seanome/kmerseek

Split "kmerseek index" into "index-create-sketch", "index-get-kmers", "index-rocksdb"

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#7 opened on Feb 14, 2025

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Description

Currently kmerseek index wraps three commands in Sourmash/Branchwater:

  • index-create-sketch: sourmash scripts manysketch (uses as many CPUs as available, low-medium memory)
  • index-get-kmers: sourmash sig kmers (takes a long time, but only 1 CPU and low memory)
  • index-create-rocksdb: sourmash scripts index (uses as many CPUs as available, low-medium memory)

These were combined for convenience on the command line, but for creating Nextflow pipelines, we probably want to add the option to separate them so that they can be put into separate processes. For example, sourmash sig kmers only uses one CPU and takes a really long time, like 24hrs+ on larger datasets, but shouldn't be blocking on proceeding with doing kmerseek search.

To clarify, kmerseek-index would still wrap the call to all three of index-create-sketch, index-get-kmers, index-rocksdb.

Notice that each command is named search-VERB-something -- I like this style for clarity. Also taking suggestions on naming, the hardest problem!

Contributor guide

Research direction
Examine the current implementation of `kmerseek index` in the codebase and identify how to break it into three separate subcommands following the naming convention `index create sketch`, `index get kmers`, `index rocksdb`. Start by looking at the existing command structure in main.rs or cli module, then refactor the command dispatch accordingly.
Tech stack
rust
Domain
cli
Issue type
Refactor
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
Half day
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
Rust
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
60