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/utils/nibCheck/makefile src/utils/nibCheck/makefile
index 897ff87..7a7fe76 100644
--- src/utils/nibCheck/makefile
+++ src/utils/nibCheck/makefile
@@ -1,17 +1,18 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 
 L += -lm
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkweb.a
 
 O = nibCheck.o
 
 nibCheck: $O $(MYLIBS)
 	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibCheck $O $(MYLIBS) $L
 	${CC} ${COPT} ${CFLAGS} $O $(MYLIBS) ${L} -lm
 	mv ${AOUT} nibCheck
 	chmod a+rx nibCheck
 
 clean::
 	rm -f ${O}