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1. Commits on Nov 11, 2025

   • bump version to 3.0.3

     gpertea

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2. Commits on Nov 10, 2025

   • fixed duplicate guides printing in mergeMode (#493)

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3. Commits on Oct 9, 2025

   • fix: -e sometimes losing track of 0-cov tx; may fix #238, #434, #451, #484

     gpertea

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4. Commits on Sep 27, 2025

   • Poly verbose v2 (#4)

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     ishinder

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5. Commits on Sep 24, 2025

   • Feature/tts poly a graph (#3)

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     ishinder

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6. Commits on Aug 22, 2025

   • restored debug/dev comment blocks

     gpertea

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7. Commits on Aug 10, 2025

   • clean-up old code, adding self-contained source package

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8. Commits on Jul 27, 2025

   • Fix: correct validation for -s (singlethr) parameter

     

     Martin Smith

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9. Commits on Apr 27, 2025

   • partial fix for #253, but -e -N still prints nascents though it should not

     gpertea

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10. Commits on Mar 17, 2025

    • updated htslib to upstream 1.21 to support newer CRAM files as input

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11. Commits on Jan 6, 2025

    • merged v3.0.0 changes

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12. Commits on May 6, 2024

    • backport LR fix from dev-2.2.3

      gpertea

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13. Commits on Apr 20, 2024

    • patchfix release 2.2.2

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14. Commits on Oct 6, 2023

    • fixed out of bounds error for sparsely covered guides

      mpertea

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15. Commits on Jun 13, 2022

    • fix #348 . Adds mutex to manage concurrent writing to covered reference transcript file

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16. Commits on Mar 3, 2022

    • ignoring terminal hanging introns, addressing issue #356

      gpertea

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17. Commits on Jan 25, 2022

    • ver bump to 2.2.1, test output included in distribution

      gpertea

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    • fixed bug that forced a hardcoded >=1 coverage output threshold

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18. Commits on Jan 10, 2022

    • addressing PTF loading bug reported in #347

      gpertea

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19. Commits on Dec 4, 2021

    • version bump to 2.2.0

      gpertea

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20. Commits on Nov 5, 2021

    • merging htslib

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21. Commits on Jun 25, 2021

    • fixed bug in fwd_to_sink_fast_long and back_to_source_fast_long deleting nodes from pathpat

      gpertea

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22. Commits on Jun 19, 2021

    • --merge works, transition to htslib completed

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23. Commits on Jun 17, 2021

    • build ok, needs testing

      gpertea

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24. Commits on Jun 14, 2021

    • fixed --mix bug

      gpertea

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25. Commits on Jun 4, 2021

    • merged mix-merge branch

      gpertea

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26. Commits on May 28, 2021

    • reverted intron+deletion fix

      gpertea

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    • v2.1.5b

      gpertea

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27. Commits on Apr 18, 2021

    • modified stringtie to see tiebrush YC tag

      

      Mihaela Pertea

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28. Commits on Mar 9, 2021

    • exiting transfrag fix

      

      Mihaela Pertea

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29. Commits on Mar 7, 2021

    • cds work in progress, load_cds_param done

      

      Mihaela Pertea

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30. Commits on Mar 5, 2021

    • v2.1.5 fix: adjust coverage estimation for long reads

      gpertea

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31. Commits on Feb 19, 2021

    • switching to new gclib GHashMap

      gpertea

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32. Commits on Jan 2, 2021

    • mix mode branch created

      gpertea

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33. Commits on Aug 25, 2020

    • shorten sleep duration while waiting for threads

      gpertea

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