Mavis

Bugfixes:
* fix error on empty columns
* fix chromosome comparison check

Improvements

* Update mavis summary

Bugfixes

* Fix ref alt calculation
* Fix tests so tests can run again on github

BugFixes
- Require mavis config v1.2.2+ to fix snakemake dependency error (335)

New Features
- Support for new SV(like) callers arriba and straglr

Improvements
- code refactoring to improve validate module readability

Breaking Changes
- Uses snakemake instead of internal scheduler code
- Use JSON config instead of large number of command-line arguments
- Use nested translations to allow polycistronic transcripts in annotations file
- Do not use to start header line in mavis tab files

New Features
- Add conversion tool for upgrading v3 annotations files and converting gtf/gff3 files

Improvements
- Upgraded pysam (no longer being used to load vcfs)

Improvements
* https://github.com/bcgsc/mavis/pull/326 Adding arriba support to v2
* https://github.com/bcgsc/mavis/pull/352 update imprecise breakpoints to v2

Bugfixes
* 237 Fix paths in annotation doc
* Fix mavis config TypeError when invalid tool is given
* Bugfix/debug dependency install

Improvements
* add formal support for MuTect input
* 253 adding qos priority to slurm