475424b5d722b4ff761681f1d3bd91ad666fb2d6
angie
  Wed Apr 1 10:17:03 2020 -0700
For nested clades, add all clade samples to per-clade VCF.  Also generate Newick (.nh) tree file and tweak sample name separator, in preparation for drawing the nextstrain tree in the VCF left label area.  refs #25188

diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh
index cd735e1..299f077 100755
--- src/hg/utils/otto/nextstrainNcov/doUpdate.sh
+++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh
@@ -42,24 +42,26 @@
 done
 
 # bigBed-ify the gene names and "clades"
 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
 
 # Archive
 mkdir -p $ottoDir/archive/$today
 cp -p $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
     $runDir/nextstrainSamples*.vcf.gz{,.tbi} \
+    $runDir/nextstrain.nh \
+    $runDir/ncov.json \
     $ottoDir/archive/$today
-cp -p $runDir/ncov.json $ottoDir/archive/$today
 
 # Install
 ln -sf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
     $runDir/nextstrainSamples*.vcf.gz{,.tbi} \
+    $runDir/nextstrain.nh \
     $gbdbDir/
 
 echo "Updated nextstrain/ncov `date` (ncov.json date $latestDate)"