fc7f1b9f5e16f4128f56760ac87a5649ee422b9d
angie
  Thu Mar 26 15:07:25 2020 -0700
Add TreeTime date and administrative division (location) info for clades to nextstrainClade.  refs #25188

diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh
index 1905778..32a4b01 100755
--- src/hg/utils/otto/nextstrainNcov/doUpdate.sh
+++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh
@@ -30,30 +30,30 @@
 runDir=$ottoDir/$today
 cd $runDir
 
 #Generate bed and VCF files
 $ottoDir/nextstrain.py
 
 # bgzip & tabix the VCF
 bgzip -f nextstrainSamples.vcf
 tabix -p vcf nextstrainSamples.vcf.gz
 
 # 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=$ottoDir/nextstrainClade.as -type=bed12+2 -tab -verbose=0 \
+bedToBigBed -as=$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} \
     $ottoDir/archive/$today
 cp -p $runDir/ncov.json $ottoDir/archive/$today
 
 # Install
 ln -sf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb $runDir/nextstrainSamples.vcf.gz{,.tbi} \
     $gbdbDir/
 
 echo "Updated nextstrain/ncov `date` (ncov.json date $latestDate)"