Re: Any volunter to write a test for bamclipper?
On 2021-03-26 01:58, Andreas Tille wrote:
> Hi folks,
>
> I have packaged bamclipper[1] since it is a precondition for the
> pipeline covpipe[2] which is developed and used in my institute.
> (@Steffen, possibly another column in the spreadsheet.)
>
> Despite bamclipper is pretty easy I would love to have some autopkgtest
> but I'm lacking the needed files (bam + bam.bai as well as bedpe). The
> README.md[3] has an example that could be used as autopkgtest - so it
> should not be a hard job for someone who has such files / knows how to
> find some examples.
I found those files here[1] inside examples/ dir -- it also has
outputted *.primer.bam* files, so I think it is sensible
to assume that these files work.
I follow this in other packages as well, when on adding certain bam or
sam files, "something" happens which is good for
at least a preliminary functioning test :-)
I added a autopkgtest to the salsa repo, please take in a look.
PS: Please consider enabling salsa CI for any new packages that you
might push. I did so for this one for now.
[1]: https://github.com/tommyau/bamclipper
Nilesh
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