search

bcgsc / mavis

Merging, Annotation, Validation, and Illustration of Structural variants
http://mavis.bcgsc.ca
GNU General Public License v3.0
72 stars 13 forks source link

add formal support for MuTect input #251

Closed mattdoug604 closed 2 years ago

mattdoug604 commented 3 years ago

Same as https://github.com/bcgsc/mavis/pull/249 but to the develop_v3 branch.

codecov[bot] commented 3 years ago

Codecov Report

Merging #251 (c01be75) into develop_v3 (027c403) will decrease coverage by 5.18%. The diff coverage is 100.00%.

:exclamation: Current head c01be75 differs from pull request most recent head e716f21. Consider uploading reports for the commit e716f21 to get more accurate results Impacted file tree graph

@@              Coverage Diff               @@
##           develop_v3     #251      +/-   ##
==============================================
- Coverage       86.66%   81.48%   -5.19%     
==============================================
  Files              53       57       +4     
  Lines            8842    10319    +1477     
  Branches         2234        0    -2234     
==============================================
+ Hits             7663     8408     +745     
- Misses            719     1911    +1192     
+ Partials          460        0     -460
Flag Coverage Δ
unittests 81.48% <100.00%> (-5.19%) :arrow_down:

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

Impacted Files Coverage Δ
mavis/constants.py 93.61% <100.00%> (ø)
src/mavis/config.py
src/mavis/cluster/main.py
src/mavis/annotate/constants.py
src/mavis/annotate/base.py
src/mavis/annotate/main.py
src/mavis/main.py
src/mavis/interval.py
src/mavis/tools/constants.py
src/mavis/util.py
... and 101 more

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update e3b1d98...e716f21. Read the comment docs.

mattdoug604 commented 3 years ago

Looks like the failing builds are related to snakemake/Docker. Are we expecting those to pass right now?

creisle commented 3 years ago

Looks like the failing builds are related to snakemake/Docker. Are we expecting those to pass right now?

yup, all the tests should be runnable/passing

mattdoug604 commented 2 years ago

There was a change of plans and we won't be routinely running mutect2 through MAVIS going forward. Since you could already run mutect2 as a generic 'vcf' input without this PR, I'm not in a hurry to add support for a named 'mutect2' input type. I'm going to close this PR since we can always revisit this later.