Multi-threading
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- Dominant language
- Python
- Stars
- 302
- Forks
- 25
- PR merge metrics
- No merged PRs in 30d
Description
Is your feature request related to a problem? Please describe.
The simulator is very slow when it comes to
- Adjusting the lengths of reference contigs. This might be not an issue for human genomes, but it is a big issue for the transcriptome (>180K vs. 23)
- Generating reads.
Both of these steps should have straighforward data parallelism
Describe the solution you'd like
Multithreading of the two steps (and possible others?)
Describe alternatives you've considered
Adding a program command to prepare the reference contigs and pickle the results so rerunning won't be slow. That won't really resolve the read generation speed thu
Additional context
I am building a wrapper around Badread for transcriptomic reads. It's still in the design stage. I plan to code the multithreading described above on a separate branch and make PR
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
Start by locating the entry points for adjusting reference contig lengths and generating reads; the issue does not name specific files or tests. Define completion around parallelizing both steps safely and confirming that the simulator's runtime improves for transcriptome-scale inputs.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100