X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=a6d863c7b6616901a058418c56fa60c9828d1cc7;hb=97554bbac838f2ed578d81f98e421dac0669e74e;hp=45ab35d11cee55d44654949830bf4c0b43869d66;hpb=757263aa0ff5367f826468db30d983282e51e7f0;p=rsem.git

diff --git a/makefile b/makefile
index 45ab35d..a6d863c 100644
--- a/makefile
+++ b/makefile
@@ -4,14 +4,14 @@ 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
 
 
-all : build-sam $(PROGRAMS)
+all : $(PROGRAMS)
 
-build-sam : 
+sam/libbam.a :
 	cd sam ; ${MAKE} all
 
 Transcript.h : utils.h
 
-Transcripts.h : Transcript.h
+Transcripts.h : my_assert.h Transcript.h
 
 rsem-extract-reference-transcripts : utils.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
 	$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
@@ -47,13 +47,13 @@ PairedEndHit.h : SingleHit.h
 HitContainer.h : GroupInfo.h
 
 
-SamParser.h : sam/sam.h sam/bam.h utils.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h RefSeq.h Refs.h
+SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h
 
 
 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 RefSeq.h Refs.h sam/sam.h sam/bam.h parseIt.cpp
+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