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/gsid/makefile src/hg/gsid/makefile
index 98d9ce3..055f87f 100644
--- src/hg/gsid/makefile
+++ src/hg/gsid/makefile
@@ -1,40 +1,41 @@
+kentSrc = ../..
 # Build all directories in utils
 
 include ../../inc/common.mk
 
 all::    utils
 
 utils:
 	@for D in $(USE_DIRS) x; do \
             if test "$$D" != "x" ; then \
                 ( cd $$D && echo $$D && $(MAKE) ) ;\
                 x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
             fi ;\
 	done
 
 # List of directories to build
 USE_DIRS = $(DIRS)
 
 clean: 
 	@for D in ${USE_DIRS}; do \
 		(cd $${D} && ${MAKE} clean;) \
 	done
 
 # no makefile for:
 #       pfamXref
 #	spXref2
 
 
 DIRS = \
 	gsidSubj \
 	gsidTable \
         gsIdXref \
         gsidAaMsa \
         gsidGetConsensus \
         gsidMsa \
         gsidMsaToTab \
         gsidPbGateway \
         pbGsid \
 	pwdtest \
 	gsidMember