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/geneBounds/makefile src/hg/geneBounds/makefile
index 4ff731b..69c6036 100644
--- src/hg/geneBounds/makefile
+++ src/hg/geneBounds/makefile
@@ -1,56 +1,57 @@
+kentSrc = ../..
 include ../../inc/common.mk
 # Build all directories in makeDb 
 
 # List of directories to build
 USE_DIRS = $(DIRS)
 
 DIRS = \
 	assessLibs \
 	averagExp \
 	axtForEst \
 	bedCons \
 	checkableBorf \
 	clusterGenes \
 	clusterPsl \
 	clusterRna \
 	dnaMotifFind \
 	eisenInput \
 	emblMatrixToMotif \
 	estLibStats \
 	expToRna \
 	iriToControlTable \
 	iriToDnaMotif \
 	lib \
 	liftPromoHits \
 	motifLogo \
 	motifSig \
 	orf \
 	orfStats \
 	polyInfo \
 	promoSeqFromCluster \
 	raToCds \
 	twinOrf \
 	twinOrf2 \
 	twinOrf3 \
 	twinOrfStats \
 	twinOrfStats2 \
 	twinOrfStats3 
 
 
 all: $(USE_DIRS:%=%.all)
 
 lib.all:
 	cd lib && $(MAKE)
 
 # make sure lib is built first, even in a parallel make
 
 %.all: lib.all
 	cd $* && echo $* && $(MAKE)
 
 test::
 	cd clusterGenes && ${MAKE} test
 
 clean:: $(USE_DIRS:%=%.clean)
 
 %.clean::
 	cd $* && echo $* && $(MAKE) clean