#350 fix overlapping imprecise breakpoints in mavis v2

[calchoo]

Fix for limiting the breakpoints start/ends when they overlap too much

[zhemingfan]

Hi @calchoo, can you lint the files and add some quick test cases for this scenario in developv2? I should have some examples at: https://github.com/bcgsc/mavis/blob/master/tests/test_mavis/convert/test_tools_vcf.py#L68

[codecov]

Codecov Report

Patch coverage: 82.45% and project coverage change: +8.72 🎉

Comparison is base (cfc68d4) 81.52% compared to head (d8092b2) 90.24%.

Additional details and impacted files

@@              Coverage Diff               @@
##           develop_v2     #352      +/-   ##
==============================================
+ Coverage       81.52%   90.24%   +8.72%     
==============================================
  Files              58       59       +1     
  Lines           10348    10599     +251     
==============================================
+ Hits             8436     9565    +1129     
+ Misses           1912     1034     -878     

Flag	Coverage Δ
unittests	90.24% <82.45%> (+8.72%)	⬆️

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

Impacted Files	Coverage Δ
mavis/annotate/file_io.py	88.73% <ø> (+2.25%)	⬆️
mavis/annotate/variant.py	92.80% <ø> (+11.91%)	⬆️
mavis/assemble.py	95.60% <ø> (+2.93%)	⬆️
mavis/config.py	88.69% <ø> (+0.50%)	⬆️
mavis/illustrate/util.py	92.06% <ø> (ø)
mavis/pairing/pairing.py	95.17% <0.00%> (+11.03%)	⬆️
mavis/summary/summary.py	65.71% <ø> (+41.42%)	⬆️
mavis/tools/__init__.py	90.90% <ø> (ø)
mavis/validate/base.py	87.05% <ø> (+32.37%)	⬆️
mavis/tools/vcf.py	89.56% <83.63%> (-8.03%)	⬇️
... and 1 more

... and 22 files with indirect coverage changes

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