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1. Commits on Mar 20, 2026

   • added note to streamline in the future

     brianjohnhaas

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   • updated pasa example for streamlined approach

     brianjohnhaas

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   • adding pasa assemblies test starting from GTF

     brianjohnhaas

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   • Run cufflinks example via pyTransdecoder driver

     brianjohnhaas

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   • Streamline stringtie example around pyTransdecoder

     brianjohnhaas

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   • revised stringtie example for streamlined approach

     brianjohnhaas

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2. Commits on Jan 24, 2026

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

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     brianjohnhaas

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   • Add CLI support for gene_trans_map and fix output directory

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     brianjohnhaas

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   • Fix coordinate boundary handling in Phase 2

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     brianjohnhaas

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   • Make PyTransDecoder self-contained: add util/ directory

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     brianjohnhaas

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   • Add sample_data test compatibility

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     brianjohnhaas

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   • Complete Phase 2 implementation and fix critical bugs

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     brianjohnhaas

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   • Fix ORF length calculation for implicit 3' stops

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     brianjohnhaas

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   • Fix ORF finding algorithm to match Perl exactly

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     brianjohnhaas

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