--- src/utils/htslib/Makefile.orig	2021-01-23 19:33:26 UTC
+++ src/utils/htslib/Makefile
@@ -22,20 +22,23 @@
 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 # DEALINGS IN THE SOFTWARE.
 
-CC     = gcc
-AR     = ar
-RANLIB = ranlib
+# Defaults if not provided by the environment or make args
+CC     ?= gcc
+AR     ?= ar
+RANLIB ?= ranlib
 
 # Default libraries to link if configure is not used
 htslib_default_libs = -lz -lm -lbz2 -llzma
 
-CPPFLAGS =
+# Defaults if not provided by the environment or make args
+CPPFLAGS ?=
+CFLAGS   ?= -g -Wall -O2
+LDFLAGS  ?=
+
 # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
 # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
 #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
-CFLAGS   = -g -Wall -O2
 EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS  =
 LIBS     = $(htslib_default_libs)
 
 prefix      = /usr/local