Expand description
FM-Index Long Read Corrector v2
This library provides access to the functionality used by FMLRC2 to perform read correction using a Burrows Wheeler Transform (BWT). Currently, the BWT is assumed to have been generated externally (typically with a tool like ropebwt2) and stored in the same numpy format as FMLRC v1. FMLRC load a binary representation of the BWT into memory for performing very fast queries at the cost of memory usage. This particular implementation is accelerated over FMLRC v1 by using a cache to pre-compute common queries to the BWT.
Example
use fmlrc::bv_bwt::BitVectorBWT;
use fmlrc::bwt_converter::convert_to_vec;
use fmlrc::ropebwt2_util::create_bwt_from_strings;
use fmlrc::string_util::convert_stoi;
use std::io::Cursor;
//example with in-memory BWT
let data: Vec<&str> = vec!["ACGT", "CCGG"];
let seq = create_bwt_from_strings(&data).unwrap();
let cursor_seq = Cursor::new(seq);
let vec_form = convert_to_vec(cursor_seq);
let mut bwt = BitVectorBWT::new();
bwt.load_vector(vec_form);
//bwt.load_numpy_file(filename); <- if in a numpy file
//do a count
let kmer: Vec<u8> = convert_stoi(&"ACGT");
let kmer_count = bwt.count_kmer(&kmer); //ACGT
assert_eq!(kmer_count, 1);Modules
Contains the alignment methods for comparing corrections
Contains the bit vector implementation of the BWT
Contains the function for reformating a BWT string into the expected run-length format or numpy file
Contains bit vector with basic rank support; other crates exist with this, but they tended to be slow for some reason
Contains a wrapper around the rust-bio FASTA writer, but forces an ordering on the reads
Contains the logic for performing the read correction
Contains wrapper functions for ropebwt2, most will fail if ropebwt2 is not on the PATH
Contains special statistics functions, mainly an ignored median score
Contains inline functions for converting between strings and integer formats