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/bdfToGem/makefile src/utils/bdfToGem/makefile
index 8d2e241..bd4538d 100644
--- src/utils/bdfToGem/makefile
+++ src/utils/bdfToGem/makefile
@@ -1,96 +1,97 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lm ${MYSQLLIBS}
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS = ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a 
 
 XINC=-I../../lib
 
 O = bdfToGem.o
 
 A = bdfToGem
 
 all::	${A} mgTinyFont.c mgSmallFont.c mgMediumFont.c mgLargeFont.c \
 		mgHugeFont.c
 
 bold::	${A} tinyBold smallBold mediumBold largeBold hugeBold
 
 fixed::	${A} tinyFixed smallFixed mediumFixed largeFixed hugeFixed
 
 allThree::	all bold fixed
 
 $A: $O ${MYLIBS}
 	${CC} ${COPT} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} $L
 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
 
 compile:	${O} ${MYLIBS}
 	${CC} ${COPT} -o ${A}${EXE} $O ${MYLIBS} $L
 
 install:: compile
 	rm -f ${DESTDIR}${BINDIR}/${A}${EXE}
 	cp -p ${A}${EXE} ${DESTDIR}${BINDIR}/${A}${EXE}
 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
 
 mgTinyFont.c:	${O}
 	bdfToGem -verbose=2 -name="Tiny" 75dpi/helvR08-L1.bdf mgTinyFont.c
 
 mgSmallFont.c:	${O}
 	bdfToGem -verbose=2 -name="Small" 75dpi/helvR10-L1.bdf mgSmallFont.c
 
 mgMediumFont.c:	${O}
 	bdfToGem -verbose=2 -name="Medium" 75dpi/helvR14-L1.bdf mgMediumFont.c
 
 mgLargeFont.c:	${O}
 	bdfToGem -verbose=2 -name="Large" 75dpi/helvR18-L1.bdf mgLargeFont.c
 
 mgHugeFont.c:	${O}
 	bdfToGem -verbose=2 -name="Huge" 100dpi/helvR24-L1.bdf mgHugeFont.c
 
 tinyBold:	mgTinyFont.c
 	bdfToGem -noHeader -verbose=2 -name="TinyBold" \
 		75dpi/helvB08-L1.bdf stdout >> mgTinyFont.c
 
 smallBold:	mgSmallFont.c
 	bdfToGem -noHeader -verbose=2 -name="SmallBold" \
 		75dpi/helvB10-L1.bdf stdout >> mgSmallFont.c
 
 mediumBold:	mgMediumFont.c
 	bdfToGem -noHeader -verbose=2 -name="MediumBold" \
 		75dpi/helvB14-L1.bdf stdout >> mgMediumFont.c
 
 largeBold:	mgLargeFont.c
 	bdfToGem -noHeader -verbose=2 -name="LargeBold" \
 		75dpi/helvB18-L1.bdf stdout >> mgLargeFont.c
 
 hugeBold:	mgHugeFont.c
 	bdfToGem -noHeader -verbose=2 -name="HugeBold" \
 		100dpi/helvB24-L1.bdf stdout >> mgHugeFont.c
 
 
 tinyFixed:	mgTinyFont.c
 	bdfToGem -noHeader -verbose=2 -name="TinyFixed" \
 		misc/5x8-L1.bdf stdout >> mgTinyFont.c
 
 smallFixed:	mgSmallFont.c
 	bdfToGem -noHeader -verbose=2 -name="SmallFixed" \
 		misc/6x10-L1.bdf stdout >> mgSmallFont.c
 
 mediumFixed:	mgMediumFont.c
 	bdfToGem -noHeader -verbose=2 -name="MediumFixed" \
 		misc/8x13-L1.bdf stdout >> mgMediumFont.c
 
 largeFixed:	mgLargeFont.c
 	bdfToGem -noHeader -verbose=2 -name="LargeFixed" \
 		misc/9x15-L1.bdf stdout >> mgLargeFont.c
 
 #	there is a 12x24 misc font, but it is different than
 #	the other fixed fonts
 
 hugeFixed:	mgHugeFont.c
 	bdfToGem -noHeader -verbose=2 -name="HugeFixed" \
 		misc/10x20-L1.bdf stdout >> mgHugeFont.c
 
 clean:
 	rm -f ${BINDIR}/${A} $O \
 		mgTinyFont.c mgSmallFont.c mgMediumFont.c mgLargeFont.c \
 		mgHugeFont.c