Fix edge case where dangling end merging creates cycles #5960
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Thanks @davidbenjamin! Please let me know when the merge is complete and we will rerun gnomAD analysis. |
Codecov Report
@@ Coverage Diff @@
## master #5960 +/- ##
==============================================
+ Coverage 86.823% 86.84% +0.017%
- Complexity 32360 32429 +69
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Files 1993 1993
Lines 149509 149725 +216
Branches 16524 16598 +74
==============================================
+ Hits 129808 130021 +213
+ Misses 13676 13673 -3
- Partials 6025 6031 +6
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meganshand
approved these changes
May 22, 2019
| return getAssemblyResult(refHaplotype, kmerSize, rtgraph, aligner); | ||
| final AssemblyResult result = getAssemblyResult(refHaplotype, kmerSize, rtgraph, aligner); | ||
| // check whether recovering dangling ends created cycles | ||
| if (recoverAllDanglingBranches && rtgraph.hasCycles()) { |
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It doesn't actually matter if recoverAllDanglingBranches right? You want to return null if there are cycles regardless?
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You're right but I'm being conservative about runtime here. This is all going to be overhauled soon anyway.
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And don't worry about the code coverage. It's effectively a random number generator.
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Sounds good, merge away!
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@meganshand This fixes the Sarah's recent bug, and just makes sense in general.
I am not adding a regression test because our work on linked de Bruijn graphs is going to moot stuff like this soon.