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/htdocs/makefile src/hg/htdocs/makefile
index 2527f41..d867dcb 100644
--- src/hg/htdocs/makefile
+++ src/hg/htdocs/makefile
@@ -1,51 +1,52 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 GIT = git
 GITUP = ${GIT} pull
 FIND=gitFiles
 
 # if you need to pick up files not checked-in yet for rsync,
 # you can run it like this:
 #
 #   make FIND=find
 #
 # but be careful as it will rsync everything over including junk
 
 # REMEMBER: HTDOCSEXTRA 
 # htdocsExtra is a repository that contains large files that we
 # do not wish to burden the main kent repo with.
 # You can check it out and make there too.
 # If you think there is a file missing, see if it is under the htdocsExtra repo.
 
 ifeq (${DOCUMENTROOT_USER},)
     DOCUMENTROOT_USER=${DOCUMENTROOT}-${USER}
 endif
 
 user:
 	if test -d ${DOCUMENTROOT_USER}; then \
 	    ${MAKE} doInstall destDir=${DOCUMENTROOT_USER} ; \
 	fi
 
 alpha:
 	${MAKE} doInstall destDir=${DOCUMENTROOT} 
 
 beta:
 	${GITUP}
 	${MAKE} doInstall destDir=qateam@hgwbeta:${DOCUMENTROOT} 
 	${MAKE} doInstall destDir=${DOCUMENTROOT}-beta
 
 # Run rsync.  Care is taking to preserve times and mode on files.  rsync is
 # smart about recreating file under the current users so that times and
 # permissions maybe modified.  However, problems happen when a directory
 # is not owned by the current users.  These options attemp to work around it.
 # use care in changing
 rsyncOpts = --times --recursive --omit-dir-times --relative --cvs-exclude --exclude='makefile' --exclude='cpAndLinkToResourceFiles.pl' --exclude='style/*'
 doInstall:
 	umask 002; rsync ${rsyncOpts} ${excl} ${incl} `$(FIND)` ${destDir}
 
 # Other targets that may be invoked by ../makefile:
 compile:
 
 install: alpha
 
 clean: