|0.2.5||Sep 28, 2022|
|0.2.4||Jul 26, 2022|
|0.1.8||Jul 21, 2022|
#183 in Science
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Used in 3 crates
A barebones fastx reader for rust.
This crate attempts to be a faster and more lightweight alternative to
bio-rs and provides a standardized interface to working with fasta and fastq formats.
The goal of this crate is to be fast and flexible - it is about twice as fast as
bio-rs on average but about half as fast than
fastq for standard fastx files.
The difference between the different crates is reduced heavily though once gzip files are included (see benchmark).
The speed up can be attributed to reducing the total number of vectors allocated for each record - but the limitation compared to
fastq is that each record has ownership over its data and is allocated once.
This creates extra overhead, but is very convenient as you can treat the reader directly as an iterator.
Some benefits of this interface is that each
FastqReader share the
FastxReader trait and act as iterators over
initialize_reader can determine the fastq format from the path name
use fxread::initialize_reader; let path = "example/sequences.fq"; let reader = initialize_reader(path).unwrap(); assert_eq!(reader.count(), 10);
initialize_reader can handle if the file is gzip or not without changing the downstream usage
use fxread::initialize_reader; let path = "example/sequences.fq.gz"; let reader = initialize_reader(path).unwrap(); assert_eq!(reader.count(), 10);
Check out the API Documentation for usage