fd84fe49fb0697a08c40b8cdbd1b4b003c06330b
angie
  Mon Nov 29 12:59:31 2021 -0800
Now that Problematic Sites track has been updated, no need to patch in masking of site 21987 (S:142).

diff --git src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
index bc5c2a7..0f07cda 100755
--- src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
+++ src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
@@ -267,29 +267,24 @@
     | sed -re 's/ /_/g' \
         >> $renaming
     set -o pipefail
 fi
 if [ -s newGisaid.filtered.fa ]; then
     zcat $gisaidDir/metadata_batch_$today.tsv.gz \
     | grep -Fwf <(fastaNames newGisaid.filtered.fa) \
     | tawk '{print $3 "\t" $1 "|" $3 "|" $5;}' \
         >> $renaming
 fi
 wc -l $renaming
 
 # Make masked VCF
 tawk '{ if ($1 ~ /^#/) { print; } else if ($7 == "mask") { $1 = "NC_045512v2"; print; } }' \
     $problematicSitesVcf > mask.vcf
-# Add masked VCF to previous protobuf
-#*** With horrible hack for time being, to mask 21987 (because it messes up the Delta branch)...
-#*** TODO: make hgPhyloPlace handle protobufs that don't have all of the latest problematic sites
-#*** masked more gracefully, and update the Problematic Sites track.
 time cat <(twoBitToFa $ref2bit stdout) $alignedFa \
 | faToVcf -maxDiff=1000 \
     -excludeFile=<(cat ../tooManyEpps.ids ../badBranchSeed.ids) \
     -verbose=2 stdin stdout \
 | vcfRenameAndPrune stdin $renaming stdout \
 | vcfFilter -excludeVcf=mask.vcf stdin \
-| tawk '$2 != 21987' \
 | gzip -c \
     > new.masked.vcf.gz