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/blat/makefile src/blat/makefile
index be9a2da..d42f2c2 100644
--- src/blat/makefile
+++ src/blat/makefile
@@ -1,34 +1,35 @@
+kentSrc = ..
 include ../inc/common.mk
 
 L += -lm $(SOCKETLIB)
 MYLIBDIR = ../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkOwnLib.a $(MYLIBDIR)/jkweb.a 
 
 O = blat.o
 
 blat: $O $(MYLIBS)
 	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/blat $O $(MYLIBS) $L
 	${STRIP} ${DESTDIR}${BINDIR}/blat${EXE}
 
 all:
 	cd ../lib && ${MAKE}
 	make
 tags:
 	ctags *.c *.h ../lib/*.c ../inc/*.h
 
 test::
 	blat -verbose=0 hCrea.geno hCrea.mrna testRna.psl
 	cmp testRna.psl refRna.psl
 	blat -verbose=0 -prot hCrea.pep mCrea.pep testProt.psl
 	cmp testProt.psl refProt.psl
 	blat -verbose=0 -t=dnax -q=prot hCrea.geno mCrea.pep testProtX.psl
 	cmp testProtX.psl refProtX.psl
 	blat -verbose=0 -t=dnax -q=rnax hCrea.geno mCrea.mrna testRnaX.psl
 	cmp testRnaX.psl refRnaX.psl
 	blat -verbose=0 -fine hCrea.geno hCrea.mrna testFine.psl
 	cmp testFine.psl refFine.psl
 	cd test && ${MAKE}
 
 clean::
 	rm -f testRna.psl testProt.psl testProtX.psl testRnaX.psl \
 	testFine.psl $(O) blat