bcgsc / mavis

Merging, Annotation, Validation, and Illustration of Structural variants
http://mavis.bcgsc.ca
GNU General Public License v3.0
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Feature/gff support #306

Closed creisle closed 2 years ago

creisle commented 2 years ago

Breaking Changes

Improvements

closes #302

codecov[bot] commented 2 years ago

Codecov Report

Merging #306 (42fa682) into develop_v3 (2987227) will decrease coverage by 0.76%. The diff coverage is 76.30%.

Impacted file tree graph

@@              Coverage Diff               @@
##           develop_v3     #306      +/-   ##
==============================================
- Coverage       87.10%   86.34%   -0.77%     
==============================================
  Files              53       54       +1     
  Lines            8835     9256     +421     
  Branches         2293     2394     +101     
==============================================
+ Hits             7696     7992     +296     
- Misses            692      781      +89     
- Partials          447      483      +36     
Flag Coverage Δ
unittests 86.34% <76.30%> (-0.77%) :arrow_down:

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Impacted Files Coverage Δ
src/mavis/annotate/genomic.py 88.09% <ø> (ø)
src/mavis/annotate/main.py 87.75% <ø> (-2.73%) :arrow_down:
src/mavis/annotate/splicing.py 90.47% <ø> (-0.55%) :arrow_down:
src/mavis/blat.py 85.45% <ø> (ø)
src/mavis/cluster/cluster.py 89.47% <ø> (ø)
src/mavis/align.py 84.81% <33.33%> (-0.55%) :arrow_down:
src/mavis/bam/stats.py 85.71% <50.00%> (-0.96%) :arrow_down:
src/mavis/types.py 71.42% <60.00%> (-28.58%) :arrow_down:
src/mavis/annotate/file_io.py 76.41% <63.26%> (-0.43%) :arrow_down:
src/mavis/util.py 78.09% <66.66%> (-0.56%) :arrow_down:
... and 19 more

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oneillkza commented 2 years ago

Thanks @creisle ! I don't think I'm currently familiar enough with the code to be reviewing it in depth, but if Jeremy's testing on the internal sample work's, then I'm happy to approve.