1715fcf5e6c59c033d9f6dfb341e62b1f1b7c629
angie
  Tue Dec 7 18:38:36 2021 -0800
Mask 21846 (S:95) in Delta branch - Cornelius Roemer and Chris Ruis pointed out phylogeny problems it caused.

diff --git src/hg/utils/otto/sarscov2phylo/maskDelta.sh src/hg/utils/otto/sarscov2phylo/maskDelta.sh
index 6d767e5..30cba66 100755
--- src/hg/utils/otto/sarscov2phylo/maskDelta.sh
+++ src/hg/utils/otto/sarscov2phylo/maskDelta.sh
@@ -31,18 +31,22 @@
 deltaNode=$(grep IND/GBRC714b/2021 $samplePaths | awk '{print $NF;}' | sed -re 's/:.*//;')
 
 # Delta has deletions at S:157-158 (22029-22034), ORF8:119-120 (28248-28253) and 28271.
 # Mask those locations and some adjacent bases where we get a ton of spurious "mutations".
 maskFile=$(basename $treeInPb .pb).maskForDelta.tsv
 set +x
 for ((i=22027;  $i <= 22034;  i++)); do
     echo -e "N${i}N\t$deltaNode"
 done > $maskFile
 for ((i=28246;  $i <= 28253;  i++)); do
     echo -e "N${i}N\t$deltaNode"
 done >> $maskFile
 echo -e "N28271N\t$deltaNode" >> $maskFile
 set -x
 
+# S:95 (21846) is also very unreliably detected in Delta.  Mask it off to avoid tree trouble,
+# like split AY.100.
+echo -e "N21846N\t$deltaNode" >> $maskFile
+
 time $matUtils mask -i $treeInPb \
     -m $maskFile \
     -o $treeOutPb