e90f5a2fd5cdd909496615dacb99216c05dcfde1
angie
  Wed Aug 9 13:42:51 2017 -0700
new util vcfToHgvs: translate genomic variants from VCF into HGVS terms using latest RefSeq transcript PSL, CDS and sequence. Tested against Personalis's "ground truth set", see PMID:28122645 and https://github.com/AngieHinrichs/hgvslib/. refs #19968

diff --git src/hg/utils/makefile src/hg/utils/makefile
index 04eacf4..5d53f96 100644
--- src/hg/utils/makefile
+++ src/hg/utils/makefile
@@ -55,50 +55,54 @@
 SCRIPT_FILES = \
 	dbNsfpToBed.pl \
 	dumpDb.pl \
 	mergeOverlapBed4.pl \
 	mergeSortedBed3Plus.pl \
 	${USER_APP_SCRIPTS}
 
 APP_SCRIPTS = ${SCRIPT_FILES}
 
 # List of directories to build of interest only at UCSC
 DIRS = ${buildRefresh} \
 	automation \
 	buildReleaseLog \
 	checkUrlsInTable \
 	geoMirrorNode \
+	hgvsToVcf \
 	makeTrackIndex \
 	mysqlSecurityCheck \
 	pslUniq \
 	refSeqGet \
 	safePush \
 	toDev64 \
+	vcfToHgvs \
 	wigBedToStep
 
 TEST_DIRS = \
 	genePredFilter \
 	genePredToProt \
 	gff3ToGenePred \
 	gff3ToPsl \
 	gtfToGenePred \
+	hgvsToVcf \
 	hubCheck \
 	overlapSelect \
 	pslMap \
 	pslToBigPsl \
 	refSeqGet \
-	transMapPslToGenePred
+	transMapPslToGenePred \
+	vcfToHgvs
 
 APPS = $(DIRS) $(UTILS_APPLIST)
 
 all:: utils
 
 utils: $(APPS:%=%.utils) $(APP_SCRIPTS:%=%.appScript)
 %.utils:
 	cd $* && echo $* && $(MAKE)
 %.appScript:
 	chmod +x $*
 	rm -f ${DESTDIR}${SCRIPTS}/$*
 	cp -p $* ${DESTDIR}${SCRIPTS}/$*
 
 userApps: $(UTILS_APPLIST:%=%.userApp) $(USER_APP_SCRIPTS:%=%.userAppScript)
 %.userApp: