feat: secondary/supplementary alignments inherit from AuxAlignment #208
+437
−290
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Outdated suggestions cannot be applied.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.
This is a draft PR to explore a common hierarchy for "alignments from SAM tags".
Motivated by:
The diff is ugly but there are only 3 classes. I suggest reviewing like:
AuxAlignment
: abstract parent with some common concrete shared functionsSecondaryAlignment
: functionality specific to secondary alignmentsSupplementaryAlignment
: functionality specific to supplementary alignmentsI was able to make almost everything backwards compatible except:
SupplementaryAlignment
is now a dataclass vs attrsSupplementaryAlignment
had a few init fields renamed@tfenne what do you think?
I'm looking for a quick 👍 👎 so I can abandon the idea, or merge it into my actual feature branch for additional polish and a real round of review.