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/agpMergeChromScaf/makefile src/hg/agpMergeChromScaf/makefile
index e6dd236..8617122 100644
--- src/hg/agpMergeChromScaf/makefile
+++ src/hg/agpMergeChromScaf/makefile
@@ -1,15 +1,16 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 A = agpMergeChromScaf
 O = ${A}.o
 
 agpToFa: $O ${MYLIBS}
 	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/${A} \
 		$O ${MYLIBS} $L
 	${STRIP} ${BINDIR}/${A}${EXE}
 
 compile: ${O} ${MYLIBS}