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/baseMask/makefile src/hg/baseMask/makefile
index 02e5d10..1406683 100644
--- src/hg/baseMask/makefile
+++ src/hg/baseMask/makefile
@@ -1,62 +1,63 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 XINC = -I$(MYSQLINC)
 L += -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 O = cachedMask.o trackToBaseMask.o bedToBaseMask.o baseMaskToBed.o baseMask.o
 B = cachedMask trackToBaseMask bedToBaseMask baseMaskToBed baseMask
 
 all: $B
 
 cachedMask: ${MYLIBS} cachedMaskUsage.msg cachedMask.o 
 	${CC} ${COPT} ${CFLAGS} ${XINC} -o cachedMask cachedMask.o ${MYLIBS} ${MYSQLLIBS} $L
 
 trackToBaseMask: ${MYLIBS} trackToBaseMaskUsage.msg trackToBaseMask.o
 	${CC} ${COPT} ${CFLAGS} -o trackToBaseMask trackToBaseMask.o ${MYLIBS} ${MYSQLLIBS} $L
 
 bedToBaseMask: ${MYLIBS} bedToBaseMaskUsage.msg bedToBaseMask.o
 	${CC} ${COPT} ${CFLAGS} -o bedToBaseMask bedToBaseMask.o ${MYLIBS} ${MYSQLLIBS} $L
 
 baseMaskToBed: ${MYLIBS} baseMaskToBedUsage.msg baseMaskToBed.o
 	${CC} ${COPT} ${CFLAGS} -o baseMaskToBed baseMaskToBed.o ${MYLIBS} ${MYSQLLIBS} $L
 
 baseMask: ${MYLIBS} baseMaskUsage.msg baseMask.o
 	${CC} ${COPT} ${CFLAGS} -o baseMask baseMask.o ${MYLIBS} ${MYSQLLIBS} $L
 
 
 # create usage msg from text
 cachedMaskUsage.msg: cachedMaskUsage.txt
 	echo '/* GENERATED CODE, DO NOT EDIT */' > $@.tmp
 	${STRINGIFY} $< >> $@.tmp
 	mv -f $@.tmp $@
 
 baseMaskUsage.msg: baseMaskUsage.txt
 	echo '/* GENERATED CODE, DO NOT EDIT */' > $@.tmp
 	${STRINGIFY} $< >> $@.tmp
 	mv -f $@.tmp $@
 
 baseMaskToBedUsage.msg: baseMaskToBedUsage.txt
 	echo '/* GENERATED CODE, DO NOT EDIT */' > $@.tmp
 	${STRINGIFY} $< >> $@.tmp
 	mv -f $@.tmp $@
 
 trackToBaseMaskUsage.msg: trackToBaseMaskUsage.txt
 	echo '/* GENERATED CODE, DO NOT EDIT */' > $@.tmp
 	${STRINGIFY} $< >> $@.tmp
 	mv -f $@.tmp $@
 
 bedToBaseMaskUsage.msg: bedToBaseMaskUsage.txt
 	echo '/* GENERATED CODE, DO NOT EDIT */' > $@.tmp
 	${STRINGIFY} $< >> $@.tmp
 	mv -f $@.tmp $@
 
 test:
 	cd tests && ${MAKE} test
 
 clean:
 	rm -f $O $B
 	rm -f cachedMaskUsage.msg baseMaskUsage.msg trackToBaseMaskUsage.msg bedToBaseMaskUsage.msg baseMaskToBedUsage.msg
 	cd tests && ${MAKE} clean