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/blatz/makefile src/blatz/makefile
index f45fe4d..fb337d9 100644
--- src/blatz/makefile
+++ src/blatz/makefile
@@ -1,33 +1,34 @@
+kentSrc = ..
 include ../inc/common.mk
 
 L += -lm $(SOCKETLIB)
 MYLIBDIR = ../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkOwnLib.a ${MYLIBDIR}/jkweb.a
 
 O = align.o bzp.o gapless.o index.o output.o
 
 all: blatz blatzClient blatzServer 
 	echo made
 
 blatz: standalone.o $O ${MYLIBS}
 	${CC} ${COPT} -o ${DESTDIR}${BINDIR}/blatz standalone.o $O ${MYLIBS} $L
 #	${STRIP} ${DESTDIR}${BINDIR}/blatz${EXE}
 
 blatzServer: server.o $O ${MYLIBS}
 	${CC} ${COPT} -o ${DESTDIR}${BINDIR}/blatzServer server.o $O ${MYLIBS} $L
 	${STRIP} ${DESTDIR}${BINDIR}/blatzServer${EXE}
 
 blatzClient: client.o bzp.o ${MYLIBS}
 	${CC} ${COPT} -o ${DESTDIR}${BINDIR}/blatzClient client.o bzp.o ${MYLIBS} $L
 	${STRIP} ${DESTDIR}${BINDIR}/blatzClient${EXE}
 
 clean:
 	rm -f $O standalone.o server.o client.o
 
 test:	doTest
 
 doTest:
 	blatz test/clock/human.fa test/clock/mouse.fa test/clock/test.chain
 	diff test/clock/expected.chain test/clock/test.chain
 	blatz test/100k/human.fa test/100k/mouse.fa test/100k/test.chain
 	diff test/100k/expected.chain test/100k/test.chain