Koeng101 comments

Results 79 comments of


                                            Koeng101

Pileup parsing deletion with .

(This is commenting on something that could come up when we want a "pileup.AnalyzeSequence" function)

Pileup parsing deletion with .

Added labels I think, also I think generally this is gonna be "sequencing result from pileup file"

Create top-level `types.go` to define types shared across packages

This is gonna be entirely unhelpful, but lemme just put some comments below - 1. When I physically get oligos from IDT, I often add in modifications to the sequence....

Create top-level `types.go` to define types shared across packages

I also think I agree that methylationSites should be separate - perhaps like `map[int]MethylationSite` where MethylationSite is just a byte that representing that specific internal mutation. For the sequence itself...

slow5 doesn't detect newline

[Fixed in ](https://github.com/TimothyStiles/poly/pull/339#issuecomment-1713159345) Need that io to bio review

Failed to parse Saccharomyces cerevisiae S288C chromosome IX

I know what the code means, but it is pretty unclear what it biologically means. All 3 of those are referring to the same gene/mRNA/CDS... but each one uses a...

Failed to parse Saccharomyces cerevisiae S288C chromosome IX

I don't think it has been fixed. It does need fixing I think the difficult part here is parsing out the join properly - without keeping a map of locus_tags,...

Failed to parse Saccharomyces cerevisiae S288C chromosome IX

Probably not. I think the time to fix this would be after the merge of ioToBio.

Add a newline normalizing wrapper for io.Readers

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

Add a newline normalizing wrapper for io.Readers

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