Description: don't build local copy of samtools
Author: Michael R. Crusoe <crusoe@ucdavis.edu>
--- a/Makefile
+++ b/Makefile
@@ -7,9 +7,6 @@
 
 all : $(PROGRAMS)
 
-sam/libbam.a :
-	cd sam ; ${MAKE} all
-
 Transcript.h : utils.h
 
 Transcripts.h : utils.h my_assert.h Transcript.h
@@ -48,13 +45,13 @@
 HitContainer.h : GroupInfo.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
+SamParser.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 -lpthread 
+rsem-parse-alignments : parseIt.o
+	$(CC) -o rsem-parse-alignments parseIt.o /usr/lib/libbam.a -lz -lpthread 
 
-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
+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 parseIt.cpp
 	$(CC) -Wall -O2 -c -I. parseIt.cpp
 
 
@@ -76,36 +73,32 @@
 
 HitWrapper.h : HitContainer.h
 
-sam_rsem_aux.h : sam/bam.h
-
-sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
+sam_rsem_cvt.h : Transcript.h Transcripts.h
 
-BamWriter.h : sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
+BamWriter.h : sam_rsem_aux.h sam_rsem_cvt.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
 
 sampling.h : boost/random.hpp
 
 WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h
 
-rsem-run-em : EM.o sam/libbam.a
-	$(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
+rsem-run-em : EM.o
+	$(CC) -o rsem-run-em EM.o /usr/lib/libbam.a -lz -lpthread
 
-EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp
+EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp
 	$(CC) $(COFLAGS) EM.cpp
 
-bc_aux.h : sam/bam.h
-
-BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
+BamConverter.h : utils.h my_assert.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 -lpthread -o $@
+rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp
+	$(CC) -O3 -Wall tbam2gbam.cpp /usr/lib/libbam.a -lz -lpthread -o $@
 
-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 -lpthread -o $@
+rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o bam2wig.cpp
+	$(CC) -O3 -Wall bam2wig.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
 
-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 -lpthread -o $@
+rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o bam2readdepth.cpp
+	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
 
-wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
+wiggle.o: wiggle.cpp wiggle.h
 	$(CC) $(COFLAGS) wiggle.cpp
 
 rsem-simulate-reads : simulation.o
@@ -130,19 +123,17 @@
 calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp
 	$(CC) $(COFLAGS) calcCI.cpp
 
-rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
-	$(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
+rsem-get-unique : getUnique.cpp
+	$(CC) -O3 -Wall getUnique.cpp /usr/lib/libbam.a -lz -lpthread -o $@
 
-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 -lpthread -o $@
+rsem-sam-validator : my_assert.h samValidator.cpp
+	$(CC) -O3 -Wall samValidator.cpp /usr/lib/libbam.a -lz -lpthread -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 -lpthread -o $@
+rsem-scan-for-paired-end-reads : my_assert.h scanForPairedEndReads.cpp
+	$(CC) -O3 -Wall scanForPairedEndReads.cpp /usr/lib/libbam.a -lz -lpthread -o $@
 
 ebseq :
 	cd EBSeq ; ${MAKE} all
 
 clean :
 	rm -f *.o *~ $(PROGRAMS)
-	cd sam ; ${MAKE} clean
-	cd EBSeq ; ${MAKE} clean
