--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin	2017-04-28 21:53:55.811777276 +0200
@@ -28,7 +28,7 @@
 LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
 LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
 STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++
-BLDFLAGS             = -O3 ${STDFLAGS}
+BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}
 
 
 FLAGS                = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/bedextract/src/Makefile	2017-04-28 21:54:05.952048644 +0200
@@ -24,7 +24,7 @@
 INCLUDES                = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
 LIBLOCATION             = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
 LIBRARIES               = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
-BLDFLAGS                = -Wall -pedantic -O3 -std=c++11
+BLDFLAGS                = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
 SFLAGS                  = -static
 
 dependency_names        = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
@@ -64,4 +64,4 @@
 	rm -rf $(OBJDIR)
 	rm -f $(BINDIR)/$(PROG)
 	rm -f $(BINDIR)/*.$(PROG)
-	rm -rf $(BINDIR)
\ No newline at end of file
+	rm -rf $(BINDIR)
--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin	2017-04-28 21:54:12.162214836 +0200
@@ -28,7 +28,7 @@
 LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
 LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
 STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++
-BLDFLAGS             = -O3 ${STDFLAGS}
+BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}
 
 FLAGS                = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
 
--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/bedmap/src/Makefile	2017-04-28 21:54:19.472410465 +0200
@@ -23,7 +23,7 @@
 INCLUDES            = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
 LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
 LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
-BLDFLAGS            = -Wall -pedantic -O3 -std=c++11 
+BLDFLAGS            = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11 
 SFLAGS              = -static
 
 dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
--- bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin	2017-04-28 21:54:25.422569698 +0200
@@ -1,7 +1,7 @@
 MIN_OSX_VERSION           = 10.7
 BLDFLAGS                  = -Wall -Wextra -pedantic -std=c99
 COMMONFLAGS               = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
-CFLAGS                    = -O3
+CFLAGS                    = ${CXXFLAGS:--O3}
 CDFLAGS                   = -DDEBUG=1 -g -O0 -fno-inline
 CPFLAGS                   = -pg
 LIBS                      = -lpthread
--- bedops-2.4.26/applications/bed/conversion/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/conversion/src/Makefile	2017-04-28 21:54:30.832714482 +0200
@@ -1,6 +1,6 @@
 BLDFLAGS                  = -Wall -Wextra -pedantic -std=c99
 COMMONFLAGS               = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
-CFLAGS                    = -O3
+CFLAGS                    = ${CXXFLAGS:--O3}
 CDFLAGS                   = -DDEBUG=1 -g -O0 -fno-inline
 CPFLAGS                   = -pg
 LIBS                      = -lpthread
--- bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin	2017-04-28 21:54:37.312887898 +0200
@@ -27,7 +27,7 @@
 LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
 LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
 STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++
-BLDFLAGS             = -O3 ${STDFLAGS}
+BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}
 
 FLAGS                = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
 
--- bedops-2.4.26/applications/bed/bedops/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/bedops/src/Makefile	2017-04-28 21:54:43.513053823 +0200
@@ -25,7 +25,7 @@
 INCLUDES            = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
 LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
 LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
-BLDFLAGS            = -Wall -pedantic -O3 -std=c++11
+BLDFLAGS            = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
 SFLAGS              = -static
 
 dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin	2017-04-28 21:54:49.093203153 +0200
@@ -28,7 +28,7 @@
 LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
 LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
 STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++
-BLDFLAGS             = -O3 ${STDFLAGS}
+BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}
 
 FLAGS                = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
 
--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile	2017-04-28 21:54:54.283342049 +0200
@@ -23,7 +23,7 @@
 INCLUDES            = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
 LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
 LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
-BLDFLAGS            = -Wall -pedantic -O3 -std=c++11
+BLDFLAGS            = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
 SFLAGS              = -static
 
 dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin	2017-04-28 21:55:00.023495662 +0200
@@ -7,7 +7,7 @@
 PROG                 = sort-bed
 DIST_DIR             = ../bin
 OBJ_DIR              = objects_${ARCH}
-OPTIMIZE             = -O3 -std=c++11 -stdlib=libc++
+OPTIMIZE             = ${CXXFLAGS:--O3} -std=c++11 -stdlib=libc++
 WARNINGS             = -Wall
 MAIN                 = ../../../..
 HEAD                 = ${MAIN}/interfaces/general-headers
--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
+++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile	2017-04-28 21:55:05.663646597 +0200
@@ -29,7 +29,7 @@
 BINDIR              = ../bin
 OBJDIR             = objects
 WARNINGS            = -Wall -Wextra -pedantic
-BLDFLAGS            = ${WARNINGS} -O3 -std=c++11
+BLDFLAGS            = ${WARNINGS} ${CXXFLAGS:--O3} -std=c++11
 SFLAGS              = -static
 
 dependency_names    = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort