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/baseMask/makefile src/hg/baseMask/makefile
index 02e5d10..1406683 100644
--- src/hg/baseMask/makefile
+++ src/hg/baseMask/makefile
@@ -1,15 +1,16 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 XINC = -I$(MYSQLINC)
 L += -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 O = cachedMask.o trackToBaseMask.o bedToBaseMask.o baseMaskToBed.o baseMask.o
 B = cachedMask trackToBaseMask bedToBaseMask baseMaskToBed baseMask
 
 all: $B
 
 cachedMask: ${MYLIBS} cachedMaskUsage.msg cachedMask.o 
 	${CC} ${COPT} ${CFLAGS} ${XINC} -o cachedMask cachedMask.o ${MYLIBS} ${MYSQLLIBS} $L