ngless-toolkit / ngless-toolkit/ngless
Add read_length() to ShortRead type
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enhancement
- Dominant language
- Rust
- Stars
- 152
- Forks
- 23
- PR merge metrics
- No merged PRs in 30d
Description
This was something that was requested in an offline discussion.
Given a Fastq file with variable read length (e.g. after preprocessing):
mapped = select(mapped) using |mr|:
mr = mr.filter(min_match_size={read_length}, action={drop})
if not mr.flag({mapped}): ^^^^^^^^^^^^^
discard
here {read_length} could be mr.read_length().
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Locate the ShortRead type and the Fastq handling code, then read how existing read properties are exposed. Implement the read_length() behavior described for variable-length reads, and verify that the example can use it as mr.read_length() when setting min_match_size.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- rust
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100