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Bug in superbubble removal #212

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paoloczi opened this issue Nov 9, 2020 · 2 comments
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Bug in superbubble removal #212

paoloczi opened this issue Nov 9, 2020 · 2 comments
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@paoloczi
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paoloczi commented Nov 9, 2020

There is a bug in the algorithm that chooses assembly paths during superbubble removal (under control of command line option --MarkerGraph.simplifyMaxLength). The code does not always chooses the optimal path. This can occasionally result in locally low assembled accuracy. There is no quantitative estimate of the effect of this bug on assembled accuracy, but the events where the bug has an effect are believe to be relatively infrequent.
@paoloczi paoloczi added the bug Something isn't working label Nov 9, 2020
paoloczi added a commit that referenced this issue Nov 9, 2020
@paoloczi
Fix bug in superbubble removal (issue #212).
c052640
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This bug is present in Shasta 0.6.0 and previous releases. It is fixed in the latest code and the fix will be available in the next release. To download a current test build containing the fix, follow the directions here.

@paoloczi paoloczi added the fix pushed but not released A fix is in the repository but not yet in a release label Nov 10, 2020
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paoloczi commented Dec 3, 2020

The fix is in Shasta release 0.7.0.

@paoloczi paoloczi removed the fix pushed but not released A fix is in the repository but not yet in a release label Dec 3, 2020
@paoloczi paoloczi closed this as completed Dec 3, 2020
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