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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 May 11, 2018

   • cleanup

     brianjohnhaas

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   • more cleanup

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   • better cleanup in sample area

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3. Commits on Apr 27, 2018

   • echo done

     brianjohnhaas

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   • support gene-gtf format for final outputs

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4. Commits on Apr 21, 2018

   • cleanup

     brianjohnhaas

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5. Commits on Apr 18, 2018

   • including pfam and blast as part of the test run

     brianjohnhaas

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   • adding mini pfam db

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   • adding mini sprot

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   • pullmerge

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   • removing old blast results

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

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6. Commits on Oct 13, 2017

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

     brianjohnhaas

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7. Commits on Oct 12, 2017

   • update

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   • added supertranscripts

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   • add

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   • add

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   • removed cufflinks from names

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8. Commits on Sep 8, 2017

   • included support for gmap-aligned transcripts

     brianjohnhaas

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9. Commits on Jul 29, 2017

   • updated tests

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10. Commits on Jul 8, 2017

    • improved resume mode

      brianjohnhaas

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11. Commits on Apr 21, 2017

    • include stringtie example

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    • add stringtie example

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12. Commits on Apr 26, 2016

    • autotesting

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    • adding autorun

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    • update, improved reporting

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    • prioritize according to model len not gene len

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    • use pfam and blast by default in example

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    • adding precomputed blast and pfam here

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    • additional reporting of kept cats

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    • include pasa gene-to-trans mapping

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    • updating pasa assembly test

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    • include phasing info, allow for single best orf

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13. Commits on Apr 23, 2016

    • Make the sample data reproducible

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      mr-c

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