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/hg/secure/makefile src/hg/secure/makefile
index dda3a24..98594b2 100644
--- src/hg/secure/makefile
+++ src/hg/secure/makefile
@@ -1,41 +1,42 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 
 L += $(MYSQLLIBS) -lm 
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a
 
 A = secure
 
 O = $A.o
 
 my: compile
 	mv $A /usr/local/apache/cgi-bin-$(USER)/$A
 
 alpha: compile
 	mv $A /usr/local/apache/cgi-bin/$A
 
 beta: compile
 	mv $A /usr/local/apache/cgi-bin-beta/$A
 
 mgsc: compile
 	mv $A /usr/local/apache/cgi-bin-mgsc/$A
 
 compile: $O 
 	${CC} ${COPT} ${CFLAGS} $O $(MYLIBS) $(L) 
 	mv ${AOUT} $A${EXE}
 	${STRIP} $A${EXE}
 	chmod a+rx $A
 
 debug: $O
 	${CC} ${COPT} ${CFLAGS} $O $(MYLIBS) $(L) 
 	mv ${AOUT} $A${EXE}
 
 lib:
 	cd ../../lib && ${MAKE}
 
 tags:  
 	ctags *.h *.c ../lib/*.c ../inc/*.h ../../lib/*.c ../../inc/*.h
 
 clean::
 	rm -f ${O}