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Datastores for reads, not your papa's FASTQ files.

License: MIT License

Julia 100.00%

biojulia sequencing files storage format bioinformatics bioinformatics-data biology genomics genomics-data

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gitter-badger stjordanis banhbio m-persic

readdatastores.jl's Issues

Use explicit imports, not `using FASTX`

Writing using FASTX (or any other package) is bad for two reasons:

If FASTX in a new version exports a new name, it may conflict with an existing names in ReadDatastores, causing an error. This means that even adding new features to FASTX can break this package
It makes it harder to find the definition the used functions

All of these should be replaced with using FASTX: Foo, Bar, baz, or, if FASTX internals is used, using FASTX: FASTX, Foo, Bar, baz, such that e.g. FASTX.qux can be accessed.

Release version 0.1.0

ReadDatastores.jl is ready for a 0.1 release.

Paired end read sequence datastores.

Are there any plans on making a release of the latest version of this package? (with BioSequences v3 and FASTX v2)
I've been adding the package to my projects using the GitHub URL, but for registered packages it'd be nice to have an up-to-date release of ReadDatastores.

If no: are there any other ways of randomly accessing FASTQ records that I could use instead? (or some equivalent to FASTX's FASTA index)

Thanks :)

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