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/oneShot/checkLayout/makefile src/oneShot/checkLayout/makefile
index 326552a..24dc495 100644
--- src/oneShot/checkLayout/makefile
+++ src/oneShot/checkLayout/makefile
@@ -1,11 +1,12 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 
 O = checkLayout.o 
 
 checkLayout: $(O)
 	${CC} ${COPT} ${CFLAGS} -o ../../cgi-bin/checkLayout $O ../../lib/$(MACHTYPE)/jkweb.a ${L}
 	${STRIP} ../../cgi-bin/checkLayout${EXE}
 
 clean::
 	rm -f ${O}