Medaka

Models, features and fixes release

Fixed
- Fix to methylation aggregation.
Added
- Consensus models for Guppy 3.6.0.
- Add functionality for auto-download of older models.
- VCF annotation tool.

Minor release.

Changed
- Harmonised versions of htslib/samtools dependencies.

Models, features and fixes release

Fixed
- Minor speed improvement.
- Fix bug where force overwrite of output was always enabled.
- Fix bug where variant calling of a region crashed if the region began with a deletion.
Added
- Variant calling models for R10.3 and R9.4.1 and updated benchmarks.
- Consensus models for Guppy 3.5.1.
- Add read group (RG) tag filtering.
- Add option to create consensus sequence via intermediate .vcf file.
- Update to methylation calling documentation.
- Addition of all-context modified-base aggregation.

R10.3 model and small fixes

Fixed
- Fix index/compression issue with RLE workflow
- Fix a rare memory error during feature generation caused by very long indels.
Added
- Add model for R10.3 on MinION.
- Write and empty vcf when no variants are found in medaka_variant.

Bugfix release

Fixed
- Fix invalid specification of variant calling model.

Model release

Added
- Models for guppy 3.4.4.