAMS)
        cd sam ; ${MAKE} clean
-
+       cd EBSeq ; ${MAKE} clean