bug: prelim checks for complete repeat block dups#836
Open
Peter-J-Freeman wants to merge 1 commit into
Open
Conversation
Expanded repeat blocks where the gap is exactly 1 repeat block with respect to the transcript cause vv_hgvs and VV to miss duplicaations at the g>t conversion. Refer to #810. The patterns can be identified as shown in the code. However, the conditional if statements may need to be expanded with additional variants over time. We also need to identify similar variants in antisense genes wrt to the chr reference. However this sets the framework and fixes the test variant in the linked issue
| import logging | ||
| import vvhgvs.exceptions | ||
| from . import utils as fn | ||
| from sqlparse.utils import offset |
Collaborator
There was a problem hiding this comment.
We don't want this imported
Collaborator
|
My brain is a bit fried today to go into the details on this one. I need to work through it step-wise to check the logic on the more complex conditional(pair), which could take a while. |
Collaborator
Author
|
Yeah, these are a pain. FYI, the reason these are not merged in the hard push code, the variants overlap, so cannot be merged by the current tool, so it goes through the path you see where it is spotted. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Expanded repeat blocks where the gap is exactly 1
repeat block with respect to the transcript cause
vv_hgvs and VV to miss duplicaations at the g>t
conversion. Refer to #810. The patterns can be
identified as shown in the code. However,
the conditional if statements may need to be
expanded with additional variants over time.
We also need to identify similar variants in
antisense genes wrt to the chr reference. However
this sets the framework and fixes the test variant in the linked issue