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

diff --git src/hg/utils/otto/sarscov2phylo/mapPublic.sh src/hg/utils/otto/sarscov2phylo/mapPublic.sh
new file mode 100755
index 0000000..aa43d05
--- /dev/null
+++ src/hg/utils/otto/sarscov2phylo/mapPublic.sh
@@ -0,0 +1,103 @@
+#!/bin/bash
+set -beEu -x -o pipefail
+
+#	Do not modify this script, modify the source tree copy:
+#	kent/src/hg/utils/otto/sarscov2phylo/mapPublic.sh
+
+usage() {
+    echo "usage: $0 releaseLabel problematic_sites_sarsCov2.vcf epiToPublic"
+}
+
+if [ $# != 3 ]; then
+  usage
+  exit 1
+fi
+
+releaseLabel=$1
+problematicSitesVcf=$2
+epiToPublic=$3
+
+usherDir=~angie/github/usher
+usher=$usherDir/build/usher
+matToVcf=$usherDir/build/matToVcf
+find_parsimonious_assignments=~angie/github/strain_phylogenetics/build/find_parsimonious_assignments
+
+echo "releaseLabel=$releaseLabel problematicSitesVcf=$problematicSitesVcf epiToPublic=$epiToPublic"
+
+# Now extract public-sequence-only subtree and VCF.  Start by making new names with shortened year:
+tawk '{if ($4 == "") { print $1, $3 "|" $2;} else { print $1, $3 "|" $2 "|" $4;} }' $epiToPublic \
+| sed -re 's/20([0-9][0-9])(-[0-9-]+)?$/\1\2/; s/, /_/g; s/[, ]/_/g;' \
+    > epiToPublicName
+wc -l epiToPublicName
+
+join -t$'\t' tree.renaming epiToPublicName | cut -f 2,3 > treeToPublic
+wc -l treeToPublic
+
+phyloRenameAndPrune ft_SH.reroot.collapsed.nh treeToPublic ft_SH.reroot.public.nh
+sed -re 's/,/,\n/g' ft_SH.reroot.public.nh | wc -l
+
+# Run usher to collapse (having removed GISAID-only variants) and make protobuf for public set too,
+# on unmasked VCF, and use matToVcf to get ambig-resolved VCF from that for hgTracks
+time vcfRenameAndPrune gisaid-$releaseLabel.unfiltered.vcf.gz treeToPublic stdout \
+| gzip -c \
+    > public-$releaseLabel.unfiltered.vcf.gz
+time $usher -c -u \
+    -v public-$releaseLabel.unfiltered.vcf.gz \
+    -t ft_SH.reroot.public.nh \
+    -o public-$releaseLabel.notMasked.pb
+time $matToVcf -i public-$releaseLabel.notMasked.pb \
+    -v public-$releaseLabel.vcf
+bgzip -f public-$releaseLabel.vcf
+tabix -p vcf public-$releaseLabel.vcf.gz
+
+# Run usher on masked public VCF to collapse tree and get protobuf for usher/hgPhyloPlace:
+time vcfFilter -excludeVcf=mask.vcf public-$releaseLabel.unfiltered.vcf.gz \
+| gzip -c \
+    > public-$releaseLabel.unfiltered.masked.vcf.gz
+time $usher -c -u \
+    -v public-$releaseLabel.unfiltered.masked.vcf.gz \
+    -t ft_SH.reroot.public.nh \
+    -o public-$releaseLabel.masked.pb
+mv uncondensed-final-tree.nh ft_SH.reroot.collapsed.public-$releaseLabel.nwk
+
+# Parsimony scores on collapsed tree
+time $find_parsimonious_assignments --tree ft_SH.reroot.collapsed.public-$releaseLabel.nwk \
+    --vcf <(gunzip -c public-$releaseLabel.vcf.gz) \
+| tail -n+2 \
+| sed -re 's/^[A-Z]([0-9]+)[A-Z,]+.*parsimony_score=([0-9]+).*/\1\t\2/;' \
+| tawk '{print "NC_045512v2", $1-1, $1, $2;}' \
+| sort -k2n,2n \
+    > public-$releaseLabel.parsimony.bg
+bedGraphToBigWig public-$releaseLabel.parsimony.bg /hive/data/genomes/wuhCor1/chrom.sizes \
+    public-$releaseLabel.parsimony.bw
+
+# Make allele-frequency-filtered versions
+# Disregard pipefail just for this pipe because head prevents the cat from completing:
+set +o pipefail
+sampleCount=$(zcat public-$releaseLabel.vcf.gz | head | grep ^#CHROM | sed -re 's/\t/\n/g' \
+              | tail -n+10 | wc -l)
+set -o pipefail
+minAc001=$(( (($sampleCount + 999) / 1000) ))
+vcfFilter -minAc=$minAc001 -rename public-$releaseLabel.vcf.gz \
+    > public-$releaseLabel.minAf.001.vcf
+wc -l public-$releaseLabel.minAf.001.vcf
+bgzip -f public-$releaseLabel.minAf.001.vcf
+tabix -p vcf public-$releaseLabel.minAf.001.vcf.gz
+
+minAc01=$(( (($sampleCount + 99) / 100) ))
+vcfFilter -minAc=$minAc01 -rename public-$releaseLabel.minAf.001.vcf.gz \
+    > public-$releaseLabel.minAf.01.vcf
+wc -l public-$releaseLabel.minAf.01.vcf
+bgzip -f public-$releaseLabel.minAf.01.vcf
+tabix -p vcf public-$releaseLabel.minAf.01.vcf.gz
+
+# And the lineage colors:
+# TODO: add Nextstrain clade colors
+for source in gisaid lineage nextstrain; do
+    Source=${source^}
+    zcat ${source}Colors.gz \
+    | subColumn -miss=/dev/null 1 stdin treeToPublic stdout \
+    | grep -v EPI_ISL > public${Source}Colors
+    wc -l public${Source}Colors
+    gzip -f public${Source}Colors
+done