Release/v3.1.0

[creisle]

BugFixes

• Require mavis config v1.2.2+ to fix snakemake dependency error (snakemake.exceptions.WorkflowError: Config file is not valid JSON or YAML #335)

New Features

• Support for new SV(like) callers arriba and straglr

Improvements

• code refactoring to improve validate module readability

[codecov]

Codecov Report

Base: 86.44% // Head: 86.69% // Increases project coverage by +0.24% 🎉

Coverage data is based on head (60817e7) compared to base (479fdeb).
Patch coverage: 84.64% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #339      +/-   ##
==========================================
+ Coverage   86.44%   86.69%   +0.24%     
==========================================
  Files          54       57       +3     
  Lines        9281     9342      +61     
  Branches     2397     2342      -55     
==========================================
+ Hits         8023     8099      +76     
+ Misses        778      762      -16     
- Partials      480      481       +1     

Flag	Coverage Δ
unittests	86.69% <84.64%> (+0.24%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/mavis/validate/evidence.py	93.96% <ø> (ø)
src/mavis/util.py	78.09% <33.33%> (ø)
src/mavis/breakpoint.py	91.23% <69.44%> (-0.03%)	⬇️
src/mavis/summary/summary.py	64.58% <80.00%> (+9.65%)	⬆️
src/mavis/validate/base.py	78.84% <83.33%> (-2.25%)	⬇️
src/mavis/validate/gather.py	83.88% <83.88%> (ø)
src/mavis/convert/__init__.py	87.76% <87.50%> (+0.55%)	⬆️
src/mavis/convert/arriba.py	91.30% <91.30%> (ø)
src/mavis/validate/call.py	87.93% <91.66%> (+0.76%)	⬆️
src/mavis/convert/vcf.py	94.11% <92.30%> (-0.66%)	⬇️
... and 12 more

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