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/qa/makefile src/hg/qa/makefile
index 0beda9d..6ccf6a1 100644
--- src/hg/qa/makefile
+++ src/hg/qa/makefile
@@ -1,19 +1,20 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += ${MYSQLLIBS} -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 progs = apacheMonitor checkCardinality countNib \
     dumpNib gbSeqCheck reviewIndexes seqCheck \
     getChroms checkChain testSearch timePosTable
 
 all: ${progs}
 
 %: %.c ${MYLIBS}
 	${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o ${DESTDIR}${BINDIR}/$* $*.c ${MYLIBS} $L
 
 clean::
 	rm -f apacheMonitor.o checkCardinality.o countNib.o \
 	dumpNib.o gbSeqCheck.o reviewIndexes.o seqCheck.o \
 	getChroms.o checkChain.o testSearch.o timePosTable.o