11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/makefile src/makefile
index bb2d162..78c9d0e 100644
--- src/makefile
+++ src/makefile
@@ -7,30 +7,31 @@
 	${MAKE} utils-alpha cgi-alpha blatSuite
 
 beta: check-beta clean cgi-beta
 
 # do a git update and clean
 update:
 	git pull
 	${MAKE} clean
 
 topLibs:
 	@./checkUmask.sh
 	@MACHTYPE=${MACHTYPE} ./machTest.sh
 	cd lib && ${MAKE}
 	cd jkOwnLib && ${MAKE}
 	cd parasol/lib && ${MAKE}
+	cd htslib && ${MAKE}
 
 hgLib:
 	@./hg/sqlEnvTest.sh
 	cd hg/lib && ${MAKE}
 
 libs: topLibs hgLib
 
 cgi: libs
 	cd hg && ${MAKE} cgi
 
 cgi-alpha: libs
 	cd hg && ${MAKE} alpha
 
 cgi-beta: check-beta libs
 	cd hg && ${MAKE} beta
@@ -76,30 +77,31 @@
 destBin:
 	${MKDIR} ${DESTBINDIR}
 
 clean:
 	@for D in ${DIRS} x; do \
             if test "$$D" != "x" ; then \
                 ( cd $$D && echo $$D && ${MAKE} clean ) ;\
                 x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
             fi ;\
 	done
 	cd parasol && ${MAKE} clean
 	cd lib && ${MAKE} clean 
 	cd hg && ${MAKE} clean
 	cd hg && ${MAKE} clean_utils
 	cd jkOwnLib && ${MAKE} clean
+	cd htslib && ${MAKE} clean
 	cd utils && ${MAKE} clean
 	cd webBlat && ${MAKE} clean
 	cd isPcr && ${MAKE} clean
 	touch non-empty-rm.o
 	- find . -name \*.o -print | xargs rm
 	rm -f tags TAGS
 	rm -f cscope.out cscope.files cscope.po.out
 
 testDirs = lib utils blat gfServer hg
 test:: $(testDirs:%=%.test)
 %.test:
 	cd $* && ${MAKE} test
 
 LIB_TAGS_IN = lib/*.[hc] */lib/*.[hc] */*/lib/*.[hc] */*/*/lib/*.[hc] jkOwnLib/*.c \
 	inc/*.h */inc/*.h */*/inc/*.h */*/*/inc/*.h