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/hgBatch/makefile src/hg/hgBatch/makefile
index d65c23a..1b0ff76 100644
--- src/hg/hgBatch/makefile
+++ src/hg/hgBatch/makefile
@@ -1,41 +1,42 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 
 L += $(MYSQLLIBS) -lm
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a
 
 O = hgBatch.o
 
 A = hgBatch
 
 my: compile
 	mv $A ${CGI_BIN}-${USER}/$A
 
 alpha: compile
 	mv $A ${CGI_BIN}/$A
 
 beta: compile
 	mv $A ${CGI_BIN}-beta/$A
 
 
 compile: $O $(MYLIBS)
 	${CC} ${COPT} ${CFLAGS} -o $A $O $(MYLIBS) $L
 	${STRIP} $A${EXE}
 	chmod a+rx $A
 
 install:	compile
 	@if [ ! -d "${DESTDIR}${CGI_BIN}" ]; then \
 		${MKDIR} "${DESTDIR}${CGI_BIN}"; \
 	fi
 	mv $A ${DESTDIR}${CGI_BIN}/$A
 
 lib:
 	cd ../lib && ${MAKE}
 	cd ../../lib && ${MAKE}
 
 tags: 
 	ctags *.h *.c ../lib/*.c ../inc/*.h ../../lib/*.c ../../inc/*.h
 
 clean::
 	rm -f ${O}