feature: support IUPAC bases #53
Closed
Conversation
This file contains 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
nh13
commented
Feb 6, 2025
| @@ -6,7 +6,7 @@ authors = [ | |||
| ] | |||
| name = "fqtk" | |||
| version = "0.3.2-rc.1" | |||
| edition = "2021" | |||
| edition = "2024" | |||
There was a problem hiding this comment.
Soon! 2025-02-20 https://doc.rust-lang.org/edition-guide/rust-2024/index.html
nh13
commented
Feb 6, 2025
| @@ -1,3 +1,3 @@ | |||
| [toolchain] | |||
| channel = "1.65.0" | |||
| channel = "nightly" | |||
tfenne
approved these changes
Feb 6, 2025
There was a problem hiding this comment.
I'm 👍 on functionality. But I think one of @theJasonFan or @jdidion should review too.
src/lib/barcode_matching.rs
Outdated
Comment on lines
95
to
96
| // Note: this allows IUPAC fuzzy matching with IUPAC bases in the expected barcodes, but not in the observed barcodes. | ||
| if expected_base & observed_base != observed_base { |
There was a problem hiding this comment.
Technically I think this will allow IUPAC in the observed ... so long as it's at least as specific at the expected, right? For example, if both are N then it will pass. But if expected is R and observed is N it will fail?
|
Did some benchmarking on some data I had lying around. No timing differences across 100M reads across 24 samples. |
jdidion
reviewed
Feb 7, 2025
|
Waiting for rust v1.85 to go out on 2025-02-20. |
|
Closing in favor of #54 |
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Outdated suggestions cannot be applied.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.
Closes #52
This is much slower when we have a lot unmatched reads, so this needs to be investigated before we merge.