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/liftOver/makefile src/hg/liftOver/makefile
index 83144e2..fbf9c6c 100644
--- src/hg/liftOver/makefile
+++ src/hg/liftOver/makefile
@@ -1,29 +1,30 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 
 L += ${MYSQLLIBS} -lm 
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 A = liftOver
 O = liftOver.o
 
 all: liftOver liftOverMerge
 
 liftOver: $O ${MYLIBS}
 	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} $L
 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
 
 liftOverMerge:  liftOverMerge.o ${MYLIBS}
 	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/liftOverMerge liftOverMerge.o ${MYLIBS} $L
 	${STRIP} ${DESTDIR}${BINDIR}/liftOverMerge${EXE}
 
 compile:: ${O} liftOverMerge.o
 	${CC} ${COPT} ${CFLAGS} -o ${A} $O ${MYLIBS} $L
 	${CC} ${COPT} ${CFLAGS} -o liftOverMerge liftOverMerge.o ${MYLIBS} $L
 
 clean::
 	rm -f ${A} ${O} liftOverMerge liftOverMerge.o
 
 test::
 	cd tests && ${MAKE} test