0b3aed10ba50cdda1d27a4b3cb170fbde09b6060
angie
  Thu Jun 6 10:55:24 2024 -0700
Minor: move compression of new*.fa files into updateCombinedTree.sh to make manual copy-paste run completion a little easier.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh
index 3d71b94..fbdd66d 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublic.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh
@@ -65,18 +65,15 @@
 cut -f 1 $scriptDir/pango.clade-mutations.tsv  \
 | grep -E '^(AY|[B-Z][A-Z])' | grep -v _ | sort -u \
     > $TMPDIR/cladeMutDoubleLetters
 missingLineages=$(comm -23 $TMPDIR/designatedDoubleLetters $TMPDIR/cladeMutDoubleLetters)
 if [[ "$missingLineages" != "" ]]; then
     echo "LINEAGES MISSING FROM lineages.csv:"
     echo $missingLineages
 fi
 extraLineages=$(comm -13 $TMPDIR/designatedDoubleLetters $TMPDIR/cladeMutDoubleLetters)
 if [[ "$extraLineages" != "" ]]; then
     echo "EXTRA LINEAGES (withdrawn?) in pango.clade-mutations.tsv:"
     echo $extraLineages
 fi
 set -o pipefail
 set -x
-
-# Clean up
-nice xz -f new*fa &