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/utils/wigAsciiToBinary/makefile src/utils/wigAsciiToBinary/makefile
index 4c6e4c8..2163763 100644
--- src/utils/wigAsciiToBinary/makefile
+++ src/utils/wigAsciiToBinary/makefile
@@ -1,44 +1,45 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lm ${MYSQLLIBS}
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS = ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a 
 
 XINC=-I../../hg/inc
 
 O = wigAsciiToBinary.o
 
 A = wigAsciiToBinary
 
 all::	${A} wigZoom wigBedToBinary
 
 $A: $O ${MYLIBS}
 	${CC} ${COPT} -o ${BINDIR}/${A} $O ${MYLIBS} $L
 	${STRIP} ${BINDIR}/${A}${EXE}
 
 wigZoom: wigZoom.o ${MYLIBS}
 	${CC} ${COPT} -o ${BINDIR}/wigZoom wigZoom.o ${MYLIBS} $L
 	${STRIP} ${BINDIR}/wigZoom${EXE}
 
 wigBedToBinary: wigBedToBinary.o ${MYLIBS}
 	${CC} ${COPT} -o ${BINDIR}/wigBedToBinary wigBedToBinary.o ${MYLIBS} $L
 
 test:
 	@echo "The testing is out of date and needs to be fixed"
 
 #	cd test_data && ./runtest
 
 clean:
 	rm -f ${BINDIR}/${A} $O \
 	${BINDIR}/wigZoom wigZoom.o \
 	${BINDIR}/wigBedToBinary wigBedToBinary.o \
 	test_data/chrM.ascii test_data/chr0.wib test_data/chr0.wig \
 	test_data/chrM_256.ascii test_data/chrS.wib test_data/chrS.wig \
 	test_data/chrM_256.wib test_data/chrM_256.wig \
 	test_data/chr_1K.ascii test_data/chr_1M.ascii \
 	test_data/chr1M.wib test_data/chr1M.wig \
 	test_data/chr_4M.ascii test_data/chr4M.wib \
 	test_data/chr4M.wig test_data/chrK.wib \
 	test_data/chrK.wig test_data/chrM_1K.ascii \
 	test_data/chrM.ascii test_data/chrS.wib \
 	test_data/chrS.wig