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 e1a47f25bd7f1c033550ac205393212ddb896921..d706f55ba04e7cf91ac376310e21c5b1fc5de55e 100644 (file)
--- a/makefile
+++ b/makefile
@@ -1,8 +1,7 @@
 CC = g++
 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 rsem-for-ebseq-calculate-clustering-info
-
+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)
 
@@ -136,10 +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 $@
 
-rsem-for-ebseq-calculate-clustering-info : calcClusteringInfo.cpp
-       $(CC) -O3 -Wall calcClusteringInfo.cpp -o $@
+ebseq :
+       cd EBSeq ; ${MAKE} all
 
-clean:
+clean :
        rm -f *.o *~ $(PROGRAMS)
        cd sam ; ${MAKE} clean
-
+       cd EBSeq ; ${MAKE} clean