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/blastToPsl/makefile src/hg/blastToPsl/makefile
index 4b3a70e..b356678 100644
--- src/hg/blastToPsl/makefile
+++ src/hg/blastToPsl/makefile
@@ -1,36 +1,37 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += $(MYSQLLIBS) -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  $(MYLIBDIR)/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 blastToPsl_objs = blastToPsl.o pslBuild.o
 blastXmlToPsl_objs = blastXmlToPsl.o ncbiBlast.o pslBuild.o
 
 all: blastToPsl blastXmlToPsl
 
 blastXmlToPsl: ${blastXmlToPsl_objs} ${MYLIBS}
 	${CC} ${COPT} -o ${DESTDIR}${BINDIR}/blastXmlToPsl${EXE} ${blastXmlToPsl_objs} ${MYLIBS} $L
 	${STRIP} ${DESTDIR}${BINDIR}/blastXmlToPsl${EXE}
 
 blastToPsl: ${blastToPsl_objs} ${MYLIBS}
 	${CC} ${COPT} -o ${DESTDIR}${BINDIR}/blastToPsl${EXE} ${blastToPsl_objs} ${MYLIBS} $L
 	${STRIP} ${DESTDIR}${BINDIR}/blastToPsl${EXE}
 
 compile: ${blastXmlToPsl_objs} ${blastToPsl_objs}
 	${CC} ${COPT} -o blastXmlToPsl${EXE} ${blastXmlToPsl_objs} ${MYLIBS} $L
 	${CC} ${COPT} -o blastToPsl${EXE} ${blastToPsl_objs} ${MYLIBS} $L
 
 test:: compile
 	cd tests && ${MAKE} test
 	rm -fr tests/output blastXmlToPsl${EXE} blastToPsl${EXE}
 
 clean::
 	rm -fr tests/output
 	rm -f ${blastToPsl_objs} ${blastXmlToPsl_objs}
 	rm -f blastXmlToPsl${EXE} blastToPsl${EXE}
 
 ncbiBlast.o: ncbiBlast.c ncbiBlast.h
 pslBuild.o: pslBuild.c pslBuild.h
 blastXmlToPsl.o: blastXmlToPsl.c ncbiBlast.h pslBuild.h
 blastToPsl.o: blastToPsl.c pslBuild.h