Fix throwing out wildtype hdr #16
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hsiaut
reviewed
Jul 26, 2018
ice/classes/sanger_analysis.py
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| """ | ||
| Indels larger than min cutoff that overlap in size with donor are not considered as an edit proposal | ||
| """ | ||
| return self.donor_odn and self.HDR_OVERLAP_FILTER_CUTOFF < indel_size == self.donor_alignment.hdr_indel_size |
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This line is not clear. There are too many logical operations in the right hand side. Can you clean it up?
hsiaut
reviewed
Jul 26, 2018
ice/classes/sanger_analysis.py
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| for deletion_before in deletion_befores: | ||
| for deletion_after in deletion_afters: | ||
| if self._should_skip_proposal(deletion_before + deletion_after): | ||
| continue |
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_should_skip_proposal treats deletions and insertions the same way?
self.donor_alignment.hdr_indel_size ==> if there is a 10bp deletion, is this value 10 or -10?
If there is a 10bp insertion, would it also throw out the 10bp deletion edit proposal?
Maybe have some more comments in the docstring for _should_skip_proposal
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Good catch. Don't see any reason you would want to throw out both the insertion and deletion. hdr_indel_size is negative for deletions (added a deletion only test case to hdr_indel_size).
Pull Request Test Coverage Report for Build 49
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added 2 commits
July 26, 2018 11:49
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Slight change to the proposal skipping where proposals less than a defined cutoff magnitude (3 right now) are NOT thrown out even if they are the same size as the insert.
Also, there was a +1 missing on the range to consider +20 inserts.
Lastly, adds a test for the substitution only case.