fda84c0982a6c223bde5a3c295890b8ca6189e05
angie
  Fri Aug 26 11:45:28 2022 -0700
When maintaining consistent mappings of duplicated items, make sure the names really match.

diff --git src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
index 88afe9f..296a339 100755
--- src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
+++ src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
@@ -59,36 +59,44 @@
 # Look for duplicate ID swizzles relative to existing ncov-ingest mappings
 cut -f 1,2 epiToPublicAndDate.$today \
 | egrep $'\t''[A-Z][A-Z][0-9]+\.[0-9]+' \
 | sort > latestEpiToGb
 zcat ~angie/github/ncov-ingest/source-data/accessions.tsv.gz \
 | tail -n+2 \
 | tawk '{print $2, $1;}' \
 | sort > ncovEpiToGb
 wc -l latestEpiToGb ncovEpiToGb
 # But allow version updates (e.g. .1 --> .2)
 join -t$'\t' ncovEpiToGb latestEpiToGb \
 | tawk '{ ncovNoDot = substr($2, 0, index($2, ".")-1);
           latestNoDot = substr($3, 0, index($3, ".")-1);
           if (ncovNoDot != latestNoDot) {print $3, $2;} }' \
     > latestToNcov.sub
+# But watch out for name mismatches which indicate bad name matches; get rid of those.
+tawk '{print $1, $1, $2, $2;}' latestToNcov.sub \
+| subColumn -skipMiss 2 stdin <(cut -f 1,6 $ncbiDir/ncbi_dataset.plusBioSample.tsv) stdout \
+| subColumn -skipMiss 4 stdin <(cut -f 1,6 $ncbiDir/ncbi_dataset.plusBioSample.tsv) stdout \
+| tawk '$2 != $4' > latestToNcov.nameMismatch
+grep -vFwf <(cut -f 1 latestToNcov.nameMismatch) latestToNcov.sub > tmp
+mv tmp latestToNcov.sub
+
 subColumn -miss=/dev/null 2 epiToPublicAndDate.$today latestToNcov.sub tmp
 mv tmp epiToPublicAndDate.$today
 
 ln -sf epiToPublicAndDate.$today epiToPublicAndDate.latest
 
 # Now that mapping is updated, add GenBank accessions to 4th column of metadata
 zcat $nextmeta | cut -f 4 | grep ... | wc -l
 set +o pipefail
 zcat $nextmeta | head -1 > tmp
 set -o pipefail
 zcat $nextmeta \
 | tail -n+2 \
 | sort -t $'\t' -k3,3 \
 | join -t$'\t' -a 1 -1 3 - <(tawk '$2 ~ /^[A-Z][A-Z][0-9]+/' epiToPublicAndDate.latest) \
     -o 1.1,1.2,1.3,2.2,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,1.14,1.15,1.16,1.17,1.18,1.19,1.20,1.21,1.22,1.23,1.24,1.25,1.26,1.27 \
 | sort \
     >> tmp
 wc -l tmp
-gzip tmp
+pigz -p 8 tmp
 mv tmp.gz $nextmeta
 zcat $nextmeta | cut -f 4 | grep ... | wc -l