Kevin Bonham

icon indicating a website link http://blog.bonham.ch

icon company Tufts Medical Center icon location Boston, MA icon location I'm a scientist interested in fermented foods, microbes, and immune systems. My code should be considered CRAPL licenced (http://matt.might.net/articles/crapl/)

Results 260 comments of Kevin Bonham

Rename `get_mark` to `Mark`

Is this supplanted by #183 ?

A test `windows_newlines` seems wrong

is this closed by #218 ?

BUG: collect not working on YAML.load_all

Somewhat related to #104 and #145, I think @Paalon is planning an overhaul of that part of the API

Duplicate keys in mapping

Using `insert!` from Dictionaries.jl is how I would do it (though to be clear, I'm not advocating adding that dependency)

Discussion: Make `LongSequence` fixed-length?

@jakobnissen Do we have a decent list of dependents? We could maybe use juliahub to query this, or use some of the work that Timothy has been doing. If we...

Has flag() renamed to flags()?

Looks like this: https://github.com/BioJulia/XAM.jl/blame/develop/src/flags.jl#L27 from @CiaranOMara , and it appears to me that the answer to > Is that XAM.flags() is just a rename of BAM.flag() in the current and...

Hide inner constructors of objects in this package

Is this behavior documented? One could argue that it's not breaking if it's an internal representation and not documented, even if the method currently exists. Then again, the fact that...

Read sequences don't have overlapping with gene, but eachoverlap() reported there're.

Copying from Slack > jbieler > Today at 3:16 AM > Hum, I think the issue is that those reads do overlap the gene (they start before and end after)...

Read sequences don't have overlapping with gene, but eachoverlap() reported there're.

We have some CIGAR functionality in BioAlignments.jl and some in XAM.jl. @jakobnissen recently started https://github.com/BioJulia/CIGARStrings.jl, but I think that's just a prototype

Remove `convert` for biosequences

I saw the slack gripe on this. Doesn't feel like a huge loss, especially if we put in constructors that can do the conversion for us (eg it would be...