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Restore gene and transcript metadata without opening annotation files - #436
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coverage: 92.106% (+0.04%) from 92.07% — fix/435-lazy-locus-database into main |
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Restoring a Gene or Transcript from complete locus metadata currently opens the annotation database immediately. A missing original GTF consequently blocks metadata-only deserialization and downstream Vaxrank policy replay (openvax/vaxrank#563).
Defer database resolution to the existing
dbaccess boundary, with Genome retaining normal cache/index handling and explicit missing-reference errors. Identity, coordinates, essential serialization and biological methods remain intact. This does not substitute an annotation or make annotation-dependent operations resource-free.Regression proof: both unavailable-reference constructors failed before the change; metadata round trips now pass and annotation access still fails clearly. An actual supplied GTF exercises restored gene/transcript/exon queries and shared database caching.
./lint.shand./test.shpassed: 527 tests, one existing optional skip, 92% coverage. Version 2.22.2.Closes #435.