Limiting the search to the first n characters
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- Dominant language
- Python
- Stars
- 587
- Forks
- 144
- Avg merge
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- Merged PRs (30d)
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Description
Hi there,
I was wondering if there is a way of limiting the search for adapters to the first n characters (or the last n characters) of each sequence. I find that particularly useful when demultiplexing: if there are a considerable number of barcodes to match, it is often the problem that one of the barcodes matches somewhere in the middle of the read. As many sequencing experiments return data with known structure, one can expect the demultiplexing information to be located in the first n characters, so it will be more precise and quicker to find that info if it was possible to limit the seach to those first characters
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Research direction
The issue names no files, tests, or entry points. Start by locating the adapter-search command and its tests, then determine how a configurable prefix or suffix search boundary should be exposed. Done means matching can be limited to the first or last n characters without changing unrestricted search behavior.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100