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End coordinate should not be compared when sorting PE evidence #7835

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merged 2 commits into from
May 6, 2022

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mwalker174
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  • Use start position as end for purposes of sorting PE evidence
  • Adds regression test to MultiFeatureWalker

@mwalker174 mwalker174 requested a review from tedsharpe May 5, 2022 20:09
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Always thought that the definition of getEnd() was totally weird. This is much more sensible.
I notice that the little test file that you added has no instances of startContig==endContig, so it won't actually test the change you made to the definition of getEnd(), but otherwise this looks fine.
Sorry that I didn't anticipate the bug.

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codecov bot commented May 5, 2022

Codecov Report

Merging #7835 (20f2ef8) into master (e0e6669) will increase coverage by 0.000%.
The diff coverage is 92.857%.

@@             Coverage Diff             @@
##              master     #7835   +/-   ##
===========================================
  Coverage     86.954%   86.954%           
- Complexity     36897     36898    +1     
===========================================
  Files           2214      2214           
  Lines         173540    173551   +11     
  Branches       18736     18738    +2     
===========================================
+ Hits          150900    150910   +10     
- Misses         16037     16039    +2     
+ Partials        6603      6602    -1     
Impacted Files Coverage Δ
...ples/ExampleMultiFeatureWalkerIntegrationTest.java 91.667% <92.308%> (+0.100%) ⬆️
...te/hellbender/tools/sv/DiscordantPairEvidence.java 73.333% <100.000%> (-1.667%) ⬇️
...titute/hellbender/tools/walkers/sv/SVAnnotate.java 98.701% <0.000%> (ø)
...itute/hellbender/tools/LocalAssemblerUnitTest.java 92.448% <0.000%> (ø)

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2 participants