df04c1f66cdd6895471998c6d9c70b1a413f7d4e
angie
  Sat Mar 12 20:33:25 2022 -0800
Use new --include-nt option when generating taxonium protobufs.  Also watch out for EPI_ISL as part of GenBank name.

diff --git src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
index 659623d..5fa1334 100755
--- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
@@ -134,22 +134,23 @@
         $dir/public.plusGisaid.latest.metadata.tsv.gz
     ln -sf `pwd`/hgPhyloPlace.plusGisaid.description.txt $dir/public.plusGisaid.latest.version.txt
     ln -sf `pwd`/epiToPublic.latest $dir/
 done
 
 # Make Taxodium-formatted protobuf for display
 zcat /hive/data/genomes/wuhCor1/goldenPath/bigZips/genes/ncbiGenes.gtf.gz \
 | grep -v '"ORF1a"' > ncbiGenes.gtf
 zcat /hive/data/genomes/wuhCor1/wuhCor1.fa.gz > wuhCor1.fa
 zcat gisaidAndPublic.$today.metadata.tsv.gz > metadata.tmp.tsv
 time $matUtils extract -i gisaidAndPublic.$today.masked.pb \
     -f wuhCor1.fa \
     -g ncbiGenes.gtf \
     -M metadata.tmp.tsv \
     --extra-fields pango_lineage_usher \
+    --include-nt \
     --write-taxodium gisaidAndPublic.$today.masked.taxodium.pb
 rm metadata.tmp.tsv wuhCor1.fa
 gzip -f gisaidAndPublic.$today.masked.taxodium.pb
 
 $scriptDir/extractPublicTree.sh $today
 
 grep skipping annotate*