Expand description
Encoder implementation for an iterator over PseudoAln records.
Implements the Encoder struct that can be used to encode data from any other struct that implements an iterator returning PseudoAln data.
Calling next on Encoder will return a single block consisting of encoded bytes representing all records in the block.
To create a valid .ahda record, Encoder::encode_file_header_and_flags should be called first and its output included as the first bytes in the record. This method encodes the FileHeader and FileFlags corresponding to the data stored in the Encoder.
Block size can be controlled using Encoder::set_block_size. Larger blocks may result in better compression ratios but require more memory to encode and decode.
Encoder will store the pseudoalignment using a RoaringBitmap if the number of target sequences times the number of query sequences is less than 2^32. Otherwise, a RoaringTreemap will be used.
§Usage
§Encoding plain text data
Create a Parser on the plaintext input and pass it to Encoder
use ahda::encoder::Encoder;
use ahda::parser::Parser;
use ahda::{decode_from_read, PseudoAln};
use std::io::{Cursor, Seek, Write};
// Mock inputs that will be store in FileHeader and FileFlags
let targets = vec!["chr.fasta".as_bytes().to_vec(), "plasmid.fasta".as_bytes().to_vec(), "virus.fasta".as_bytes().to_vec()];
let queries = vec![b"r1".to_vec(), b"r2".to_vec(), b"r651903".to_vec(), b"r7543".to_vec(), b"r16".to_vec()];
let name = "sample".as_bytes().to_vec();
// Have this Metagraph input data:
// 3 r7543 chr.fasta:virus.fasta
// 0 r1 virus.fasta
// 4 r16 chr.fasta:plasmid.fasta:virus.fasta
// 2 r651903
//
let mut plaintext: Vec<u8> = Vec::new();
plaintext.append(&mut b"0\tr1\tvirus.fasta\n".to_vec());
plaintext.append(&mut b"3\tr7543\tchr.fasta:virus.fasta\n".to_vec());
plaintext.append(&mut b"4\tr16\tchr.fasta:plasmid.fasta:virus.fasta\n".to_vec());
plaintext.append(&mut b"2\tr651903\t\n".to_vec());
let mut input: Cursor<Vec<u8>> = Cursor::new(plaintext.clone());
// Create a Parser to convert the plain text data to PseudoAln and initialize Encoder on this parser to encode it
let n_queries = queries.len();
let mut it = queries.into_iter();
let mut t_it = targets.into_iter();
let mut parser = Parser::new(&mut input, Some(&mut it), Some(&mut t_it)).unwrap();
let targets = parser.get_targets().unwrap();
let mut parser_unwrapped = parser.map(|record| record.unwrap());
let mut encoder = Encoder::new(&mut parser_unwrapped, &targets, &name, n_queries).unwrap();
encoder.set_block_size(3);
let mut output: Cursor<Vec<u8>> = Cursor::new(Vec::new());
// Encode the file header and flags
let bytes = encoder.encode_file_header_and_flags().unwrap();
output.write_all(&bytes).unwrap();
// Iterate over `encoder` to get the 2 encoded blocks
for block in encoder.by_ref() {
output.write_all(&block.unwrap()).unwrap();
}
// The alignments can be decoded from `output`
output.rewind();
let (_file_header, _file_flags, alns) = decode_from_read(&mut output).unwrap();
assert_eq!(alns[0], PseudoAln { ones: Some(vec![2]), ones_names: Some(vec!["virus.fasta".as_bytes().to_vec()]), query_id: Some(0), query_name: Some("r1".as_bytes().to_vec()) });
assert_eq!(alns[1], PseudoAln { ones: Some(vec![0, 2]), ones_names: Some(vec!["chr.fasta".as_bytes().to_vec(), "virus.fasta".as_bytes().to_vec()]), query_id: Some(3), query_name: Some("r7543".as_bytes().to_vec()) });
assert_eq!(alns[2], PseudoAln { ones: Some(vec![0, 1, 2]), ones_names: Some(vec!["chr.fasta".as_bytes().to_vec(), "plasmid.fasta".as_bytes().to_vec(), "virus.fasta".as_bytes().to_vec()]), query_id: Some(4), query_name: Some("r16".as_bytes().to_vec()) });
assert_eq!(alns[3], PseudoAln { ones: Some(vec![]), ones_names: Some(vec![]), query_id: Some(2), query_name: Some("r651903".as_bytes().to_vec()) });
assert_eq!(alns.len(), 4);§Encoding alignments stored in memory
Create an iterator over some container storing PseudoAln and pass it to a new Encoder
use ahda::encoder::Encoder;
use ahda::{decode_from_read, PseudoAln};
use std::io::{Cursor, Seek, Write};
let targets = vec!["chr.fasta".as_bytes().to_vec(), "plasmid.fasta".as_bytes().to_vec(), "virus.fasta".as_bytes().to_vec()];
let queries = vec!["r1".as_bytes().to_vec(), "r2".as_bytes().to_vec(), "r651903".as_bytes().to_vec(), "r7543".as_bytes().to_vec(), "r16".as_bytes().to_vec()];
let name = "sample".as_bytes().to_vec();
let data: Vec<PseudoAln> = vec![
PseudoAln { ones: Some(vec![2]), ones_names: Some(vec!["virus.fasta".as_bytes().to_vec()]), query_id: Some(0), query_name: Some("r1".as_bytes().to_vec()) },
PseudoAln { ones: Some(vec![0, 2]), ones_names: Some(vec!["chr.fasta".as_bytes().to_vec(), "virus.fasta".as_bytes().to_vec()]), query_id: Some(3), query_name: Some("r7543".as_bytes().to_vec()) },
PseudoAln { ones: Some(vec![0, 1, 2]), ones_names: Some(vec!["chr.fasta".as_bytes().to_vec(), "plasmid.fasta".as_bytes().to_vec(), "virus.fasta".as_bytes().to_vec()]), query_id: Some(4), query_name: Some("r16".as_bytes().to_vec()) },
PseudoAln { ones: Some(vec![]), ones_names: Some(vec![]), query_id: Some(2), query_name: Some("r651903".as_bytes().to_vec()) }
];
let mut iter = data.into_iter(); // Encoder::new expects PseudoAln and doesn't work on &PseudoAln
let mut encoder = Encoder::new(&mut iter, &targets, &name, queries.len()).unwrap();
// Encode the file header and flags
let bytes = encoder.encode_file_header_and_flags().unwrap();
let mut output: Cursor<Vec<u8>> = Cursor::new(Vec::new());
output.write_all(&bytes).unwrap();
// Iterate over `encoder` to get the 2 encoded blocks
for block in encoder.by_ref() {
output.write_all(&block.unwrap()).unwrap();
}
// The alignments can be decoded from `output`
output.rewind();
let (_file_header, _file_flags, alns) = decode_from_read(&mut output).unwrap();
assert_eq!(alns[0], PseudoAln { ones: Some(vec![2]), ones_names: Some(vec!["virus.fasta".as_bytes().to_vec()]), query_id: Some(0), query_name: Some("r1".as_bytes().to_vec()) });
assert_eq!(alns[1], PseudoAln { ones: Some(vec![0, 2]), ones_names: Some(vec!["chr.fasta".as_bytes().to_vec(), "virus.fasta".as_bytes().to_vec()]), query_id: Some(3), query_name: Some("r7543".as_bytes().to_vec()) });
assert_eq!(alns[2], PseudoAln { ones: Some(vec![0, 1, 2]), ones_names: Some(vec!["chr.fasta".as_bytes().to_vec(), "plasmid.fasta".as_bytes().to_vec(), "virus.fasta".as_bytes().to_vec()]), query_id: Some(4), query_name: Some("r16".as_bytes().to_vec()) });
assert_eq!(alns[3], PseudoAln { ones: Some(vec![]), ones_names: Some(vec![]), query_id: Some(2), query_name: Some("r651903".as_bytes().to_vec()) });
assert_eq!(alns.len(), 4);Modules§
- bitmap_
encoder - Encoder implementation for an iterator over set bit indexes.