X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=e1a47f25bd7f1c033550ac205393212ddb896921;hb=1b2999c4407ef8419fb89b66b843b7141caff4da;hp=900a8b3d3a7d47db5cc29ada4e1c78fb08d38b64;hpb=d5639baddcd4bdf09dd31237e914afb987954472;p=rsem.git

diff --git a/makefile b/makefile
index 900a8b3..e1a47f2 100644
--- a/makefile
+++ b/makefile
@@ -1,7 +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
+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
 
 
 all : $(PROGRAMS)
@@ -54,7 +54,7 @@ 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 Transcripts.h sam/sam.h sam/bam.h parseIt.cpp
-	$(CC) $(COFLAGS) parseIt.cpp
+	$(CC) -Wall -O2 -c -I. parseIt.cpp
 
 
 rsem-build-read-index : utils.h buildReadIndex.cpp
@@ -96,10 +96,10 @@ 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
@@ -132,10 +132,13 @@ rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
 
 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 $@
-	
+
 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 $@
+
 clean:
 	rm -f *.o *~ $(PROGRAMS)
 	cd sam ; ${MAKE} clean