Pyseer

- Bugfix for covariates samples mismatching for LMM
- Bugfix for numeric sample names
- Bugfix for crashes happening during enet variants filtering
- Fix pip and setup.py installs (glmnet_py)
- Remove deprecation warnings for fastlmm

- Update installation from pip and setup.py
- Allow multiple intervals for a single burden tests

- Fix for multiple reported alignments from bwa

- Features, bugfixes and documentation for prediction
- Bugfix for multiple hits/overlapping regions in annotate hits

- Handle API changes between different statsmodels versions
- Handle corner cases where no distance matrix is provided but --no-distances should be used

- Handle missing variants as missing (with new `--max-missing` option to control maximum allowed)
- Unit testing for enet functionality
- Added option to perform midpoint rooting on tree used by `phylogeny_distance.py`
- Updated docs with a new section about the use of unitigs
- Various bugfixes
- Checks on phenotypes file
- Improved BWA command and results handling
- New optimizer for `fit_null`
- Avoid deprecation warnings from pandas
- Report to user if multiple chromosome/contigs are found while mapping
- Use the correct samples order when using lineages and covariates