LtFmIndex

LtFmIndex is a Rust library for building and using a FM-index that contains a lookup table of the first k-mer of a pattern. This index can be used to (1) count the number of occurrences and (2) locate the positions of a pattern in an indexed text.

Usage

Add to dependency

To use this library, add lt_fm_index to your Cargo.toml:

[dependencies]
lt_fm_index = "0.7.0"

Example code

use lt_fm_index::LtFmIndex;
use lt_fm_index::blocks::Block2; // `Block2` can index 3 types of characters.

// (1) Define characters to use
let characters_by_index: &[&[u8]] = &[
    &[b'A', b'a'], // 'A' and 'a' are treated as the same
    &[b'C', b'c'], // 'C' and 'c' are treated as the same
    &[b'G', b'g'], // 'G' and 'g' are treated as the same
];
// Alternatively, you can use this simpler syntax:
let characters_by_index: &[&[u8]] = &[
    b"Aa", b"Cc", b"Gg"
];

// (2) Build index
let text = b"CTCCGTACACCTGTTTCGTATCGGAXXYYZZ".to_vec();
let lt_fm_index= LtFmIndex::<u32, Block2<u128>>::build(
    text,
    characters_by_index,
    2,
    4,
).unwrap();

// (3) Match with pattern
let pattern = b"TA";
//   - count
let count = lt_fm_index.count(pattern);
assert_eq!(count, 2);
//   - locate
let mut locations = lt_fm_index.locate(pattern);
locations.sort();  // The locations may not be in order.
assert_eq!(locations, vec![5,18]);
// All unindexed characters are treated as the same character.
// In the text, X, Y, and Z can match any other unindexed character
let mut locations = lt_fm_index.locate(b"UNDEF");
locations.sort();
// Using the b"XXXXX", b"YYYYY", or b"!@#$%" gives the same result.
assert_eq!(locations, vec![25,26]);

// (4) Save and load
let mut buffer = Vec::new();
lt_fm_index.save_to(&mut buffer).unwrap();
let loaded = LtFmIndex::load_from(&buffer[..]).unwrap();
assert_eq!(lt_fm_index, loaded);

Features

• fastbwt: This feature can accelerate the indexing, but needs cmake to build libdivsufsort and cannot be built as WASM.
• async-io: This feature enables asynchronous I/O operations using Tokio for saving and loading the index. It adds support for async methods like async_save_to and async_load_from which can be used in asynchronous contexts.

Repository

https://github.com/baku4/lt-fm-index

API Doc

https://docs.rs/lt-fm-index/

Reference

• Ferragina, P., et al. (2004). An Alphabet-Friendly FM-Index, Springer Berlin Heidelberg: 150-160.
• Anderson, T. and T. J. Wheeler (2021). An optimized FM-index library for nucleotide and amino acid search, Cold Spring Harbor Laboratory.
• Wang, Y., X. Li, D. Zang, G. Tan and N. Sun (2018). Accelerating FM-index Search for Genomic Data Processing, ACM.
• Yuta Mori. libdivsufsort