seanome/kmerseek

Figure out why "manysearch" and "multisearch" aren't working with rocksdbs

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#4 opened on Feb 11, 2025

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Rustenhancementgood first issuehelp wanted

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Description

Right now, have to use zipped signatures for both manysearch and multisearch, but theoretically, RocksDB indices should work, according to the branchwater documentation. I don't know why this isn't working, but this will require some digging into the Branchwater Rust code, specifically multicollection::from_rocksdb here: https://github.com/sourmash-bio/sourmash_plugin_branchwater/blob/776727091d78af7de4990578ec6d07b12882c1b8/src/utils/multicollection.rs#L193

Will also need to create a custom conda environment with development versions of both sourmash_plugin_branchwater, kmerseek, so this one is a bit advanced.

Contributor guide

Research direction
Examine the multicollection::from rocksdb function in sourmash plugin branchwater/src/utils/multicollection.rs to understand why RocksDB indices are not supported for manysearch and multisearch. Trace the code paths to identify where the restriction to zipped signatures occurs.
Tech stack
rust
Domain
backend
Issue type
Bug
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
3
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.
Mostly clear
Prerequisites
GitRust
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
35