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/kehayden/alphaChain/makefile src/kehayden/alphaChain/makefile
index 9e99cbe..6c3993f 100644
--- src/kehayden/alphaChain/makefile
+++ src/kehayden/alphaChain/makefile
@@ -1,15 +1,16 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkweb.a
 
 A = alphaChain
 O = alphaChain.o
 
 alphaChain: ${O} ${MYLIBS}
 	${CC} ${COPT} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} $L
 #       ${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
 
 compile:: ${O}
 	${CC} ${COPT} -o ${A}${EXE} ${O} ${MYLIBS} $L