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/cbAli/makefile src/xenoAli/cbAli/makefile
index 9fd7d31..611d6d4 100644
--- src/xenoAli/cbAli/makefile
+++ src/xenoAli/cbAli/makefile
@@ -1,11 +1,12 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 
 O = cbAli.o 
 
 cbAli: $(O)
 	${CC} ${COPT} ${CFLAGS} $O ../../lib/$(MACHTYPE)/jkOwnLib.a ../../lib/$(MACHTYPE)/jkweb.a ${L}
 	mv ${AOUT} ${BINDIR}/cbAli
 
 clean::
 	rm -f ${O}