X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=e2711b532be12b82ff45a01d845597c0ed8d0ff8;hb=9210a5fece7ec2854eb834d5b2dcbe2d12fbebf1;hp=a6d863c7b6616901a058418c56fa60c9828d1cc7;hpb=97554bbac838f2ed578d81f98e421dac0669e74e;p=rsem.git

diff --git a/makefile b/makefile
index a6d863c..e2711b5 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
+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)
@@ -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
@@ -65,13 +65,13 @@ simul.h : boost/random.hpp
 
 ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
 
-SingleModel.h : utils.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h
+SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h
 
-SingleQModel.h : utils.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h
+SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h
 
-PairedEndModel.h : utils.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h 
+PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h 
 
-PairedEndQModel.h : utils.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h
+PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h
 
 HitWrapper.h : HitContainer.h
 
@@ -130,6 +130,12 @@ calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h
 rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
 	$(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -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 $@
+
+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 $@
+
 clean:
 	rm -f *.o *~ $(PROGRAMS)
 	cd sam ; ${MAKE} clean