Crate msbwt2

MSBWT v2

This library provides access to a rust-based implementation of Multi-String BWT (MSBWT) queries. Currently, the BWT is assumed to be stored in the same numpy format as expected by the original msbwt tool. It could have been generated by the built-in msbwt2-build tool or externally.

Current BWT Types

• RleBWT - This is short for the Run-length encoded BWT, which stores the data in a compressed format identical to the msbwt numpy format. FM-indices are built from the data after loading. This structure is not dynamic, and must currently be loaded from disk before usage. However, if your data is fixed, this is generally a faster structure.
• DynamicBWT - This format is intended to allow for dynamic addition of strings to the structure at run-time. This means it can be used for BWT construction (msbwt2-build uses this under the hood) or simply for adding more data to an existing BWT on the fly. However, the dynamic ability comes at a run-time cost for queries If you only need to query the BWT, it is recommended you use one of the fixed data structures.

Examples

Basic load and query

use msbwt2::msbwt_core::BWT;
use msbwt2::rle_bwt::RleBWT;
use msbwt2::string_util;
let mut bwt = RleBWT::new();
let filename: String = "test_data/two_string.npy".to_string();
bwt.load_numpy_file(&filename);
assert_eq!(bwt.count_kmer(&string_util::convert_stoi(&"ACGT")), 1);

Creation from FASTX files and adding string dynamically

use msbwt2::dynamic_bwt::{create_from_fastx,DynamicBWT};
use msbwt2::msbwt_core::BWT;
use msbwt2::string_util;
let single_file = vec!["./test_data/two_string.fa"];
let mut bwt = create_from_fastx(&single_file, true).unwrap();
assert_eq!(bwt.count_kmer(&string_util::convert_stoi(&"$")), 2);
assert_eq!(bwt.count_kmer(&string_util::convert_stoi(&"ACGT")), 1);
//adds an identical sorted string
bwt.insert_string(&"ACGT", true);
assert_eq!(bwt.count_kmer(&string_util::convert_stoi(&"$")), 3);
assert_eq!(bwt.count_kmer(&string_util::convert_stoi(&"ACGT")), 2);

Modules

bwt_converter

Contains the function for reformating a BWT string into the expected run-length format or numpy file

bwt_util

Contains helper functions related to BWT construction, primarily for testing purposes

dynamic_bwt

Contains the implementation of a dynamic BWT structure. Reads can be added to this BWT during run-time, so it is useful for construction of a new BWT.

msbwt_core

Includes the trait for a multi-string BWT

rle_bplus_tree

Contains the implementation of a run-length encoded B+ tree

rle_bwt

This is the classic RLE implementation from the original msbwt package

run_block_av_flat

Contains a block structure for capturing runs of data in a more succinct but dynamic format

string_util

Contains inline functions for converting between strings and integer formats