Medaka

Fixed
- medaka variant IndexError on long insertion

Added
- capability to fill gaps in consensus sequence with a designated character
(e.g. 'N') instead of content from a reference sequence.
- option `-r` in `medaka_consensus` to set the designated fill character.
- option `--fill_char` in `medaka stitch` to set the designated fill character.
Fixed
- CUDA initialization errors during `medaka smolecule`s stitch phase.

Added
- New models for R10.4.1 E8.2 400bps based sequencing chemistries.

Fixed
- DiploidZygosityLabelScheme renaming.

Changed
- Updated to tensorflow~=2.7.0.
- Do not always force recreation of minimap2 index in helper scripts.
- PyPI wheel releases now built with libdeflate for faster BAM reading.
Fixed
- Inclusion of inserted bases immediately after deletion in pileup counts.
Added
- Makefile can now build environment for macOS M1.
- Publish ARMv8 wheels compatible with NVIDIA's [Jetpack 4.6.1 binary](https://developer.download.nvidia.com/compute/redist/jp/v461/tensorflow).
- `--qualities` option for `smolecule` and `stitch` to output consensus fastq.

Changed
- Updated tensorflow requirement to ~=2.5.2.
- Spruced-up documentation.
Added
- Light testing of Docker build.
Removed
- Remove `medaka_variant` in deference of clair3.

Changed
- Updated tensorflow requirement to ~=2.4.4.
Added
- Light testing of Docker build.