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/hgGene/makefile src/hg/hgGene/makefile
index 53e73ae..56d4d5e 100644
--- src/hg/hgGene/makefile
+++ src/hg/hgGene/makefile
@@ -1,46 +1,47 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += $(MYSQLLIBS) -lm
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a
 
 A = hgGene
 
 O = hgGene.o alleles.o altSplice.o ctd.o dnaBindMotif.o domains.o gad.o malaCards.o\
     flyBaseInfo.o gtex.o go.o info.o links.o microarray.o \
     method.o localization.o mrnaDescriptions.o otherOrgs.o\
     pathways.o pseudoGene.o rgdInfo.o rnaStructure.o sequence.o swissProtComments.o \
     synonym.o wikiTrack.o geneReviews.o
 
 include ../../inc/cgi_build_rules.mk
 
 my::
 	rm -fr ${CGI_BIN}-${USER}/hgGeneData
 	rsync -ar --exclude=CVS/ --exclude=.svn/ --delete hgGeneData ${CGI_BIN}-${USER}/
 	chmod -R a+rX ${CGI_BIN}-${USER}/hgGeneData
 
 install::
 	rm -fr ${DESTDIR}${CGI_BIN}/hgGeneData
 	rsync -ar --exclude=CVS/ --exclude=.svn/ --delete hgGeneData \
 		${DESTDIR}${CGI_BIN}/
 	chmod -R a+rX ${DESTDIR}${CGI_BIN}/hgGeneData
 
 alpha::
 	rm -fr ${CGI_BIN}/hgGeneData
 	rsync -ar --exclude=CVS/ --exclude=.svn/ --delete hgGeneData ${CGI_BIN}/
 	chmod -R g+w ${CGI_BIN}/hgGeneData
 	chmod -R a+rX ${CGI_BIN}/hgGeneData
 
 beta::
 	rm -fr ${CGI_BIN}-beta/hgGeneData
 	rsync -ar --exclude=CVS/ --exclude=.svn/ --delete hgGeneData ${CGI_BIN}-beta/
 	chmod -R g+w ${CGI_BIN}-beta/hgGeneData
 	chmod -R a+rX ${CGI_BIN}-beta/hgGeneData
 
 compile: $O 
 	${CC} $O ${MYLIBS} ${L}
 	mv ${AOUT} $A${EXE}
 
 test:
 	${CGI_BIN}-${USER}/$A hgg_gene=D43968 hgg_chrom=chr21 hgg_start=35080500 hgg_end=35181383 db=hg16 hgsid=68172