06d7be056190c14b85e71bc12523f18ea6815b5e
markd
  Mon Dec 7 00:50:29 2020 -0800
BLAT mmap index support merge with master

diff --git src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
new file mode 100755
index 0000000..be70d07
--- /dev/null
+++ src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
@@ -0,0 +1,66 @@
+#!/bin/bash
+set -beEu -x -o pipefail
+
+#	Do not modify this script, modify the source tree copy:
+#	kent/src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
+
+usage() {
+    echo "usage: $0 metadata_date.tsv.gz sequences_date.fasta.gz"
+}
+
+if [ $# != 2 ]; then
+  usage
+  exit 1
+fi
+
+nextmeta=$1
+nextfasta=$2
+
+scriptDir=$(dirname "${BASH_SOURCE[0]}")
+source $scriptDir/util.sh
+
+today=$(date +%F)
+ottoDir=/hive/data/outside/otto/sarscov2phylo
+mapScriptDir=~/chris_ncov
+# Should use a better location than this...
+installDir=/hive/users/angie/gisaid
+
+ncbiDir=$ottoDir/ncbi.$today
+mkdir -p $ncbiDir
+cd $ncbiDir
+$scriptDir/getNcbi.sh >& getNcbi.log
+
+cogUkDir=$ottoDir/cogUk.$today
+mkdir -p $cogUkDir
+cd $cogUkDir
+$scriptDir/getCogUk.sh >& getCogUk.log
+
+# Last time I checked, CNCB had not updated since September, just keep using what we have
+cncbDir=$ottoDir/cncb.latest
+
+# Set up input files for Chris's scripts to map GISAID <--> public sequences
+cd $mapScriptDir
+mkdir input/$today
+cd input/$today
+ln -sf $cncbDir/cncb.nonGenBank.fasta .
+ln -sf $ncbiDir/genbank.fa.xz .
+ln -sf $cogUkDir/cog_all.fasta.xz .
+ln -sf $nextfasta .
+xcat $nextmeta | tail -n+2 | cut -f1,3 > seqToEpi
+
+cd $mapScriptDir
+./build.sh -t $today
+
+cd $installDir
+
+gbToDate=$ncbiDir/gbToDate
+cogUkToDate=$cogUkDir/cogUkToDate
+cncbToDate=$cncbDir/cncbToDate
+
+join -t$'\t' -a 1 -1 2 -o 1.1,1.2,1.3,2.2 \
+    <(sort -k2,2 ~/chris_ncov/epiToPublicIdName.$today.txt) \
+    <(sort $gbToDate $cncbToDate $cogUkToDate) \
+| sort \
+    > epiToPublicAndDate.$today
+
+ln -sf epiToPublicAndDate.$today epiToPublicAndDate.latest