Medaka

Bug fix and feature release

Fixed
Added
- Fix issues in command-line argument parsing.
- Add true ploidy-1 variant caller.
- Do not break contigs at unpolished regions (fill with input instead).
- Add multi-nucleotide variant decomposition to be compatible with DeepVariant.

Bux fix release.

Fixed
- Remove python version check preventing Python >3.6 builds from running.

Update with new models and features.

Fixed
- Fix a few bugs in variant annotation program.
Added
- Add ARM builds to PyPI release.
- Add Python 3.7 and 3.8 builds for x86-64.
- Add PromethION model for Guppy 4.0.11.
Changed
- Upgrade to Tensorflow 2.2.
- Option to split MNPs to independent SNPs (for compatibility with DeepVariant).
- Single molecule consensus program now uses `pyspoa`.
Removed
- Remove methylation aggregation functionality.

Minor fixes release.

Fixed
- Fix occasional mangled sam output in guppy2sam.
Changed
- Update htslib ecosystem to 1.10 to fix conda installation issue.

Minor fixes and models release.

Fixed
- VCF GQ is now an integer in line with VCF spec.
- Fixed issue requiring a previous model for training.
- Fixed issue causing -p option of medaka_variant to crash.
- Fixed issue preventing installation in a virtualenv with python <3.6.
Added
- R9.4.1 variant calling models for Guppy 3.6.0 and updated benchmarks.
- Made r941_min_high_g360 the default consensus model.

Minor fixes release, resolving issues introduced in v1.0.0.

Fixed
- Fix default model for SNP calling.
- Fix issue causing medaka_consensus to crash.