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/pslDiff/makefile src/hg/pslDiff/makefile
index 3a33fc8..7c87381 100644
--- src/hg/pslDiff/makefile
+++ src/hg/pslDiff/makefile
@@ -1,30 +1,31 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += ${MYSQLLIBS} -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 
 O = pslSets.o pslDiff.o
 # pslDiff.o
 A =  pslDiff
 
 $A: $O ${MYLIBS}
 	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L}
 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
 
 compile:: ${O}
 	${CC} ${COPT} ${CFLAGS} -o ${A}${EXE} $O ${MYLIBS} ${L}
 
 pslDiff.o: pslDiff.c pslSets.h
 
 test: compile
 	cd tests && ${MAKE} test
 	rm -f ${A}${EXE}
 
 clean:
 	rm -f $O $B pslDiff
 	cd tests && ${MAKE} clean
 
 savebak:
 	savebak pslDiff makefile *.c