Change support for MAVIS input

[zhemingfan]

Addresses issues in https://github.com/bcgsc/mavis/issues/307

[codecov[bot]]

Codecov Report

Merging #327 (3189534) into develop_v3 (9e64e59) will increase coverage by 0.24%. The diff coverage is 91.66%.

:exclamation: Current head 3189534 differs from pull request most recent head 2f4144c. Consider uploading reports for the commit 2f4144c to get more accurate results

@@              Coverage Diff               @@
##           develop_v3     #327      +/-   ##
==============================================
+ Coverage       86.43%   86.68%   +0.24%     
==============================================
  Files              55       57       +2     
  Lines            9306     9347      +41     
  Branches         2404     2409       +5     
==============================================
+ Hits             8044     8102      +58     
+ Misses            779      761      -18     
- Partials          483      484       +1     

Flag	Coverage Δ
unittests	86.68% <91.66%> (+0.24%)	:arrow_up:

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Impacted Files	Coverage Δ
src/mavis/summary/main.py	77.30% <ø> (ø)
src/mavis/annotate/file_io.py	74.63% <83.33%> (-1.78%)	:arrow_down:
src/mavis/pairing/pairing.py	89.86% <100.00%> (+0.13%)	:arrow_up:
src/mavis/summary/summary.py	62.77% <100.00%> (+7.84%)	:arrow_up:
src/mavis/validate/base.py	78.84% <0.00%> (-2.25%)	:arrow_down:
src/mavis/convert/constants.py	100.00% <0.00%> (ø)
src/mavis/validate/evidence.py	93.96% <0.00%> (ø)
src/mavis/align.py
src/mavis/blat.py
... and 12 more

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