ecbbcd78daf00901ca5eac7cde487effd342a376
angie
  Thu Jan 13 11:33:31 2022 -0800
Increase max-path-length so we don't lop off all of BA.2 and BA.3 which due to Delta contam & back-muts are on super-long paths.

diff --git src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
index 958a9ff..659623d 100755
--- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
@@ -35,31 +35,31 @@
 
 usherDir=~angie/github/usher
 usher=$usherDir/build/usher
 matUtils=$usherDir/build/matUtils
 
 if [ ! -s new.masked.vcf.gz ]; then
     $scriptDir/makeNewMaskedVcf.sh $prevDate $today $problematicSitesVcf $baseProtobuf
 fi
 
 if [ ! -s gisaidAndPublic.$today.masked.pb ]; then
     $scriptDir/usherClusterRun.sh $today
     # Prune samples with too many private mutations and internal branches that are too long.
     $matUtils extract -i gisaidAndPublic.$today.masked.preTrim.pb \
         --max-parsimony 20 \
         --max-branch-length 45 \
-        --max-path-length 100 \
+        --max-path-length 150 \
         -O -o gisaidAndPublic.$today.masked.pb
 fi
 
 # Exclude sequences with a very high number of EPPs from future runs
 grep ^Current usher.addNew.log \
 | awk '$16 >= 10 {print $8;}' \
 | awk -F\| '{ if ($3 == "") { print $1; } else { print $2; } }' \
     > tooManyEpps.ids
 cat tooManyEpps.ids >> ../tooManyEpps.ids
 
 $matUtils extract -i gisaidAndPublic.$today.masked.pb -u samples.$today
 
 $scriptDir/combineMetadata.sh $prevDate $today
 
 # version/description files