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/hgBlatTest/makefile src/hg/hgBlatTest/makefile
index e736e8e..ca4f2e0 100644
--- src/hg/hgBlatTest/makefile
+++ src/hg/hgBlatTest/makefile
@@ -1,32 +1,33 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += ${MYSQLLIBS} -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 O = hgBlatTest.o
 
 hgBlatTest: $O ${MYLIBS}
 	${CC} ${COPT} -o ${BINDIR}/hgBlatTest $O ${MYLIBS} $L
 #	${STRIP} ${BINDIR}/hgBlatTest${EXE}
 
 test:
 	hgBlatTest hgwdev-${USER}.cse.ucsc.edu/cgi-bin/hgBlat test.log org=human db=hg16 type=DNA sort=score output=psl repeat=1 
 
 test2:
 	hgBlatTest hgwbeta.cse.ucsc.edu/cgi-bin/hgBlat test.log org=chimp type=DNA sort=score output=psl repeat=1 
 
 test3:
 	hgBlatTest hgwdev.cse.ucsc.edu/cgi-bin/hgBlat test.log type=DNA sort=score output=psl repeat=1 
 
 backup: clean
 	date +%Y-%m-%d-%H-%M | gawk '{printf("zip hgBlatTest%s.zip *\n",$$1);}' > tempX
 	chmod 755 tempX
 	./tempX
 	rm tempX 
 	scp *.zip screech:/scratch/backups/
 	rm *.zip
 
 clean:
 	rm -f $O
 	rm -f *.log