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--- 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
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