Fix gene field alignment in removeLowScoreGenes - #706
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edkerk merged 1 commit intoAug 28, 2026
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Ports the fix from #670 (merged to develop) to develop3, which carried the identical bug in its reworked removeLowScoreGenes. removeLowScoreGenes regenerated model.genes from getGenesFromGrRules, which returns a sorted list, but trimmed the gene-associated fields (geneShortNames, proteins, geneMiriams, geneFrom, geneComps) with a mask in the original gene order. When model.genes was not already sorted, this left every annotation field shifted relative to model.genes, corrupting the gene ID to gene symbol mapping in ftINIT-reconstructed models (removeGenes=true). Retain the remaining genes in their original order and reorder the rxnGeneMat columns to match, so the trimmed annotation fields stay aligned. Reproduced on develop3 with an unsorted-genes model: removing one isozyme gene paired G2->short3 and G3->short2; after the fix G2->short2, G3->short3. Adds removeLowScoreGenesKeepsFieldsAligned to tINIT covering exactly this.
Function test results303 tests 277 ✅ 1m 8s ⏱️ Results for commit 8f6b233. |
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Ports the fix from #670 (merged to
develop) todevelop3, which carried the identical bug in its reworkedremoveLowScoreGenes.removeLowScoreGenesregeneratedmodel.genesfromgetGenesFromGrRules, which returns a sorted list, but trimmed the gene-associated fields (geneShortNames,proteins,geneMiriams,geneFrom,geneComps) with a mask in the original gene order. Whenmodel.geneswas not already sorted, every annotation field ended up shifted relative tomodel.genes, corrupting the gene-ID → gene-symbol mapping in ftINIT-reconstructed models (removeGenes=true).The retained genes are now kept in their original order and the
rxnGeneMatcolumns reordered to match, so the trimmed annotation fields stay aligned.Reproduced on develop3 with an unsorted-genes model: removing one isozyme gene paired
G2 -> short3andG3 -> short2; after the fixG2 -> short2,G3 -> short3. AddsremoveLowScoreGenesKeepsFieldsAlignedto tINIT covering exactly this.