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/bedOverlap/makefile src/hg/bedOverlap/makefile
index f185105..d3fb4e1 100644
--- src/hg/bedOverlap/makefile
+++ src/hg/bedOverlap/makefile
@@ -1,27 +1,28 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 
 L += -lm $(MYSQLLIBS)
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a
 
 O = bedOverlap.o
 
 bedOverlap: $O $(MYLIBS)
 	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/bedOverlap $O $(MYLIBS) $L
 	${STRIP} ${BINDIR}/bedOverlap${EXE}
 
 test:	test2 test4 test5
 %:	input/%.bed
 	${MKDIR} output
 	bedOverlap -hasBin -verbose=1 input/$@.bed output/$@.bed  
 	diff expected/$@.bed output/$@.bed 
 	rm output/$@.bed
 %:	input/%.noBin
 	${MKDIR} output
 	bedOverlap input/$@.noBin output/$@.bed 
 	diff expected/$@.bed output/$@.bed 
 	rm output/$@.bed
 
 clean::
 	rm -fr ${O} output