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/affyGnf/makefile src/hg/affyGnf/makefile
index 4d13d49..84c8f1a 100644
--- src/hg/affyGnf/makefile
+++ src/hg/affyGnf/makefile
@@ -1,15 +1,16 @@
+kentSrc = ../..
 
 include ../../inc/common.mk
 
 L += $(MYSQLLIBS) -lm 
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a
 
 % : %.c
 	$(CC) $(COPT) -I../inc  -I../../inc  -o $@ $(addsuffix .c,$@) $(MYLIBS) ${L} $(MYSQLLIBS) -lm -lz
 	cp $@ ${BINDIR}
 
 O = affyUclaMergePslData affyPslAndAtlasToBed pslAffySelect
 
 
 exe: $(O)