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base repository: TransDecoder/TransDecoder
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head repository: TransDecoder/TransDecoder
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compare: devel
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  • 3 commits
  • 4 files changed
  • 3 contributors

Commits on Mar 22, 2026

  1. Add BED output for genome-propagated ORFs

    @brianjohnhaas
    brianjohnhaas committed Mar 22, 2026
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Commits on Oct 20, 2026

  1. Merge devel (genome-mode BED output) into the development line 

    Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
    @brianjohnhaas @claude
    brianjohnhaas and claude committed Oct 20, 2026
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  2. GC content from G+C counts for long-ORF retention; deterministic tie-… 

    …break in ORF selection

- TransDecoder.Predict: transcriptome GC for the dynamic long-ORF threshold is computed from the
  G and C counts in base_freqs.dat (was 2 x freq(C), wrong for stranded transcripts)
- select_best_ORFs_per_transcript.pl: ORFs tied on homology, score and length are ordered by
  position (leftmost, then plus strand)

With these, Perl and PyTransDecoder predictions are identical on all 84 benchmark inputs.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
    @brianjohnhaas @claude
    brianjohnhaas and claude committed Oct 20, 2026
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