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/txGene/makefile src/hg/txGene/makefile
index 064dc49..5b90f39 100644
--- src/hg/txGene/makefile
+++ src/hg/txGene/makefile
@@ -1,44 +1,45 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkweb.a
 
 all:
 	@for D in ${DIRS} x; do \
 	  if test "$$D" != "x" ; then \
 	    ( cd $$D && echo $$D && ${MAKE}  ) ;\
 	    x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
 	    fi ;\
 	done
 
 DIRS = \
 	txGenbankData \
 	txGeneAccession \
 	txGeneAlias \
 	txGeneAltProt \
 	txGeneCanonical \
 	txGeneCdsMap \
 	txGeneColor \
 	txGeneExplainUpdate1 \
 	txGeneFromBed \
 	txGeneProtAndRna \
 	txGeneSeparateNoncoding \
 	txGeneValidation \
 	txGeneXref
 
 clean::
 	@for D in ${DIRS} x; do \
 	  if test "$$D" != "x" ; then \
 	    ( cd $$D && echo $$D && ${MAKE} clean ) ;\
 	    x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
 	    fi ;\
 	done
 
 compile:
 	@for D in ${DIRS} x; do \
 	  if test "$$D" != "x" ; then \
 	    ( cd $$D && echo $$D && ${MAKE} compile ) ;\
 	    x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
 	    fi ;\
 	done