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pack_reference.sh: reject an empty reference file, not just a missing one #83

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pack_reference.sh: reject an empty reference file, not just a missing one #83

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6 changes: 6 additions & 0 deletions scripts/pack_reference.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,12 @@ echo "wrote $OUT ($(du -h "$OUT" | cut -f1)); $(grep -c . <<<"$members") members
for org in human mouse rat rabbit rhesus_monkey; do
for f in alleles.fasta alleles.aa.fasta markup.tsv markup.aa.tsv cdr3_anchors.tsv; do
grep -q "^vdj/$org/$f\$" <<<"$members" || { echo "ERROR: vdj/$org/$f missing"; exit 1; }
# Present is not enough: a build-db run without IgBLAST emits 0-byte alleles/markup, which pass
# the presence check, ship, and then crash every fresh install with `NoDataError: empty CSV`.
# (v2.5.7 shipped exactly this.) The smallest real file is rat/cdr3_anchors.tsv at ~24 KB, so a
# 1 KB floor catches empty without ever tripping on a valid small-repertoire organism.
sz=$(tar -xzf "$OUT" -O "vdj/$org/$f" | wc -c)
[ "$sz" -gt 1000 ] || { echo "ERROR: vdj/$org/$f is empty ($sz B) -- was build-db run without IgBLAST?"; exit 1; }
done
done
# D germlines exist only for organisms with a D locus; d_prior only where a model was published.
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