012294051c7f9ded1f8392899feebbebd26ead5c
markd
  Fri Apr 24 22:03:38 2026 -0700
makefile will initialize htslib submodule if needed

diff --git src/makefile src/makefile
index b5d253dcf6b..f04dec2c039 100644
--- src/makefile
+++ src/makefile
@@ -15,30 +15,33 @@
 	${MAKE} clean
 ##
 # topLibs
 ##
 TOP_LIBS = lib parasol/lib htslib
 ifneq ($(wildcard jkOwnLib/*),)
   TOP_LIBS += jkOwnLib
 endif
 topLibs: topChecks | ${TOP_LIBS:%=%.topLibs}
 %.topLibs:
 	${MAKE} -C $*
 
 topChecks:
 	@./checkUmask.sh
 	@MACHTYPE=${MACHTYPE} ./machTest.sh
+	@if [ ! -e htslib/.git ] ; then \
+	    set -x; git -c protocol.file.allow=always submodule update --init --recursive ; \
+	fi
 
 optLib:
 	cd optimalLeaf && ${MAKE}
 
 ##
 # hgLib
 ##
 ifneq ($(wildcard hg/makefile),)
    HGLIB_DIRS += hg/lib
    HGLIB_CHECK = hgLibChecks
 endif
 ifneq ($(wildcard hg/cgilib/makefile),)
    HGLIB_DIRS += hg/cgilib
 endif