d0ed6814b11e78dfd69dbe071b296acf46b8e24a
angie
  Fri Aug 28 08:28:16 2026 -0700
If split lineages were found, report them.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh
index 529eee0474c..4af13736e09 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublic.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh
@@ -71,17 +71,20 @@
                          | grep -vFwf $scriptDir/designatedNotAnnotated | cat)
 if [[ "$designatedNotAnnotated" != "" ]]; then
     echo "MISSING LINEAGES:"
     echo "$designatedNotAnnotated"
 else
     echo "No unexpectedly missing lineages, good."
 fi
 annotatedNotDesignated=$(comm -13 $TMPDIR/designatedLineages $TMPDIR/annotatedLineages \
                          | grep -vFwf $scriptDir/annotatedNotDesignated | cat)
 if [[ "$annotatedNotDesignated" != "" ]]; then
     echo "EXTRA LINEAGES (withdrawn?) in tree:"
     echo "$annotatedNotDesignated"
 else
     echo "No extra lineages, good."
 fi
+echo ""
+# Check for split lineages / sequences to prune:
+grep 'prune ' split_lineages.txt | cat
 set -o pipefail
 set -x