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Commits on Nov 17, 2025

• Fix gdtools APPLY of mut within INS within INV

  jeffreybarrick

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• Added default strand for ISEScan ingestion

  jeffreybarrick

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  719867c

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Commits on Jul 13, 2025

• Fixed problem introduced in multi-FASTA parsing

  jeffreybarrick

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  9473b6e

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• Fixed issue with alignment splicing when trimming extended to end

  jeffreybarrick

  committed
  a39cca3

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Commits on Jul 6, 2025

• Fixed reading in last line of FASTA that does not have a carriage return

  jeffreybarrick

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Commits on Jun 14, 2025

• Fixed alignment slice display for JC; Removed _ref_seq field that broke rentry; Removed unlinked HTML file generation.

  jeffreybarrick

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Commits on Jun 10, 2025

• Further fix for long-read CIGAR shifts

  jeffreybarrick

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Commits on Jun 8, 2025

• Updated --version to include GitHub revision if working from repository version

  jeffreybarrick

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Commits on Jun 6, 2025

• Finished new slim alignment output; updated test

  jeffreybarrick

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• Checkpoint for allowing slices of alignments to be shown and fixes for minimap2 alignments

  jeffreybarrick

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Commits on Jun 5, 2025

• Restored --repeat-header option for COMPARE

  jeffreybarrick

  committed
  9a4991c

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Commits on May 18, 2025

• Fixes for complex apply cases involving INVs and IS-mediated AMPs

  jeffreybarrick

  committed
  dcb5b46

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Commits on Apr 7, 2025

• Fixed stale feature_ptr after erase in applying INV

  jeffreybarrick

  committed
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Commits on Mar 15, 2025

• Already-applied mutation positions no longer generate errors and are re-updated; condensed adjacent/between duplicate warnings

  jeffreybarrick

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  5b9f2b1

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Commits on Mar 7, 2025

• Updated description of inactivated_genes and refactored code to make cases clearer

  jeffreybarrick

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  aed9449

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• Updated calling inactivated_genes for in-frame small INS/DEL/SUB, including looking for stop codons formed as a result of the mutation

  jeffreybarrick

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Commits on Feb 1, 2025

• Merge branch 'sgsCS-interactive-output'

  jeffreybarrick

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• Integrate list.js search box from ancient pull request; removed repeat header lie option

  jeffreybarrick

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Commits on Jan 30, 2025

• Added notes for further development

  jeffreybarrick

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  07fb7f4

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• Merge

  jeffreybarrick

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  789c7d4

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• Update to current code

  jeffreybarrick

  committed
  92b2b1f

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• Merge pull request #390 from meono/pseudo-patch

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  jeffreybarrick

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Commits on Jan 3, 2025

• fix: "pseudo" is also used in refseq gff annotations.

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  meono

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Commits on Jan 1, 2025

• Fixed APPLY of nested withins for LTEE curation

  jeffreybarrick

  committed
  c26eb1c

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Commits on Oct 31, 2024

• More updates to compile/developer directions.

  jeffreybarrick

  committed
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Commits on Oct 29, 2024

• Fixed local compile zlib issues

  jeffreybarrick

  committed
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• Updates for compiling universal binary on MacOSX and static linking to libz

  jeffreybarrick

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  36f40ce

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• Updated nanopore option name to clarify it is for datasets that use fast basecalling

  jeffreybarrick

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Commits on Oct 22, 2024

• Updated to allow true libz static linking for MacOSX binary

  jeffreybarrick

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  55cdc98

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• Fixed typo

  jeffreybarrick

  committed
  ab36f8a

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Commits on Aug 20, 2024

• Fixes for compare of GD files with INT, begin allowing hard-clipping in input SAM, typos

  jeffreybarrick

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Commits on Jul 10, 2024

• Merge branch 'master' of https://github.com/barricklab/breseq

  jeffreybarrick

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  e3d5b9e

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• Minor fixes to ChangeLog

  jeffreybarrick

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  c281aa1

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• Update README.md

  jeffreybarrick

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• Bump to 0.39.0

  jeffreybarrick

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