FASTX.jl
FASTX.jl copied to clipboard
BioJulia
Parse and process FASTA and FASTQ formatted files of biological sequences.
The new BioGenerics `@rdr_str` and `@wtr_str` macros, as well as the `defer` keyword has been a longstanding FASTX todo. This change adds this new functionality. ### TODO: - [x] Wait...
Sorry, I'm a bit confused by the doc (or lack thereof), is that one correct way one has to read a fastq file, say if I want to read N...
With Julia 1.9, package image caching significantly reduces latency, as entire function can now be completely cached. FASTX's readers and writers are parameterized by the underlying IO type. This means...
I think we would do the usability of BioJulia a lot of favours if we made it easier to use the file format packages to do the processing of HTS...
In v2, the way records are constructed (directly, not parsed from a file) is not very nice, which hints at an underlying problem. Luckily this is internal and can be...
Julia 1.8 gives us the ability to declare the data field of records const. Doing this could unlock some optimizations. However, there is currently no way of doing this in...
The reader contains a record, which is sized to the largest sequence in the file. This is wasteful if you're reading a bunch of files with large sequences. Maybe add...