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1. Commits on Oct 20, 2017

   • work w/ gzipped target fasta file

     brianjohnhaas

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2. 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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3. Commits on Aug 24, 2017

   • selection logic now consolidated and outside the pipe runner

     brianjohnhaas

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4. Commits on Aug 17, 2017

   • update to changelog inprep for v4.1 release

     brianjohnhaas

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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

     brianjohnhaas

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5. Commits on Aug 16, 2017

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

     brianjohnhaas

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6. Commits on Jul 30, 2017

   • cdhit replacement installed

     brianjohnhaas

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7. Commits on Jul 29, 2017

   • updated tests

     brianjohnhaas

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8. Commits on Jul 26, 2017

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

     brianjohnhaas

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   • update

     brianjohnhaas

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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

     brianjohnhaas

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9. Commits on Jul 8, 2017

   • improved resume mode

     brianjohnhaas

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10. Commits on Apr 25, 2017

    • added option --single_allow_score_lt0

      brianjohnhaas

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11. 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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12. Commits on Apr 8, 2017

    • now includes start codon refinement

      brianjohnhaas

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13. Commits on Mar 17, 2017

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

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14. Commits on Oct 2, 2016

    • fix typo

      mr-c

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15. Commits on Aug 13, 2016

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

      brianjohnhaas

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16. Commits on Jun 30, 2016

    • improved support for alt genetic codes

      brianjohnhaas

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17. 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

      brianjohnhaas

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    • update to documentation

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    • prioritize according to model len not gene len

      brianjohnhaas

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    • additional reporting of kept cats

      brianjohnhaas

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    • include phasing info, allow for single best orf

      brianjohnhaas

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18. Commits on Apr 25, 2016

    • cleaner comments and organization

      brianjohnhaas

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19. Commits on Mar 26, 2015

    • ok

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      brianjohnhaas

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    • documentation update

      brianjohnhaas

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20. Commits on Feb 3, 2015

    • multithreaded cd-hit-est

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      macmanes

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21. Commits on Jan 26, 2015

    • update to new format

      brianjohnhaas

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22. Commits on Jan 25, 2015

    • add, initial code revision... still requires fine-tuning to make it work now

      brianjohnhaas

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