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/extractPublicTree.sh src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
index 73717c8..1f22096 100755
--- src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
+++ src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
@@ -24,31 +24,31 @@
 usherDir=~angie/github/usher
 matUtils=$usherDir/build/matUtils
 
 cd $ottoDir/$today
 
 # Extract public samples from tree
 grep -v EPI_ISL_ samples.$today > newPublicNames
 # Dunno why, but when I tried using -s together with the filtering params, it ran for 3 hours
 # and I killed it -- stuck in a loop?  Run two commands:
 $matUtils extract -i gisaidAndPublic.$today.masked.pb \
     -s newPublicNames \
     -o public-$today.all.masked.preTrim.pb
 $matUtils extract -i public-$today.all.masked.preTrim.pb \
     --max-parsimony 20 \
     --max-branch-length 45 \
-    --max-path-length 100 \
+    --max-path-length 150 \
     -O -o public-$today.all.masked.pb
 
 # Add nextclade annotations to protobuf (completely specified by nextstrain.clade-mutations.tsv)
 grep -v EPI_ISL cladeToName > cladeToPublicName
 time $matUtils annotate -T 50 \
     -l \
     -i public-$today.all.masked.pb \
     -M $scriptDir/nextstrain.clade-mutations.tsv \
     -D details.nextclade.public \
     -o public-$today.all.masked.nextclade.pb \
     >& annotate.nextclade.public
 
 # Add pangolin lineage annotations to public protobuf
 grep -v EPI_ISL lineageToName > lineageToPublicName
 time $matUtils annotate -T 50 \