X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=c95fd14467cb0263ac6122d321cd7af4f8e0b9bb;hb=f205fc0144198dee52c71d0d5d6267d9e8880fff;hp=44d73696f1ddf63c1b09732ef84b052909ff539b;hpb=fb2aa1ca9d00710943155ef3abbbdd87df116e4a;p=rsem.git

diff --git a/makefile b/makefile
index 44d7369..c95fd14 100644
--- 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
-
+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)
 
@@ -51,10 +50,10 @@ SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h
 
 
 rsem-parse-alignments : parseIt.o sam/libbam.a
-	$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz 
+	$(CC) -o rsem-parse-alignments parseIt.o sam/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
-	$(CC) $(COFLAGS) parseIt.cpp
+	$(CC) -Wall -O2 -c -I. parseIt.cpp
 
 
 rsem-build-read-index : utils.h buildReadIndex.cpp
@@ -94,13 +93,13 @@ 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
 
 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 $@
+	$(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
 
-rsem-bam2wig : wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
-	$(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -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-bam2readdepth : wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
-	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -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 $@
 
 wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
 	$(CC) $(COFLAGS) wiggle.cpp
@@ -128,12 +127,20 @@ calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h
 	$(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 -o $@
+	$(CC) -O3 -Wall getUnique.cpp sam/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 -o $@
-	
-clean:
+	$(CC) -O3 -Wall samValidator.cpp sam/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 $@
+
+.PHONY: ebseq
+
+ebseq :
+	cd EBSeq ; ${MAKE} all
+
+clean :
 	rm -f *.o *~ $(PROGRAMS)
 	cd sam ; ${MAKE} clean
-
+	cd EBSeq ; ${MAKE} clean