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1. Commits on Mar 20, 2026

   • setting version 6.0.0

     brianjohnhaas

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2. Commits on Sep 13, 2023

   • Fix some test paths

     mr-c

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3. Commits on Jul 16, 2023

   • add test docker

     brianjohnhaas

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   • update for docker test

     brianjohnhaas

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   • rigorous definition around workdir based on output directory, needed for docker

     brianjohnhaas

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4. Commits on Jan 27, 2023

   • include --use_complete_orfs in TransDecoder.LongOrfs to avoid partials and internals

     brianjohnhaas

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   • turned of uri encoding of names by default

     brianjohnhaas

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   • support both hmmscan or hmmsearch formatting

     brianjohnhaas

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   • update

     brianjohnhaas

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   • some cleanup

     brianjohnhaas

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5. Commits on Oct 22, 2018

   • added option --output_dir | -O to both TransDecoder.LongOrfs and TransDecoder.Predict, as per request, so users can point to specific output directories rather than relying on the default ( basena…

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     brianjohnhaas

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6. Commits on May 11, 2018

   • cleanup

     brianjohnhaas

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   • more cleanup

     brianjohnhaas

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   • better cleanup in sample area

     brianjohnhaas

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7. Commits on Apr 27, 2018

   • echo done

     brianjohnhaas

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   • support gene-gtf format for final outputs

     brianjohnhaas

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8. Commits on Apr 21, 2018

   • cleanup

     brianjohnhaas

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9. Commits on Apr 18, 2018

   • including pfam and blast as part of the test run

     brianjohnhaas

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   • adding mini pfam db

     brianjohnhaas

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   • adding mini sprot

     brianjohnhaas

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   • pullmerge

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     brianjohnhaas

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   • removing old blast results

     brianjohnhaas

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   • allowing for rerun of prediction part w/ pfam or blast data

     brianjohnhaas

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10. Commits on Oct 13, 2017

    • additional validation of called orfs, looking for in-frame stops

      brianjohnhaas

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11. Commits on Oct 12, 2017

    • update

      brianjohnhaas

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    • added supertranscripts

      brianjohnhaas

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    • add

      brianjohnhaas

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    • add

      brianjohnhaas

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    • removed cufflinks from names

      brianjohnhaas

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12. Commits on Sep 8, 2017

    • included support for gmap-aligned transcripts

      brianjohnhaas

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13. Commits on Jul 29, 2017

    • updated tests

      brianjohnhaas

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14. Commits on Jul 8, 2017

    • improved resume mode

      brianjohnhaas

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15. Commits on Apr 21, 2017

    • include stringtie example

      brianjohnhaas

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    • add stringtie example

      brianjohnhaas

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16. Commits on Apr 26, 2016

    • autotesting

      brianjohnhaas

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