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Commits on Jul 25, 2026

• fix emit DEL from off-reference graph nodes

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Commits on Apr 12, 2026

• bumping version 2.3.0.dev2 to include vcf on alternative branches with respect to consensus

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• fix ref tracking for off-field snp/indels

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Commits on Apr 10, 2026

• updating development version after upstream version bump to 2.2.0

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• Merge branch 'main' into feat/vcf

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• Merge branch 'main' of https://github.com/fawaz-dabbaghieh/PanPA

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Commits on Apr 9, 2026

• updating the version

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Commits on Apr 5, 2026

• fix undefined ancestor_node and cur_node

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Commits on Apr 4, 2026

• adding vcf to single_align

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Commits on Mar 26, 2026

• Adding multiple sequence alignment position for each Node object: at `graph_from_msa.pyx`.

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• bump version to development for variant calling feature

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Commits on Mar 25, 2026

• Merge branch 'main' of https://github.com/kalininalab/PanPA-Variants

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Commits on Feb 26, 2026

• now works with up to python3.13 and some other fixes

  fawaz-dabbaghieh

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• removing the reverse_complement_fast.c and keeping the .cpp one

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• should work with more Python and cython versions, also added the compiled cython scripts, so users don't need cython to compile PanPA, which make installation much easier for the user

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Commits on Feb 2, 2025

• fixing a small bug related to python version and the commented out line in the setup file

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Commits on Nov 29, 2024

• Initial commit

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Commits on Nov 16, 2024

• adding metagraph experiment scripts

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Commits on Nov 12, 2024

• updating the version for a new tag

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• regressing setuptool version back to 45.2, the newer versions are causing some error

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• adding project.toml and adding tag for new version

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• updating version

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• fixing a small problem in outout GAF

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Commits on Oct 23, 2024

• removed forgotted debugging prints

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Commits on Oct 22, 2024

• Update _main.pyx

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Commits on Sep 23, 2024

• Merge branch 'main' of github.com:fawaz-dabbaghieh/PanPA

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• updating version and fixing a couple of bugs in indexing and buildling GFAs

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Commits on May 23, 2024

• Update _main.pyx

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Commits on Feb 9, 2024

• removing redundant data

  fawaz-dabbaghieh

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Commits on Dec 12, 2023

• Update README.md

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• adding accession numbers

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Commits on Dec 1, 2023

• addig the excel file with all the accession numbers for the data used in the paper

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Commits on Sep 12, 2023

• fixing the added tag to GAF to match the sam description of a tag

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Commits on Jul 21, 2023

• updating README

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• fixing a small problem with reading graphs, it was only assuming there are forward direction edges, now it only takes the forward direction because the assumption is that these graphs are DAGs

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