scverse / scverse/rustar-aligner
Parallel inputs (`{C,V,,}BQ` or parallel readers for `fastq`)
Nobody has claimed this yet.
- Dominant language
- Rust
- Stars
- 75
- Forks
- 7
- Avg merge
- 8m
- Merged PRs (30d)
- 1
Description
https://github.com/arcinstitute/binseq has multiple variants of sequence storage which would be suitable for input and support parallel reading
https://docs.rs/paraseq/latest/paraseq/ supports parallel fast_ reading as well it seems. Searching this repo returned no mention of binseq cc @rob-p
The current i/o pipeline with regards to inputs (i.e., https://github.com/scverse/rustar-aligner/blob/37423d10eedd70a9e661e14295071617ee6686a8/src/lib.rs#L889) seems to be
- sequential io of a "batch"
- align in parallel
- write out that batch
So we'd be targeting the first step but maybe we open a second issue for the third step
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 at src/lib.rs around line 889 and trace the current sequential batch-input step before parallel alignment. Compare the possible binseq and paraseq approaches linked in the issue, then define completion as parallel reading integrated into that input stage with the existing batch and output flow preserved.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- rust
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100