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1. 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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2. Commits on Oct 16, 2018

   • prep for release 5.4.0

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3. Commits on Aug 26, 2018

   • removed mention of --train

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4. Commits on May 11, 2018

   • back to devel mode

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   • release v5.3.0

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5. Commits on Apr 21, 2018

   • back to devel

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6. Commits on Apr 19, 2018

   • revised pipeliner and checkpointing system

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7. Commits on Apr 18, 2018

   • Release v5.2.0

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   • sync w/ latest devel

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8. Commits on Mar 27, 2018

   • always run the full final selection routines, no checkpointing

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   • release v5.1.0

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   • adding version tags

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   • improved support for genetic codes

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9. Commits on Oct 20, 2017

   • work w/ gzipped target fasta file

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10. Commits on Aug 25, 2017

    • removed --all_good_orfs option, retaining --single_best_only, and by default, reporting all good orfs that are minimally overlapping

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11. Commits on Aug 24, 2017

    • selection logic now consolidated and outside the pipe runner

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12. Commits on Aug 17, 2017

    • update to changelog inprep for v4.1 release

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    • turning off length-based auto-select

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    • update - use delim parser module to ensure proper column extraction

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    • bugfix related to new format of scores file

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13. Commits on Aug 16, 2017

    • --retain_long_orfs_mode now allows strict mode, option processing wasnt configured correctly

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14. Commits on Jul 30, 2017

    • cdhit replacement installed

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15. Commits on Jul 29, 2017

    • updated tests

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16. Commits on Jul 26, 2017

    • removed unlimited mem usage on cd-hit-est step

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    • update

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    • restrict training to coding sequences that are at most 5k long - needed to make the cdhit collapse go leaps and bounds faster

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17. Commits on Jul 8, 2017

    • improved resume mode

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18. Commits on Apr 25, 2017

    • added option --single_allow_score_lt0

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19. Commits on Apr 21, 2017

    • providing a --refine_starts parameter to envoke the new behavior for adjusting 5prime partials based on the PWM

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20. Commits on Apr 8, 2017

    • now includes start codon refinement

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21. Commits on Mar 17, 2017

    • changing functionality of --single_best_orf in Transdecoder.Predict:

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22. Commits on Oct 2, 2016

    • fix typo

      mr-c

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23. Commits on Aug 13, 2016

    • dont require ^/ in path to files found by which

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24. Commits on Jun 30, 2016

    • improved support for alt genetic codes

      brianjohnhaas

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25. Commits on Apr 26, 2016

    • removing the mRNA file as it leads to confusion, and in the multi-orf scenario - leads to a lot of redundancy

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