Fix bug with reverse complement not being normalized.#65
Open
donovan-h-parks wants to merge 1 commit intoonecodex:masterfrom
Open
Fix bug with reverse complement not being normalized.#65donovan-h-parks wants to merge 1 commit intoonecodex:masterfrom
donovan-h-parks wants to merge 1 commit intoonecodex:masterfrom
Conversation
…ng identification of canonical kmers.
Keats
reviewed
Jan 30, 2023
| let rc = seq.reverse_complement(); | ||
| for (_, kmer, is_rev_complement) in | ||
| seq.normalize(false).canonical_kmers(self.kmer_length, &rc) | ||
| let norm_seq = seq.normalize(false); |
Contributor
There was a problem hiding this comment.
I think in practice this trait is not well thought. The process function should take a &Sequence since we do not need anything from the &SequenceRecord and normalizing it here implicitly would allocate twice for normalized sequence if you need that elsewhere. In that case you would still need to call normalize before calling process though.
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Fixes bug with reverse complement of sequence not being normalized during identification of canonical kmers. This impacts both fixed and scaled sketches, and results in incorrect containment and Jaccard values.