Bugfixes:

• fix error on empty columns
• fix chromosome comparison check

Improvements

• #326 Adding arriba support to v2
• #352 update imprecise breakpoints to v2

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)

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

BugFixes

• Documentation: Update links to old docs to use new RTD links
• Documentation: Make sure column and settings files are generated when RTD builds the docs
• write logs when jobs fail running in local mode

Improvements

• #234 add better error message for mavis not found on path

BugFixes

• #227 fix_mismatched_annotation

Improvements

• Updating docs
• Updates to the ensembl json script

BugFixes

• #213 (VCF): Allow non-translocations to use BND syntax for inputs. Infer break1 orientation from BND alt notation

Improvements

• Use separate submodules for tool conversion code
• lint with black

BugFixes

#189 Fix clustering bug by shifting start of second breakpoint for intra-chromosomal breakpoint merges
#195 BugFix from the 2.2.5 release where these were defaulted to strings instead of arrays

Features

Update readthedocs configuration
Add python3.7 to the tox and travis configs
Update the contributor directions