pangolin v4.3.1

Patch update to resolve snakemake dependency issue #525. Required update to env file, pinning of snakemake-minimal version to 7.24.0 and update to github actions to pass tests. Later versions of snakemake-minimal would not solve in github actions.

pangolin v4.3

• pangoLEARN analysis mode is now deprecated due to lack of resources for updating the pangoLEARN model. If --analysis-mode fast or --analysis-mode pangolearn is given, pangolin v4.3 will print out a warning and use UShER mode instead, unless --datadir is also given specifying a directory with pangoLEARN model files. The next release of pangolin-data (v1.20) will no longer include the model files which have not been updated since v1.18). (PR #519)

• In UShER mode, in the case of multiple equally parsimony-optimal placements (EPPs), the lineage with the most EPPs will no longer override UShER's selected lineage. This "voting" logic was problematic in the case of amplicon dropout (e.g. issue #492). (PR #521)

• dependencies: snakemake-minimal is no longer pinned to <=6.8.0 and tabulate is no longer pinned to 0.8.10. (PR #514)

pangolin v4.2

Significant speed improvement for the default UShER analysis mode when running on a large number of input sequences, if the latest version of usher (v0.6.1 or later) is installed (PR #499: Use usher-sampled if installed).

pangolin v4.1.3

Patch to pin tabulate version described in issue #489.

pangolin v4.1.2

• merging PR #474
• --all-versions flag now also has faToVcf version

pangolin v4.1.1

Patch to fix --all-versions flag. Everything bar faToVcf now reported, will need faToVcf to have --version flag for this approach to be compatible.

pangolin v4.1

• Major change: In usher mode, run scorpio and report conflicts but don't override the usher call, in pangoLEARN mode continue to overwrite the call.
• Allow assignment cache to be saved to and loaded from datadir issue #444

pangolin v4.0.6

Fix for #432, from PR by pcjentsch (Thank you!). New version now can stream various compressed file types without having to write out the file.

pangolin v4.0.5

• Check draft and prerelease flags to get latest stable release.
• Tempdir bug caught from issue #419

pangolin v4.0.4

Release notes

• --no-temp issue flagged in issue #419, only when pipeline otherwise fails.
• Issue #420 fix by reording print outs in cmd script.