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/gitTools/makefile src/utils/gitTools/makefile
index 95d9963..32e9b44 100644
--- src/utils/gitTools/makefile
+++ src/utils/gitTools/makefile
@@ -1,22 +1,23 @@
+kentSrc = ../..
 include ../../inc/common.mk
 GITTOOLS= 
 GITSCRIPTS= gitFiles gilt gitu
 
 all: ${GITTOOLS:%=${BINDIR}/%} ${GITSCRIPTS:%=${SCRIPTS}/%}
 
 ${BINDIR}/%: %
 	@${MKDIR} ${BINDIR}
 	chmod a+rx $<
 	rm -f $@
 	cp -pf $< $@
 
 scripts: ${GITSCRIPTS:%=${SCRIPTS}/%}
 
 ${SCRIPTS}/%: %
 	@${MKDIR} ${SCRIPTS}
 	chmod a+rx $<
 	rm -f $@
 	cp -pf $< $@
 
 clean::
 	@echo nothing to clean in src/utils/gitTools/