Add GTF tabix adapter, inline GTF parser#5577
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GFF3: bump to gff-nostream@3.0.10, which fixes multi-segment CDS sharing one ID being dropped after the first segment. Add regression fixtures and tests (plain + tabix) for the discontinuous-feature idiom, which the existing Parent-only volvox data never exercised. GTF: replace the heavyweight gtf-nostream dependency with an inlined parseGtf (parse + transcript_id grouping). Synthesized transcripts no longer leak the first CDS child's reading frame. Add GtfTabixAdapter (redispatch off spanning transcript/gene lines), a shared aggregateGtfFeatures helper, consistent attribute quote stripping, and route .gtf.gz through the tabix adapter. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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…ingTie/UCSC demos Remove volvox.sorted.gtf (bare exon/CDS, no spanning lines) from web/plugin/cli test data and its volvox demo track. Add small real-format GTF excerpts of the same TP53 hg19 model in four tool conventions, as config_demo.json tracks: GENCODE and StringTie via GtfTabixAdapter (gene_name aggregation), AUGUSTUS via GtfTabixAdapter (gene_id; redispatches off its spanning gene/transcript lines), and UCSC genePredToGtf via the in-memory GtfAdapter (bare, so no tabix redispatch anchor; gene_id). aggregateGtfFeatures now also drops childless transcripts, e.g. AUGUSTUS's bare `transcript` line whose 9th column has no parseable attributes. Repoint the plugin and CLI GTF tests at a real GENCODE excerpt. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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GTF: replace the heavyweight gtf-nostream dependency with an inlined parseGtf (parse + transcript_id grouping). Synthesized transcripts no longer leak the first CDS child's reading frame. Add GtfTabixAdapter (redispatch off spanning transcript/gene lines), a shared aggregateGtfFeatures helper, consistent attribute quote stripping, and route .gtf.gz through the tabix adapter.
also fixes a non-released (e.g. mainline only) gff-nostream regression