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/hgc/makefile src/hg/hgc/makefile
index a405747..97c96e0 100644
--- src/hg/hgc/makefile
+++ src/hg/hgc/makefile
@@ -1,40 +1,41 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lm ${MYSQLLIBS} 
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 A = hgc
 
 O = $A.o bamClick.o bigBedClick.o dbRIP.o ccdsClick.o cgapSageClick.o encodeClick.o expClick.o \
 	gencodeClick.o gtexClick.o gvfClick.o hgdpClick.o \
 	lowelab.o lrgClick.o \
 	mafClick.o makeItemsClick.o mgcClick.o \
 	parClick.o peakClusters.o regMotif.o retroClick.o rmskJoinedClick.o \
 	rnaFoldClick.o \
 	transMapClick.o txCdsInfo.o pubs.o vcfClick.o virusClick.o wiggleClick.o \
 	wikiTrack.o variomeClick.o numtsClick.o geneReviewsClick.o
 
 include ../../inc/cgi_build_rules.mk
 
 mgsc: compile
 	mv $A ${CGI_BIN}-mgsc/$A
 
 compile: $O 
 	${CC} ${CFLAGS} $O ${F64} ${MYLIBS} ${L}
 	mv ${AOUT} $A${EXE}
 
 my::
 	rm -rf ${CGI_BIN}-${USER}/hgcData ${CGI_BIN}-${USER}/lsSnpPdbChimera.py
 	rsync -aO --exclude=CVS/ --exclude=.svn/ --delete hgcData ../lib/lsSnpPdbChimera.py ${CGI_BIN}-${USER}/
 	chmod -R a+rX ${CGI_BIN}-${USER}/hgcData ${CGI_BIN}-${USER}/lsSnpPdbChimera.py
 
 alpha::
 	rm -fr ${CGI_BIN}/hgcData ${CGI_BIN}/lsSnpPdbChimera.py
 	rsync -aO --exclude=CVS/ --exclude=.svn/ --delete hgcData ../lib/lsSnpPdbChimera.py ${CGI_BIN}/
 	chmod -R a+rX,g+w ${CGI_BIN}/hgcData ${CGI_BIN}/lsSnpPdbChimera.py
 
 beta::
 	rm -fr ${CGI_BIN}-beta/hgcData ${CGI_BIN}-beta/lsSnpPdbChimera.py
 	rsync -aO --exclude=CVS/ --exclude=.svn/ --delete hgcData ../lib/lsSnpPdbChimera.py ${CGI_BIN}-beta/
 	chmod -R a+rX,g+w ${CGI_BIN}-beta/hgcData ${CGI_BIN}-beta/lsSnpPdbChimera.py