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/txCds/makefile src/hg/txCds/makefile
index 7f83a7d..17067a2 100644
--- src/hg/txCds/makefile
+++ src/hg/txCds/makefile
@@ -1,41 +1,42 @@
+kentSrc = ../..
 # Build txGraph source
 include ../../inc/common.mk
 
 # List of directories to build
 DIRS = \
     txCdsBadBed \
     txCdsCluster \
     txCdsEvFromBed \
     txCdsEvFromBorf \
     txCdsEvFromProtein \
     txCdsEvFromRna \
     txCdsGoodBed \
     txCdsOrfInfo \
     txCdsOrtho \
     txCdsPick \
     txCdsPredict \
     txCdsRaExceptions \
     txCdsRefBestEvOnly \
     txCdsRepick \
     txCdsSuspect \
     txCdsSvmInput \
     txCdsToGene \
     txCdsWeed \
     txInfoAssemble
 
 USE_DIRS = $(DIRS)
 
 all: $(USE_DIRS:%=%.all)
 
 %.all:
 	( cd $* && echo $* && $(MAKE) )
 
 clean:: $(USE_DIRS:%=%.clean)
 
 %.clean::
 	( cd $* && echo $* && $(MAKE) clean )
 
 compile:: $(USE_DIRS:%=%.compile)
 
 %.compile::
 	( cd $* && echo $* && $(MAKE) compile )