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/nci60/makefile src/hg/nci60/makefile
index cce974d..89340f4 100644
--- src/hg/nci60/makefile
+++ src/hg/nci60/makefile
@@ -1,19 +1,20 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lm $(MYSQLLIBS)
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a $(L)
 
 O = findStanAlignments  stanToBedAndExpRecs
 
 %: %.c 
 	${CC} ${COPT} ${CFLAGS}  -Wimplicit  -I../inc -I../../inc  -o ${DESTDIR}${BINDIR}/$@ $(addsuffix .c,$@) $(MYLIBS) ${L}
 	${STRIP} ${DESTDIR}${BINDIR}/$@
 
 all: $(O)
 
 #$(O): %: %.c ../lib/$(ARCHTYPE)/libsugnet.a 
 #	${CC} ${COPT} ${CFLAGS} -Wimplicit  -I../inc -I$(KENT_DIR)/inc -I$(KENT_DIR)/hg/inc -o $@ $(addsuffix .c,$@)  $(SUGNET_LIBS) $(KENT_LIBS)
 
 clean::
 	rm -fr ${O} ${ARCHTYPE}