Megamash cannot call complicated sequences
- Dominant language
- Go
- Stars
- 38
- Forks
- 1
- PR merge metrics
- No merged PRs in 30d
Description
`seq_recovery=0.4152_0` for example, cannot be processed into a megamash table because it doesn't have any unique 16mers. This is because of a flawed assumption: ESPECIALLY in protein variant libraries, 16mer windows won't necessarily be unique - and even if a sequence is unique, a 16mer sliding window may not be able to pick it up. This is a real issue.
I'm still trying to figure out how to fix this.
[templateMap.csv](https://github.com/Koeng101/dnadesign/files/14300542/templateMap.csv)
Contributor guide
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Research direction
Start by reproducing the megamash failure with seq_recovery=0.4152_0 and inspect the attached templateMap.csv. Trace how sequences are converted into a megamash table and identify where the unique-16mer assumption rejects this input. Done means complicated protein variant sequences can be processed without requiring unique 16mers.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- go
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100