Repository navigation
WIP: Add Oligomer - #51
Draft
jakobnissen wants to merge 55 commits into
Draft
jakobnissen wants to merge 55 commits into
jakobnissen wants to merge 55 commits into
Conversation
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #51 +/- ##
==========================================
- Coverage 98.49% 97.02% -1.48%
==========================================
Files 16 18 +2
Lines 865 1480 +615
==========================================
+ Hits 852 1436 +584
- Misses 13 44 +31
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
|
This type is variable length, but backed by a single unsigned integer. The length is encoded in parts of the integer's bits. This is useful for code using a small range of kmer lengths, which would other- wise cause type instability.
Arguments were flipped before
Before skipped three _codons_, now skips three _nucleotides_
An intermediate abstraction to recode one symbols' encoding from one alphabet to another.
Construct kmers and oligomers from whole chunks of LongSequence, LongSubSeq, Kmers or Oligomers. This should speed up construction significantly.
kescobo
reviewed
Sep 10, 2026
kescobo
left a comment
kescobo
left a comment
Member
There was a problem hiding this comment.
I reviewed the docs, not the code, but this looks good to me!
I wonder if it would be worth cherry-picking or otherwise separating out all of the typo fixes that are recorded here from the actual Oligo work - it's a big PR all by itself without adding that noise. But I don't feel super strongly about this.
This branch has not been deployed
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
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 type adds
Oligomer, a kmer backed by a single unsigned integer. The length is encoded in parts of the integer's bits.This is useful for code using a small range of kmer lengths, which would other- wise cause type instability.
One user could be to represent primers, or immunogenic peptides.
I tried to back oligos with an
NTuplelike kmers are, but it's very hard to made the code efficient and type stable, so I had to resort to backing it by a single unsigned integer.TODO
Make Oligomer on level with Kmer.