[WIP] Ann io - Githubissues

biocpp / biocpp-io

BioC++ Input/Output library

https://biocpp.github.io

BSD 3-Clause "New" or "Revised" License

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[WIP] Ann io #48

Closed joshuak94 closed 1 year ago

joshuak94 commented 2 years ago

This is a very first draft/WIP for the annotation IO. This will cover annotation file types (BED, bedGraph, wiggle, etc.).

At the moment I've only implemented a very basic BED format (three columns, chrom, chromStart, chromEnd) and the BED header.

TODO

[ ] Extend BED3 format to full BED format w/ optional fields.
[ ] Implement the writer.
[ ] Add support for at the very least, bigbed (binary & indexed BED), wig, and bigwig files.
[ ] Allow reading BAM files as annotation files??

smehringer commented 2 years ago

For the naming I opened a discussion thread: https://github.com/h-2/b.i.o./discussions/51