4 releases
0.1.3 | Jul 8, 2023 |
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0.1.2 | Jan 10, 2023 |
0.1.1 | Oct 12, 2022 |
0.1.0 | Oct 7, 2022 |
#318 in Biology
241 downloads per month
29KB
624 lines
Yet another fasta/q/x parser
Well fuzzed though....
Benchmark
I don't know if this is correct or not, but it's fast enough. NOTE: This does not include I/O at all as that is outside the scope of this library (for now) and thus uniprot is included as a raw string in the binary.
Running benches/parse_fasta.rs (target/release/deps/parse_fasta-1e449f5527386a9a)
Parse UniProt SwissProt FASTA File/parse_fasta
time: [54.788 ns 54.922 ns 55.069 ns]
thrpt: [4773329 GiB/s 4786111 GiB/s 4797786 GiB/s]
Found 11 outliers among 100 measurements (11.00%)
4 (4.00%) low mild 4 (4.00%) high mild
3 (3.00%) high severe
Changelog
0.1.3
Pin bytelines to 2.2.2 to remove the tokio/futures dependency as it is not used here.
0.1.2
Change zlib-ng for flate2 to just zlib.
lib.rs
:
Yet another rust fasta/fastq parser, with a focus on speed and memory usage. Well fuzzed and performant-focused.
The basic ones to use are fasta, fastq submodules.
The ones under zerocopy:: use slightly less memory at the cost of discontiguous streams.
Dependencies
~1.5MB
~30K SLoC