8cab21c8b8a5e84a3491b796bd6590c5d6905325
angie
  Thu Dec 4 15:45:54 2025 -0800
Added a couple samples to spare for reversion-riddled LF.7.6.5

diff --git src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
index 9459bda28b0..9128b4b4a25 100755
--- src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
+++ src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
@@ -19,58 +19,61 @@
     startingTree=$2
 else
     startingTree=gisaidAndPublic.$buildDate.masked.pb.gz
 fi
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 
 usherDir=~angie/github/usher
 matUtils=$usherDir/build/matUtils
 
 today=$(date +%F)
 cd $ottoDir/$buildDate
 
 # Remove sequences that have two or more reversions relative to their assigned clade/lineage.
 $matUtils summary -i $startingTree --node-stats node-stats
-#*** Until BA.2.3.22 gets more samples that don't have bogus reversion on 25000 and 26577,
-#*** exempt some samples; also, most of JP.1 has rev on 27383,27384:
+# Until BA.2.3.22 gets more samples that don't have bogus reversion on 25000 and 26577,
+# exempt some samples; also, most of JP.1 has rev on 27383,27384 and 2 of LF.7.6.5's 4
+# samples have revs.
 cat > pruneRevsExemptions <<EOF
 Germany/HH-RKI-I-1073418/2022|EPI_ISL_16330648|2022-12-18
 Germany/SH-RKI-I-1071936/2022|EPI_ISL_16329344|2022-12-05
 Germany/SH-RKI-I-1074649/2022|EPI_ISL_16396486|2022-12-12
 Germany/SH-RKI-I-1071904/2022|EPI_ISL_16329314|2022-12-05
 Germany/SH-RKI-I-1071924/2022|EPI_ISL_16329332|2022-12-05
 Germany/SH-RKI-I-1071920/2022|EPI_ISL_16329328|2022-12-05
 Germany/SH-RKI-I-1071899/2022|EPI_ISL_16329310|2022-12-05
 Germany/HH-RKI-I-1029775/2022|EPI_ISL_15901009|2022-11-13
 Germany/HH-RKI-I-1105132/2023|EPI_ISL_16940514|2023-01-27
 OY160699.1
 OY148358.1
 OY125285.1
 OY165180.1
 OY176754.1
 OY146516.1
 OY142598.1
 OY124642.1
 OY143123.1
 OY151190.1
 SouthAfrica/NICD-N55605/2023|EPI_ISL_17859330|2023-05-22
 SouthAfrica/NICD-N56015/2023|EPI_ISL_18125227|2023-06-15
 SouthAfrica/NICD-N56013/2023|EPI_ISL_18125226|2023-06-15
 SouthAfrica/NICD-R10184/2023|EPI_ISL_18341856|2023-09-05
 SouthAfrica/NICD-R10169/2023|EPI_ISL_18341854|2023-09-05
 SouthAfrica/NICD-R10455/2023|EPI_ISL_18341867|2023-09-12
+USA/NY-PRL-250108_82B06/2024|PQ898526.1|2024-12-22
+Egypt/MOH-CPHL-0003/2025|EPI_ISL_19975232|2025-04-13
 EOF
 tawk '$5 > 1 {print $1;}' node-stats \
 | grep -vFwf pruneRevsExemptions \
     > pruneRevs
 $matUtils extract -i $startingTree \
     -p -s pruneRevs -O -o gisaidAndPublic.$buildDate.masked.pruneRevs.pb.gz
 
 # Get node ID for root of lineage A, used as reference/root by Pangolin:
 $matUtils extract -i gisaidAndPublic.$buildDate.masked.pruneRevs.pb.gz -C clade-paths.prunedRevs
 lineageARoot=$(grep ^A$'\t' clade-paths.prunedRevs | cut -f 2)
 
 # Reroot protobuf to lineage A and restrict to low mutation density (highly supported nodes):
 $matUtils extract -i gisaidAndPublic.$buildDate.masked.pruneRevs.pb.gz \
     --reroot $lineageARoot \
     --max-mutation-density 2 \