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AngieHinrichs

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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

• 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 Jun 15, 2022

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

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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.

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

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Commits on Apr 12, 2022

• Merge pull request cov-lineages#429 from AngieHinrichs/filter_prerelease

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• Remove debugging print statement inadvertently committed in 913b81.

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Commits on Apr 11, 2022

• Check draft and prerelease flags to get latest stable release.

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Commits on Apr 6, 2022

• Merge pull request cov-lineages#413 from AngieHinrichs/cacheUnassigned

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• Ignore cache row if lineage is Unassigned (because of QC failure when cache was created). Otherwise, in generate_final_report, scorpio override logic's expanded_pango_lineage.startswith() gets an e…

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Commits on Apr 5, 2022

• Merge pull request cov-lineages#411 from AngieHinrichs/run_git-lfs_install

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• Run 'git-lfs install' before installing pangolin-assignment. fixes cov-lineages#403.

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Commits on Apr 4, 2022

• Merge pull request cov-lineages#404 from hivdb/def/fd/63

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Commits on Mar 31, 2022

• Small fixes to datadir version comparison logic

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• When updating --datadir, remove destination directory if it exists; otherwise, moving the new directory into the existing directory makes a subdirectory, and fails if the subdirectory already exists..

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• Call setup_data before processing --update/--update-data options so that if --datadir is given, versions are taken from datadir instead of conda installation.

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Commits on Mar 30, 2022

• Merge pull request cov-lineages#388 from AngieHinrichs/handle_cache

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• Compare the first two columns of output from 'pangolin pangolin/test/test_seqs.fasta' with expected values.

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• Merge pull request cov-lineages#387 from AngieHinrichs/handle_cache

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• If --usher is passed in, don't allow argparse to interpret it as --usher-tree which expects a filename; instead, print out a message that it is deprecated in v4.

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Commits on Mar 18, 2022

• Merge pull request cov-lineages#384 from AngieHinrichs/handle_cache

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• fix cov-lineages#383: the final else clause in generate_final_report needed to be de-indented after the last change; it was causing lineages to be overwritten with Unassigned unless they were desig…

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Commits on Mar 17, 2022

• Merge pull request cov-lineages#381 from AngieHinrichs/handle_cache_add_scorpio

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• Use the same logic for designation cache and scorpio-overriding for assignment cache results as for inference results.

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Commits on Mar 11, 2022

• Assignment cache: optional install, usher analysis mode only

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Commits on Mar 4, 2022

• Use faToVcf -includeNoAltN (conda ucsc-fatovcf v426)

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Commits on Jul 9, 2021

• Merge pull request cov-lineages#272 from AngieHinrichs/usher_0_3_2

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• Require usher>=0.3.2 to avoid error about using options that did not exist in earlier versions as reported in cov-lineages#266

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Commits on Jun 16, 2021

• Merge pull request cov-lineages#248 from AngieHinrichs/usher_plurality

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