Medaka

Added
- Added `medaka tandem` targeted tandem repeat variant calling.

Added
* Updated features related to fetching of trimmed reads.
Changed
* Refactored smolecule module.
* Faster inference and stitching of many short contigs.
* Tensorflow version 2.10 (allows for aarch64 wheels).

Added
- Expose qualities parameter in medaka_consensus script with `-q` parameter.

Added
- Consensus and variant models for v4.1 and v4.2 basecallers.
Changed
- Changed default models to be r1041_e8.2_400bps_v4.2 models
- Clip probabilities in `_phred()` rather than adding smallest float.

Added
- Consensus polishing models for Version 4 basecallers.
- Wheel builds for newer Python versions.
Fixed
- Deprecated numpy.unicode use.
Changed
- Set minimum Python version to 3.7.
- Updated tensorflow requirement to 2.8.
- Put lower bound on numpy requirement.
Removed
- Dropped support for Python 3.6. Security support for Python 3.6 was ended on 23 Dec 2021;
as such we have removed support for Python 3.6 and suggest users update their Python version.

Added
- New models for R10.4.1 E8.2 260bps based sequencing chemistries.
Changed
- Updated Hac and Fast models for R10.4.1 E8.2 400bps based sequencing chemistries.
- Removed models for Fast basecallers from pypi package