Description: pass CXXFLAGS to compiler
Author: Michael R. Crusoe <crusoe@ucdavis.edu>
--- a/Makefile
+++ b/Makefile
@@ -12,10 +12,10 @@
 Transcripts.h : utils.h my_assert.h Transcript.h
 
 rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
-	$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
+	$(CC) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
 
 rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
-	$(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
+	$(CC) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
 
 BowtieRefSeqPolicy.h : RefSeqPolicy.h
 
@@ -25,10 +25,10 @@
 
 
 rsem-preref : preRef.o
-	$(CC) preRef.o -o rsem-preref
+	$(CC) $(CPPFLAGS) $(LDFLAGS) preRef.o -o rsem-preref
 
 preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
-	$(CC) $(COFLAGS) preRef.cpp
+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(COFLAGS) preRef.cpp
 
 
 SingleRead.h : Read.h
@@ -49,14 +49,14 @@
 
 
 rsem-parse-alignments : parseIt.o
-	$(CC) -o rsem-parse-alignments parseIt.o /usr/lib/libbam.a -lz -lpthread 
+	$(CC) $(LDFLAGS) -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 parseIt.cpp
-	$(CC) -Wall -O2 -c -I. parseIt.cpp
+	$(CC) $(CPPFLAGS) $(CXXFLAGS) -Wall -O2 -c -I. parseIt.cpp
 
 
 rsem-build-read-index : utils.h buildReadIndex.cpp
-	$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
 
 
 ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
@@ -78,55 +78,55 @@
 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
-	$(CC) -o rsem-run-em EM.o /usr/lib/libbam.a -lz -lpthread
+	$(CC) $(LDFLAGS) -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 simul.h sam_rsem_aux.h sampling.h WriteResults.h EM.cpp
-	$(CC) $(COFLAGS) EM.cpp
+	$(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) EM.cpp
 
 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_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp
-	$(CC) -O3 -Wall tbam2gbam.cpp /usr/lib/libbam.a -lz -lpthread -o $@
+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall tbam2gbam.cpp /usr/lib/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 $@
+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall bam2wig.cpp wiggle.o /usr/lib/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 $@
+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall bam2readdepth.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
 
 wiggle.o: wiggle.cpp wiggle.h
-	$(CC) $(COFLAGS) wiggle.cpp
+	$(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) wiggle.cpp
 
 rsem-simulate-reads : simulation.o
-	$(CC) -o rsem-simulate-reads simulation.o
+	$(CC) $(CPPFLAGS) $(LDFLAGS) -o rsem-simulate-reads simulation.o
 
 simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h WriteResults.h simulation.cpp
-	$(CC) $(COFLAGS) simulation.cpp
+	$(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) simulation.cpp
 
 rsem-run-gibbs : Gibbs.o
-	$(CC) -o rsem-run-gibbs Gibbs.o -lpthread
+	$(CC) $(CPPFLAGS) $(LDFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
 
 #some header files are omitted
 Gibbs.o : utils.h my_assert.h sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp 
-	$(CC) $(COFLAGS) Gibbs.cpp
+	$(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) Gibbs.cpp
 
 Buffer.h : my_assert.h
 
 rsem-calculate-credibility-intervals : calcCI.o
-	$(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
+	$(CC) $(CPPFLAGS) $(LDFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
 
 #some header files are omitted
 calcCI.o : utils.h my_assert.h 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
+	$(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) calcCI.cpp
 
 rsem-get-unique : getUnique.cpp
-	$(CC) -O3 -Wall getUnique.cpp /usr/lib/libbam.a -lz -lpthread -o $@
+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall getUnique.cpp /usr/lib/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 $@
+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall samValidator.cpp /usr/lib/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 $@
+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall scanForPairedEndReads.cpp /usr/lib/libbam.a -lz -lpthread -o $@
 
 ebseq :
 	cd EBSeq ; ${MAKE} all
