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/xenoAli/waba/makefile src/xenoAli/waba/makefile
index ddb6a29..b6bb1b5 100644
--- src/xenoAli/waba/makefile
+++ src/xenoAli/waba/makefile
@@ -1,11 +1,12 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 
 O = waba.o wabaCrude.o
 
 waba: $(O)
 	${CC} ${COPT} ${CFLAGS} $O ../../lib/$(MACHTYPE)/jkOwnLib.a ../../lib/$(MACHTYPE)/jkweb.a ${L} -lm
 	mv ${AOUT} ${BINDIR}/waba
 
 clean::
 	rm -f ${O}