1af2fddea7e6ede49cc2b334a6c8e78df998c9fa
angie
  Mon Jun 8 16:15:28 2020 -0700
Nextstrain changed to a new set of clade definitions, but they still keep the old clade assignments around in a different tag.  Make subtracks for both old and new sets of clades.  refs #25188

diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh
index 1050c03..441daa9 100755
--- src/hg/utils/otto/nextstrainNcov/doUpdate.sh
+++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh
@@ -46,76 +46,83 @@
 # bgzip & tabix the VCF files
 for f in nextstrain*.vcf; do
   bgzip -f $f
   tabix -p vcf $f.gz
 done
 
 # bigBed-ify the gene names, "clades" and discarded/blacklisted/informative tracks for David
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainGene.bed $chromSizes \
     nextstrainGene.bb
 
 sort -k2n,2n nextstrainClade.bed > nextstrainClade.sorted.bed
 bedToBigBed -as=$ottoDir/nextstrainClade.as -type=bed12+7 -tab -verbose=0 \
     nextstrainClade.sorted.bed $chromSizes \
     nextstrainClade.bb
 
+if [ -f nextstrainOldClade.bed ]; then
+    sort -k2n,2n nextstrainOldClade.bed > nextstrainOldClade.sorted.bed
+    bedToBigBed -as=$ottoDir/nextstrainClade.as -type=bed12+7 -tab -verbose=0 \
+        nextstrainOldClade.sorted.bed $chromSizes \
+        nextstrainOldClade.bb
+fi
+
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainDiscarded.bed $chromSizes \
     nextstrainDiscarded.bb
 
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainBlacklisted.bed $chromSizes \
     nextstrainBlacklisted.bb
 
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainInformative.bed $chromSizes \
     nextstrainInformative.bb
 
 # bigWig for the tree parsimony scores track for David
 bedGraphToBigWig nextstrainParsimony.bedGraph $chromSizes nextstrainParsimony.bw
 
 # Max's nextstrainSamples*.bedGraph allele count bigWigs:
 for i in nextstrainSamples*.vcf.gz; do
     base=`basename $i .vcf.gz`
     zcat $i \
     | grep -v '#' \
     | perl -wne '@w=split("\t");
                  $w[7] =~ m/AC=(\d+)[\d,]*;AN=(\d+)/ ||
                           die "Cant find AC and AN in |$w[7]|";
                  print join("\t", $w[0], $w[1]-1, $w[1], (sprintf "%.06f", $1 / $2)) . "\n";' \
       > $base.bedGraph
     bedGraphToBigWig $base.bedGraph $chromSizes $base.bigWig
 done
 
 # Install public track files
 mkdir $ottoDir/install
-cp -pf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
+cp -pf $runDir/nextstrainGene.bb $runDir/nextstrain*Clade.bb \
     $runDir/nextstrain*.vcf.gz{,.tbi} \
     $runDir/nextstrain*.nh \
     $runDir/nextstrainSamples*.bigWig \
     $ottoDir/install/
 rm -rf $ottoDir/current.bak
 mv -f $ottoDir/current $ottoDir/current.bak
 mv $ottoDir/install $ottoDir/current
 rm -r $gbdbDir
 mkdir $gbdbDir
-ln -sf $ottoDir/current/nextstrainGene.bb $ottoDir/current/nextstrainClade.bb \
+ln -sf $ottoDir/current/nextstrainGene.bb $ottoDir/current/nextstrain*Clade.bb \
     $ottoDir/current/nextstrain*.vcf.gz{,.tbi} \
     $ottoDir/current/nextstrain*.nh \
     $ottoDir/current/nextstrainSamples*.bigWig \
     $gbdbDir/
 
 # Install but don't archive (for now) the experimental tracks for David.
 cp -pf $runDir/nextstrain{Discarded,Blacklisted,Informative}.bb \
     $runDir/nextstrainParsimony.bw \
     $ottoDir/current/
 ln -sf $ottoDir/current/nextstrain{Discarded,Blacklisted,Informative}.bb \
     $ottoDir/current/nextstrainParsimony.bw \
     $gbdbDir/
 
 # Daily archive (may overwrite files from earlier today)
 mkdir -p $ottoDir/archive/$today
 rm -f $ottoDir/archive/$today/*
-cp -pf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
+cp -pf $runDir/nextstrainGene.bb $runDir/nextstrain*Clade.bb \
     $runDir/nextstrain*.vcf.gz{,.tbi} \
     $runDir/nextstrain*.nh \
     $runDir/nextstrainSamples*.bigWig \
     $ottoDir/archive/$today
 
-echo "Updated nextstrain/ncov `date` (ncov.json date $latestDate)"
+echo "Updated nextstrain/ncov `date` (ncov.json dated $ncovTime)"