https://github.com/feldroop/genedex

A small and fast FM-Index for Rust
https://github.com/feldroop/genedex

bioinformatics data-structures fmindex search sequence-analysis

Last synced: 5 months ago
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A small and fast FM-Index for Rust

• Host: GitHub
• URL: https://github.com/feldroop/genedex
• Owner: feldroop
• Created: 2025-09-06T14:03:43.000Z (5 months ago)
• Default Branch: master
• Last Pushed: 2025-09-08T13:54:44.000Z (5 months ago)
• Last Synced: 2025-09-08T15:34:29.513Z (5 months ago)
• Topics: bioinformatics, data-structures, fmindex, search, sequence-analysis
• Language: Rust
• Homepage:
• Size: 59.6 KB
• Stars: 1
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# genedex: A Small and Fast FM-Index for Rust

Coming soon!

## Possible future extensions:

- API/structure:

    - better API for construction

    - better API for alphabets

    - more alphabets + better test coverage for different alphabets

    - gate rayon/OpenMP usage behind feature flag (enabled by default)

- Optimization ideas for existing features:

    - space optimization for rarely occurring symbols (such as the sentinel and N in the human Genome),

    - improved build memory usage (maybe a configurable, slower low memory mode): 

        - add u32 saca

        - BWT view optimization 

        - suffix array, lookup table compression using unconventional int widths (e.g. 33 bit)

    - paired blocks for less memory usage when using larger alphabets (such as all possible u8 values except 0)

- Novel features (implementation + API):

    - bidirectional FM-Index

    - searches with errors and "degenerate" chars as in IUPAC fasta definition (using search schemes)

    - optimized version for single text without sentinel

    - text sampled suffix array (maybe with text ids and other annotations),

    - optimized construction directly from (fasta) file reader