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/utils/qa/makefile src/utils/qa/makefile
index 7a825a0..bb200ca 100644
--- src/utils/qa/makefile
+++ src/utils/qa/makefile
@@ -1,15 +1,16 @@
+kentSrc = ../..
 include ../../inc/common.mk
 # ${SCRIPTS} is ${HOME}/bin/scripts (defined in kent/src/inc/common.mk)
 # to install in /cluster/bin/scripts/, run (in this directory):
 # make SCRIPTS=/cluster/bin/scripts
 
 install:
 	@echo Reminder: is your sandbox up to date?
 	cp -p --remove-destination 2bitCompare             ${SCRIPTS}
 	cp -p --remove-destination activeGenbank.csh       ${SCRIPTS}
 	cp -p --remove-destination alertBqueue.csh         ${SCRIPTS}
 	cp -p --remove-destination allowTraffic.csh        ${SCRIPTS}
 	cp -p --remove-destination backupCentral.csh       ${SCRIPTS}
 	cp -p --remove-destination bamToBedGraph.csh       ${SCRIPTS}
 	cp -p --remove-destination bamToBigWig.csh         ${SCRIPTS}
 	cp -p --remove-destination bigPush.sh              ${SCRIPTS}