pangolin v3.1.14

Release notes

• Addressing issues #315 and #316, handling commas in the sequence ids.

pangolin v3.1.13

## Release notes

• Env name issue #314 fix

pangolin v3.1.12

Release notes

• Fix for snakemake update that was breaking path handling in issue #313.

pangolin v3.1.11

Release notes

• Merge @pvanheus PR additional testing logic (pytests)
• Ensure datadir is an absolute path
• Logic for model decompression flag fixed (issue #291)
• All versions flag by @fmaguire (issue #290)

pangolin v3.1.10

• Extend the false positive removal so will apply to new AY.x sublineages where the parent is a voc/vui but the lineage itself is not, but we still want to have confirmation from scorpio.
• Add developer option to skip designation hash

pangolin v3.1.9

Use scorpio to remove false positive VOC/VUI calls:

• if there is a constellation definition for a lineage, checks if scorpio also calls that lineage. If no call by scorpio, removes the pangolin lineage assignment as probably false positive.

pangolin v3.1.8

Adds support for --update-data downloading updates to --datadir. This is to support environments where pangolin does not have permission to write to its own install directories (such as HPCs or when pangolin is run from a Singularity container).

It also moves the code that looks for pangoLEARN, constellations and pango_designation files up in the file so that this searching is all done before any calls to update() etc.

Includes changes started in PR #282 with fixes to issue #283

pangolin v3.1.7

Bug fix for #274

pangolin v3.1.6

Add --list-incompatible flag to scorpio command, and process the results downstream.
Resolves the problem of over-assigning AY.1 lineages and more generally provides a way to check against VOC/VUI plus lineage assignments.
Requires an update to scorpio.

pangolin v3.1.5

Release notes

• --pangolin flag to scorpio call to call mrca instead of replacing the field with constellation
• Requires scorpio version v0.3.4 or later