Adopt cutesv error handling

[zhemingfan]

Addresses edge cases found in SV caller outputs:

• [x] change the convert module to not allow the end of breakpoint1 to be greater than the end of breakpoint2 (end1_after_end2)

  ----------================--------------- ----------------========---------------------

  should be converted into

  ----------===========--------------------- ----------------========---------------------

• [x] do not allow the start of breakpoint 2 to be lesser than the start of breakpoint 1 (start2_before_start1)

  -------------------============--------------- ----------------=================---------------------

  should be converted into

  -------------------============--------------- -------------------===============---------------------

• [x] breakpoint ends must allows be greater or equal to the same breakpoint start (throw a user warning in this case, as it should never happen, but still coerce the breakpoint to be the other)

[codecov[bot]]

Codecov Report

Merging #320 (9e64e59) into develop_v3 (59e0167) will decrease coverage by 0.01%. The diff coverage is 89.28%.

@@              Coverage Diff               @@
##           develop_v3     #320      +/-   ##
==============================================
- Coverage       86.45%   86.43%   -0.02%     
==============================================
  Files              55       55              
  Lines            9289     9306      +17     
  Branches         2398     2404       +6     
==============================================
+ Hits             8031     8044      +13     
- Misses            778      779       +1     
- Partials          480      483       +3     

Flag	Coverage Δ
unittests	86.43% <89.28%> (-0.02%)	:arrow_down:

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

Impacted Files	Coverage Δ
src/mavis/summary/summary.py	54.92% <0.00%> (ø)
src/mavis/convert/vcf.py	94.11% <92.30%> (-0.66%)	:arrow_down:
src/mavis/breakpoint.py	90.61% <100.00%> (-0.65%)	:arrow_down:

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