491395482b817cfe82cbdef4dd7f8ee0723c1a4a
angie
  Wed Mar 23 21:01:49 2011 -0700
Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc
and a customFactory.  It is a new bigDataUrl type of track; the
remote VCF file must be compressed and indexed by tabix, so like
BAM a separate index file is required.  If the VCF file has
genotypes, then each sample's two haplotypes are graphed in a
line, with one line per sample.  Otherwise, alleles and counts
(if available) are drawn using Belinda's pgSnp methods.
The source code has to be compiled with USE_TABIX=1 (which is
automatically set for us by common.mk when it finds the local
installation) in order for the CGIs to recognize the track type.

diff --git src/hg/hgTracks/makefile src/hg/hgTracks/makefile
index 2e29cf3..821d81d 100644
--- src/hg/hgTracks/makefile
+++ src/hg/hgTracks/makefile
@@ -1,71 +1,71 @@
 include ../../inc/common.mk
 
 L += ${MYSQLLIBS} -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 A = hgTracks
 
 COMMONO = altGraphXTrack.o bamTrack.o bedGraph.o bedTrack.o bigBedTrack.o bigWarn.o bigWigTrack.o \
 	chainTrack.o cgapSageTrack.o chromGraphTrack.o config.o container.o contigTrack.o \
 	coverageTrack.o cytoBandTrack.o cutterTrack.o \
         expRatioTracks.o factorSource.o hgTracks.o goldTrack.o gvfTrack.o loweLabTracks.o \
 	mafTrack.o makeItemsTrack.o multiWig.o netTrack.o pslTrack.o rmskTrack.o \
 	sampleTracks.o searchTracks.o simpleTracks.o snakeTrack.o switchGear.o transMapTracks.o \
 	wabaTrack.o wigTrack.o cds.o \
-	wigMafTrack.o encode.o variation.o transcriptome.o\
+	wigMafTrack.o encode.o variation.o vcfTrack.o transcriptome.o\
 	rnaFoldTrack.o retroGene.o hapmapTrack.o rnaPLFoldTrack.o\
 	wiki.o wikiTrack.o imageV2.o
 
 O = mainMain.o ${COMMONO} 
 
 include ../../inc/cgi_build_rules.mk
 
 ifeq (${GBROWSE}, 1)
   GBROWSE_D=-DGBROWSE
   A = gbrowseTest
   O = $A.o oneTrack.o \
       bedGraph.o cds.o chainTrack.o mafTrack.o netTrack.o pslTrack.o \
       simpleTracks.o wigMafTrack.o wigTrack.o imageV2.o
 else
   GBROWSE_D=
 endif
 
 %.o: %.c
 	${CC} ${COPT} ${CFLAGS} ${GBROWSE_D} ${LOWELAB_DEFS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
 
 mgsc: strip
 	mv $A ${CGI_BIN}/$A
 
 RENDERO = renderMain.o ${COMMONO}
 RENDERA = ./hgRenderTracks
 
 # when it is time to deliver hgRenderTracks, remove the rm and echo below
 compile: compileMain
 	@rm -f ${RENDERA}
 	@echo "run 'make hgRenderTracks' to obtain that binary"
 
 compileMain: $O
 	${CC} -o $A $O ${MYLIBS} ${L}
 
 ${RENDERA}: ${RENDERO}
 	${CC} -o ${RENDERA} ${RENDERO} ${MYLIBS} ${L}
 
 # install of RENDERA is not enabled yet.
 #	When it is desired, would need three different targets:
 #	my:: - for personal browser into ${CGI_BIN}-${USER}
 #	alpha:: - for browser into ${CGI_BIN}
 #	beta:: - for browser into ${CGI_BIN}-beta
 #	install:: - into DESTDIR/CGI_BIN
 
 wigTrack.o:	wigCommon.h
 bedGraph.o:	wigCommon.h
 
 switchGear.o:	switchGear.h
 cds.o:		cds.h
 hgTracks.o:	cds.h
 pslTrack.o:	cds.h
 
 clean::
 	rm -f ct_hgwdev_*.bed hgtIdeo_*.gif hgt_*.gif
 	rm -f ${RENDERA} ${RENDERO}