2bd08d43e884241b1e759bd87782e7bab62e1a5c
angie
  Wed Oct 6 09:19:00 2021 -0700
Oops, check more carefully for new optional arg.

diff --git src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
index 3791daa..bc5c2a7 100755
--- src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
+++ src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
@@ -5,31 +5,35 @@
 #	kent/src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
 
 usage() {
     echo "usage: $0 prevDate today problematicSitesVcf [baseProtobuf]"
     echo "This assumes that ncbi.latest and cogUk.latest links/directories have been updated."
 }
 
 if [ $# != 3 && $# != 4]; then
   usage
   exit 1
 fi
 
 prevDate=$1
 today=$2
 problematicSitesVcf=$3
+if [ $# == 4 ]; then
     baseProtobuf=$4
+else
+    baseProtobuf=
+fi
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 ncbiDir=$ottoDir/ncbi.latest
 cogUkDir=$ottoDir/cogUk.latest
 cncbDir=$ottoDir/cncb.latest
 gisaidDir=/hive/users/angie/gisaid
 minReal=20000
 ref2bit=/hive/data/genomes/wuhCor1/wuhCor1.2bit
 epiToPublic=$gisaidDir/epiToPublicAndDate.latest
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 source $scriptDir/util.sh
 
 mkdir -p $ottoDir/$today
 cd $ottoDir/$today