be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/hg/utils/otto/sarscov2phylo/updateSarsCov2Phylo.sh src/hg/utils/otto/sarscov2phylo/updateSarsCov2Phylo.sh
index 76ce0cc..0c66d53 100755
--- src/hg/utils/otto/sarscov2phylo/updateSarsCov2Phylo.sh
+++ src/hg/utils/otto/sarscov2phylo/updateSarsCov2Phylo.sh
@@ -1,40 +1,38 @@
 #!/bin/bash
 set -beEu -x -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/otto/sarscov2phylo/updateSarsCov2Phylo.sh
 
 usage() {
-    echo "usage: $0 releaseLabel metadata_date.tsv.gz sequences_date.fasta.gz epiToPublicAndDate.date"
+    echo "usage: $0 releaseLabel metadata_date.tsv.gz epiToPublicAndDate.date"
 }
 
-if [ $# != 4 ]; then
+if [ $# != 3 ]; then
   usage
   exit 1
 fi
 
 releaseLabel=$1
 nextmeta=$2
-nextfasta=$3
-epiToPublic=$4
+epiToPublic=$3
 
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 problematicSitesVcf=/hive/data/genomes/wuhCor1/bed/problematicSites/20-08-26/problematic_sites_sarsCov2.vcf
 genbankFa=$ottoDir/ncbi.latest/genbank.fa.xz
 cogUkFa=$ottoDir/cogUk.latest/cog_all.fasta.xz
 cncbFa=$ottoDir/cncb.latest/cncb.nonGenBank.fasta
 
 mkdir -p $ottoDir/$releaseLabel
 cd $ottoDir/$releaseLabel
 
-$scriptDir/getRelease.sh $releaseLabel $nextmeta $nextfasta >& getRelease.log
+$scriptDir/processGisaid.sh $releaseLabel $treeDir $msaFile $nextmeta $problematicSitesVcf \
+    >& processGisaid.log
 
-$scriptDir/processRelease.sh $releaseLabel $problematicSitesVcf >& processRelease.log
-
-$scriptDir/mapPublic.sh $releaseLabel $problematicSitesVcf $epiToPublic >& mapPublic.log
+$scriptDir/mapPublic.sh $releaseLabel $nextmeta $problematicSitesVcf $epiToPublic >& mapPublic.log
 
 $scriptDir/extractUnmappedPublic.sh $epiToPublic $genbankFa $cogUkFa $cncbFa \
     >& extractUnmappedPublic.log
 
 $scriptDir/addUnmappedPublic.sh $releaseLabel >& addUnmappedPublic.log