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/oneShot/newStitch/makefile src/oneShot/newStitch/makefile
index 0d1f873..ab411a2 100644
--- src/oneShot/newStitch/makefile
+++ src/oneShot/newStitch/makefile
@@ -1,15 +1,16 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 
 L += -lm
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a
 
 O = newStitch.o
 
 newStitch: $O $(MYLIBS)
 	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/newStitch $O $(MYLIBS) $L
 #	${STRIP} ${BINDIR}/newStitch${EXE}
 
 clean::
 	rm -f ${O}