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Merged genes: document why counts are summed, add check_merged_genes.py - #128
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Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Compares each merged gene's input genes cell by cell, reading the matrices as build_expression.py does; fails on identical values with expression. Added to the build steps and the FlyBase release issue's commands. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Explains in DESIGN.md's gene-id rules why summing the counts of merged genes is safe here: count pipelines assign each read to at most one gene. vfb-EPseq-ontology (VirtualFlyBrain/vfb-EPseq-ontology#2) works from bulk TPM, where overlapping models get identical rows. There, identical rows count once and merges with differing rows are dropped.
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scripts/check_merged_genes.py(--project/--all). It reads each project's matrices asbuild_expression.pydoes and compares the input genes behind each merged gene cell by cell. It fails on a pair with expression and identical values. It is not in CI, since it needs the matrices in.cache. It is now a build step (DESIGN.md, README) and in the commands of the FlyBase release issue.All 17 projects pass at FB2026_03. No merged pair has identical values in any cell with expression, and the pairs whose models overlap completely (CG30497 / CG45093, stg1 / CG11566) are zero in every cell.
Tests:
tests/test_check_merged_genes.py;test_ci_checks.pyupdated for the issue text.🤖 Generated with Claude Code