17ef8d906cb3af6d9426b80b1962e1948f5e9ade
angie
  Mon Apr 20 23:51:42 2020 -0700
Automatically update the experimental custom tracks for David so that they stay in sync with the updated VCF.  refs #25188

diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh
index 06d02bd..156b066 100755
--- src/hg/utils/otto/nextstrainNcov/doUpdate.sh
+++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh
@@ -35,39 +35,56 @@
 cd $runDir
 chmod 444 ncov.$ncovTime.json
 ln -sf ncov.$ncovTime.json ncov.json
 
 #Generate bed and VCF files
 $ottoDir/nextstrain.py
 
 # bgzip & tabix the VCF files
 bgzip -f nextstrainSamples.vcf
 tabix -p vcf nextstrainSamples.vcf.gz
 for clade in A1a A2 A2a A3 A6 A7 B B1 B2 B4; do
   bgzip -f nextstrainSamples$clade.vcf
   tabix -p vcf nextstrainSamples$clade.vcf.gz
 done
 
-# bigBed-ify the gene names and "clades"
+# 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
 
+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
+
+# Install
+ln -sf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
+    $runDir/nextstrainSamples*.vcf.gz{,.tbi} \
+    $runDir/nextstrain*.nh \
+    $gbdbDir/
+
+# Install but don't archive (for now) the experimental tracks for David.
+ln -sf $runDir/nextstrain{Discarded,Blacklisted,Informative}.bb \
+    $runDir/nextstrainParsimony.bw \
+    $gbdbDir/
+
 # Archive
 mkdir -p $ottoDir/archive/$today
 cp -pf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
     $runDir/nextstrainSamples*.vcf.gz{,.tbi} \
     $runDir/nextstrain*.nh \
     $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)"