mSWEEP v2.1.0

[tmaklin]

New features

• Allow adjusting zero inflation in the model with the --zero-inflation parameter. The default value is 0.01 which was used in the previous versions.

New experimental features:

• Implement the quality scores that were planned for v2.0.0. These can be enabled with the --run-rate toggle. :heavy_check_mark: (added in https://github.com/PROBIC/mSWEEP/tree/add-dirichlet-KLD-calculation)
• Implement option to ignore reference clusters that have 0 (or a higher number) alignments in the input using the --min-hits flag :heavy_check_mark: (saves memory on sparse inputs) (added in https://github.com/PROBIC/mSWEEP/tree/ignore-empty-groups)

Experimental feature implies that the user interface is not stable and is subject to change.

Enhancements

• Adjust --tol automatically to avoid convergence issues :heavy_check_mark: (resolves #25 and https://github.com/PROBIC/mSWEEP/tree/v2.0.1-dev)

Bugfixes

• Enable compression when reading plaintext alignment :heavy_check_mark: (#24)

Build changes:

• Update build pipeline to no longer require config files. :heavy_check_mark: (added in https://github.com/PROBIC/mSWEEP/tree/remove-config-files)

Continuous integration

• Compile binaries for macOS x86_64 and arm64 :heavy_check_mark: (#26 https://github.com/PROBIC/mSWEEP/tree/cross-compilation-compatibility)
• Github actions to compile binaries automatically. :heavy_check_mark: (added in https://github.com/PROBIC/mSWEEP/tree/add-prebuilt-binaries-CI-workflow)