Add a newline normalizing wrapper for io.Readers

[carreter]

Will be useful for cross-platform support.

Blocked by #339

[Koeng101]

Do you have any specific cases where this is useful? Is it like for, switching \r to \n?

[carreter]

Yes, \r and \r\n to \n.

[Koeng101]

Have you found any bioinformatics files that have \r and are so problematic?

[carreter]

No, but I'm mostly thinking about making sure clients on MacOS, which IIRC we support, can parse files without worrying about normalizing the \r newlines to \n themselves.

[Koeng101]

I see, so it would solve something like #301 . The thing I'm worried about is adding a whole generic intermediate to the parsers - I think it'd reduce readability. The tradeoffs might be worth it if we could support windows though (I use mac pretty often and haven't had this problem)

[carreter]

Hmm. I'm blanking on other ways to structure this that doesn't involve adding an intermediate. IMO we should wire this in in all the NewXXXParserWithMaxLine functions in bio/bio.go, this would minimally impact readability of the format-specific parsers themselves.

[Koeng101]

We can't put it in bio/bio.go though because it would be a circular import, but I'm sure we could put it in some utils location. Once we get ioToBio, we should revisit this for actual integration

[carreter]

I don't think there would be an import cycle. Regardless, I'm going to switch this to a draft PR until #339 is merged. Once it is, this wrapper con go in a new ioutils package:

bio/
├── util.go
└── specificFormat/
    ├── parser.go
    └── types.go
ioutils/
└── util.go

[github-actions[bot]]

Status: Blocked :x:

Issues blocking this PR:

• #339 :x:

---

This comment was automatically written by the Blocking Issues bot, and this PR will be monitored for further progress.

[github-actions[bot]]

This PR has had no activity in the past 2 months. Marking as stale.