feat: splice-junction-DB / GTF annotation config (chr_start_end TSV, gene name/type tags) - #127
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BenjaminDEMAILLE wants to merge 2 commits into
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feat: splice-junction-DB / GTF annotation config (chr_start_end TSV, gene name/type tags)#127BenjaminDEMAILLE wants to merge 2 commits into
BenjaminDEMAILLE wants to merge 2 commits into
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Parses chr/start/end/[strand] TSV files (1-based intron first/last base) into the same raw junction shape produced by GTF parsing, and unions them with any --sjdbGTFfile junctions before sjdb insertion into the genome/SA. Works standalone (no GTF): junction_db and the sjdb files are built whenever the union is non-empty; only the transcriptome index requires a GTF. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Makes the GTF attribute keys for gene name/biotype configurable (multi-candidate, last-match-in-list wins, matching STAR's find_attr_list), and fixes a latent gap where the hardcoded lookup only ever checked gene_biotype: GENCODE-style GTFs using gene_type fell back to the literal "MissingGeneType" even though STAR's default candidate list (gene_type, gene_biotype) would have picked it up. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
This was referenced Jul 24, 2026
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Summary
Groups the splice-junction-DB / GTF-annotation config knobs into one themed PR (2 commits, supersedes #122 and #124):
--sjdbFileChrStartEnd: explicit junction TSV file(s), independent of (and unionable with) a GTF's derived junctions.--sjdbGTFtagExonParentGeneName/--sjdbGTFtagExonParentGeneType: configurable candidate attribute-key lists for gene name/biotype, with STAR's "last match in list wins" semantics. Bundled fix: rustar-aligner previously only checkedgene_biotype, nevergene_type, so GENCODE-style GTFs silently fell back toMissingGeneType; the new default candidate list checks both.Test plan
cargo fmt --checkcargo clippy --workspace --all-targets -- -D warnings(0 warnings)cargo test --workspace(462 passed)genomeGeneratewith only--sjdbFileChrStartEnd(no GTF) round-trips throughsjdbList.out.tab; a GTF using onlygene_type "lncRNA"now correctly populatesgeneInfo.tabinstead ofMissingGeneType