add formal support for MuTect input

[mattdoug604]

This adds 'mutect' as a valid tool for input. Technically, mutect could already be used if it was given as generic 'vcf' input. Having a formal 'mutect' label will be helpful for the mavis pipeline at the GSC though.

[codecov[bot]]

Codecov Report

Merging #249 (fb0e0ce) into develop (c01be75) will increase coverage by 9.59%. The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop     #249      +/-   ##
===========================================
+ Coverage    81.48%   91.07%   +9.59%     
===========================================
  Files           57       57              
  Lines        10319    10319              
===========================================
+ Hits          8408     9398     +990     
+ Misses        1911      921     -990     

Flag	Coverage Δ
unittests	91.07% <100.00%> (+9.59%)	:arrow_up:

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

Impacted Files	Coverage Δ
mavis/tools/__init__.py	90.69% <ø> (ø)
mavis/tools/constants.py	100.00% <ø> (ø)
mavis/tools/vcf.py	97.59% <100.00%> (ø)
mavis/annotate/fusion.py	96.02% <0.00%> (+0.33%)	:arrow_up:
mavis/util.py	88.25% <0.00%> (+0.33%)	:arrow_up:
mavis/constants.py	94.04% <0.00%> (+0.42%)	:arrow_up:
mavis/config.py	88.69% <0.00%> (+0.50%)	:arrow_up:
mavis/bam/cigar.py	98.14% <0.00%> (+0.61%)	:arrow_up:
mavis/bam/cache.py	88.31% <0.00%> (+0.64%)	:arrow_up:
mavis/schedule/job.py	78.26% <0.00%> (+0.72%)	:arrow_up:
... and 23 more

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[creisle]

@mattdoug604 Can you also add this to the develop_v3 branch? (another PR)

Side note, we've been using bare asserts with pytest in the new version, not sure if you want to also do that here to make the inclusion simpler

@calchoo have you been looking into swapping the pipeline wrapper we have to use the newer version? (v3)

[mattdoug604]

@mattdoug604 Can you also add this to the develop_v3 branch? (another PR)

Done: https://github.com/bcgsc/mavis/pull/251

Side note, we've been using bare asserts with pytest in the new version, not sure if you want to also do that here to make the inclusion simpler

Also done.

[calchoo]

@calchoo have you been looking into swapping the pipeline wrapper we have to use the newer version? (v3)

no not yet, I'll be looking into it soon though