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/sage/makefile src/hg/sage/makefile
index 3dc669d..3f588a7 100644
--- src/hg/sage/makefile
+++ src/hg/sage/makefile
@@ -1,21 +1,22 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lm ${MYSQLLIBS}
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 A1 = addAveMedScoreToPsls
 A2 = createSageSummary
 
 all::	compile
 	rm -f ${DESTDIR}${BINDIR}/${A1}${EXE}
 	mv ${A1}${EXE} ${DESTDIR}${BINDIR}/
 	rm -f ${DESTDIR}${BINDIR}/${A2}${EXE}
 	mv ${A2}${EXE} ${DESTDIR}${BINDIR}/
 
 compile:: ${A1}.o ${A2}.o
 	${CC} ${COPT} ${CFLAGS} -o ${A1}${EXE} ${A1}.o ${MYLIBS} ${L}
 	${CC} ${COPT} ${CFLAGS} -o ${A2}${EXE} ${A2}.o ${MYLIBS} ${L}
 
 clean::
 	rm -f ${A1}.o ${A2}.o ${A1} ${A2}