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1. Commits on Oct 20, 2026

   • GC content over A/C/G/T only, no length-based retention above 80% GC, deterministic ORF tie-break

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   • genome-map: also write BED12 of the genome-coordinate ORFs

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   • Read FASTA through one helper that skips text before the first header

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   • Start refinement scores with the Kozak model as written (3 decimals), as Perl does

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   • LongOrfs: default minimum protein length 50 aa (short ORFs pass Predict's frame-contrast test)

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   • Predict: short ORFs (< --short-orf-length codons) need frame contrast >= --short-orf-min-contrast

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   • Start refinement: Kozak evidence enters the keep-or-trim cutoff additively

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   • Native genome propagation of ORFs (genome-map); transcript-level GFF3/BED as in Perl TransDecoder

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2. Commits on Oct 19, 2026

   • Kozak model in its own module, with a counts table and a sequence logo

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   • Start refinement: Kozak context of the first ATG joins frame contrast in the keep-or-trim decision

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   • Report one ORF per transcript by default, chosen by homology then coding score

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   • Start refinement: trim open 5' ends into UTRs by frame contrast; length auto-accept only for TAA/TAG/TGA codes

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3. Commits on Oct 18, 2026

   • Skip start refinement when there are too few start-site training features

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4. Commits on Oct 17, 2026

   • Long-ORF retention thresholds from a regenerated random-sequence simulation

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   • Exclude the terminal stop of the selected genetic code from Markov training and scoring

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   • Genetic codes: correct Mesodinium/Peritrich tables and accept the Perl code names

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   • Select among ORF (mRNA) records only

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   • Order and number ORFs within a transcript as LongOrfs does

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   • Count the implicit 3' stop toward the minimum ORF length, as LongOrfs does

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   • Order equal-length training candidates as the Perl pipeline does

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   • Use observed base composition as the Markov background model

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   • Start refinement: score candidates on the same window and scale used to train the threshold

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5. Commits on Mar 20, 2026

   • Fix ORF boundary and peptide stop-codon parity

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   • adding pasa assemblies test starting from GTF

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   • Add TransDecoder-style metadata to final peptide headers

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6. Commits on Mar 19, 2026

   • Fix final GFF3 output to include gene/exon/CDS hierarchy for genome propagation

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   • Add pyTransdecoder pipeline entry point with full pipeline orchestration

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7. Commits on Mar 15, 2026

   • Implement PWM-based start refinement

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8. Commits on Jan 24, 2026

   • Fix critical bug: strand-independent overlap checking

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   • Add homology-first overlap handling and document Perl/Python differences

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   • Add CLI support for gene_trans_map and fix output directory

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   • Fix coordinate boundary handling in Phase 2

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   • Replace Click with argparse for CLI compatibility

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   • Complete Phase 2 implementation and fix critical bugs

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   • Fix ORF length calculation for implicit 3' stops

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