Medaka

Fixed
- Variant annotation when counts matrix does not span variants.
Changed
- Updated Tensorflow requirement to 2.2.2

Fixed
- Off-by-one error during stitching of consensus chunks.

Minor release

Fixed
- Fixed incorrect read depth annotations in VCFs.
- Fixed missing files in PyPI source distribution.
- Fix `StopIteration` issues in newer Pythons.
Added
- Added `-n` option to `medaka_variant` to add a sample field to outputs.
- Set `HDF5_USE_FILE_LOCKING=FALSE`, which some users report as useful.
- Set `OMP_NUM_THREADS=1` required to make Tensorflow anaconda use CPU resource sensibly.

Minor release

Fixed
- Fix issue whereby variant ALTs were created equal to REF.
Added
- Build a medaka-cpu package depending on tensorflow-cpu.

Performance release

Fixed
- Fix long-standing issue where genome regions could be unprocessed.
Added
- Improve inference performance by 30%.
- Add efficient multiprocessing to `medaka stitch`.

Bug fix and feature release

Fixed
- Fix iteration error in retrieving trimmed reads.
- Work around tensorflow threading issue.
Added
- Add ability to `haploid2diploid` tool on VCFs generated by `medaka_haploid_variant`