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Commits on Nov 4, 2022

• Revert "Add entries for pangolin-data/-assignment 1.16 (cov-lineages#494)" (cov-lineages#495)

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• Add entries for pangolin-data/-assignment 1.16 (cov-lineages#494)

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Commits on Oct 11, 2022

• Merge pull request cov-lineages#491 from cov-lineages/tabulate-fix

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  aineniamh

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• fixing init conflict

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• pin tabulate number

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• Add entries for pangolin-data/-assignment 1.15.1 (cov-lineages#488) (cov-lineages#490)

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Commits on Sep 13, 2022

• Add entries for pangolin-data/-assignment 1.14 (cov-lineages#483) (cov-lineages#486)

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Commits on Aug 10, 2022

• Add entries for pangolin-data/-assignment 1.13 (cov-lineages#479) (cov-lineages#480)

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Commits on Jul 18, 2022

• Add entry for pangolin-data / -assignment 1.12 (cov-lineages#476)

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Commits on Jul 14, 2022

• Update __init__.py

  aineniamh

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• Update pangolin.yml

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• Update pangolin.yml

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• Merge pull request cov-lineages#475 from cov-lineages/all_version_dev

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Commits on Jul 13, 2022

• Merge pull request cov-lineages#474 from wm75/data-compat-file

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  aineniamh

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• Provide data packages compatibility list

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Commits on Jun 30, 2022

• cov-lineages#467 potential fatovcf version print out

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• Merge pull request cov-lineages#468 from cov-lineages/all_version_dev

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• Update __init__.py

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• fix for all versions

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• cov-lineages#467 test fix, not including faToVcf

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Commits on Jun 29, 2022

• Update __init__.py

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Commits on Jun 15, 2022

• Merge pull request cov-lineages#462 from AngieHinrichs/usher_scorpio_no_override

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• In usher mode, run scorpio and report conflicts but don't override the usher call.

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Commits on Jun 14, 2022

• skip scorpio in usher mode (cov-lineages#461)

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Commits on May 7, 2022

• Allow assignment cache to be saved to and loaded from datadir (cov-lineages#444)

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Commits on May 4, 2022

• Merge pull request cov-lineages#442 from AngieHinrichs/master

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• Bump minimum usher version to 0.5.4 to get recent bugfix.

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Commits on Apr 29, 2022

• Merge pull request cov-lineages#440 from AngieHinrichs/moreVersions

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Commits on Apr 28, 2022

• Fixing usage of subprocess.CalledProcessError, noticed while working on initialising.py's print_conda_version.

  AngieHinrichs

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• Extend pangolin --all-versions to report conda versions of important dependencies.

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  AngieHinrichs

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Commits on Apr 20, 2022

• Update __init__.py

  aineniamh

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• Merge pull request cov-lineages#436 from pcjentsch/fix-compressed-input

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Commits on Apr 18, 2022

• change < to cat

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• change xz to be singlethreaded, reduce code duplication

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• add compression_type tag, commands to pipe from xz and gz in preprocessing.smk, and support for xz in merge_files

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