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1. Commits on Nov 13, 2025

   • reverted a049f69 for a proper fix

     gpertea

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2. Commits on Nov 11, 2025

   • fix a rare crash when reads are not grouped as expected

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   • likely fix for a --mix crash in #465

     gpertea

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3. Commits on Nov 10, 2025

   • prevent guide tx output duplication in `-e` mode

     gpertea

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   • fixed duplicate guides printing in mergeMode (#493)

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4. 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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   • updated tests for v3.0.2 polyA changes, changed test data repo

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5. Commits on Oct 5, 2025

   • long read infinite loop fix for Ida`s patch

     gpertea

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6. Commits on Sep 27, 2025

   • Poly verbose v2 (#4)

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     ishinder

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7. Commits on Sep 24, 2025

   • Feature/tts poly a graph (#3)

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     ishinder

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8. Commits on Aug 22, 2025

   • restored debug/dev comment blocks

     gpertea

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9. Commits on Aug 10, 2025

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

     gpertea

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10. Commits on Apr 27, 2025

    • prevent printing of nascents in -e -N mode (#470)

      gpertea

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

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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

      gpertea

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    • OvlTracker implemented, tests passing, incl. valgrind

      gpertea

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14. Commits on Apr 19, 2024

    • wip: switching to OvlTracker instead of GVec<bool>

      gpertea

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    • adding OvlTracker class for triangular matrix tracking of overlaps

      gpertea

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15. Commits on Oct 6, 2023

    • fixed out of bounds error for sparsely covered guides

      mpertea

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16. Commits on Feb 9, 2023

    • fix rare crash in merge_read_to_group() addressing #389

      gpertea

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17. Commits on Jul 24, 2022

    • reverse & remove !eonly condition in print_predcluster L 17039

      gpertea

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18. Commits on Jun 13, 2022

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

      gsatas

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19. Commits on Mar 4, 2022

    • another take at preventing hanging terminal introns

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20. Commits on Mar 3, 2022

    • ignoring terminal hanging introns, addressing issue #356

      gpertea

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21. Commits on Jan 28, 2022

    • note about a desired jcov metric in print_predcluster()

      gpertea

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22. Commits on Jan 26, 2022

    • revert previous cov<1 check to only apply when !eonly

      gpertea

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23. Commits on Jan 25, 2022

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

      gpertea

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24. Commits on Oct 25, 2021

    • mix-merge sync: improve transcriptome assembly on mixed data w/ annotation, small exon correction

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25. Commits on Sep 16, 2021

    • fixed CRAM fidelity issue, --ref/cram-ref option added

      gpertea

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26. Commits on Sep 15, 2021

    • debugging inconsistent output vs samtools pipe

      gpertea

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27. Commits on Jun 25, 2021

    • added libbz2 build; merged mix-merge childonpath fix

      gpertea

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28. Commits on Jun 17, 2021

    • build ok, needs testing

      gpertea

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29. Commits on May 30, 2021

    • another try to rlink.cpp dealing with deletion around introns

      

      Mihaela Pertea

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