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/cbAli/makefile src/cbAli/makefile
index 4a97332..09ec5ed 100644
--- src/cbAli/makefile
+++ src/cbAli/makefile
@@ -1,12 +1,13 @@
+kentSrc = ..
 include ../inc/common.mk
 
 O = cbAli.o 
 
 cbAli.exe: $(O)
 	${CC} ${COPT} ${CFLAGS} $O ../lib/$(MACHTYPE)/jkweb.a ${L} -lm
 	mv ${AOUT} cbAli.exe
 	chmod a+rx cbAli.exe
 	mv cbAli.exe ../cgi-bin
 
 clean::
 	rm -f ${O} cbAli.exe