bioawk -c fastx sets OFS=\\t with no way to change it.

[hwalinga]

Hello,

When using bioawk with the -c fastx option the OFS parameter is set to a tab (\t) with no way to change it.

Reproduced by building from source.

Test:

bioawk -c fastx -v OFS=" " '{print OFS}' some.fasta | head -1 | od -bc

Will output:

0000000 011 012
         \t  \n
0000002

Note: some.fasta can be anything (if at least it is a fasta file), but not providing any file will not trigger this.

[ctSkennerton]

this has been fixed on my fork https://github.com/ctSkennerton/bioawk/commit/f42516d8f29f174fca26d70ea5a51754d386e203

[hwalinga]

@ctSkennerton Thank you for the bug fix. You have an interesting fork with a lot of improvement over this one.

But when using your fork I found a specific problem with the parsing of some of my fasta files. Do you mind allowing for opening github issues on your fork, so I can share what problem I found?

[ctSkennerton]

Sure. Can’t promise that I’ll be able to fix it, but we can see

On Sep 8, 2019, at 09:50, Hielke Walinga [email protected] wrote:

@ctSkennerton Thank you for the bug fix. You have an interesting fork with a lot of improvement over this one.

But when using your fork I found a specific problem with the parsing of some of my fasta files. Do you mind allowing for opening github issues on your fork, so I can share what problem I found?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[hwalinga]

@ctSkennerton Not sure if I had been clear, but can you make sure that on your fork other people can open issues.

So, on your fork: settings --> features --> tick issues.

(Forks by default have issues disabled, but since the issue I have is specific to your fork, I would like to have that issue there.)

[ctSkennerton]

Ah, I didn't know that I needed to change a setting. Try it now.