Re: python-cyvcf2 test failures (Was: python-pybedtools: fixing the failing tests)

[Liubov Chuprikova <chuprikovalv@gmail.com>]

Ouch, sorry! I first planned to write also a bit about python-cyvcf2 that is why I included it in the Subjest. Then I decided to devote to it a separate letter, but forgot to remove it from the Subject.

Since this has happened, I am to mention cyvcf2 here.

On Sun, 8 Jul 2018 at 01:23 Steffen Möller <steffen_moeller@gmx.de> wrote:

 - cyvcf2 is in a new version 0.9.0 now, but, well, tests fail.

There was a new upstream version recently in which one of the tests (issue44) was supposed to be fixed, but hadn't yet [1]. I tried to dig into this and its other test failures, but they seem to be quite tricky for me. So I think, Steffen's claim for someone's help with cyvcf2 and its dependency htslib still remains on the table:

 

It comes
with its own version of htslib, which may well contribute to the
situation since I had nothing better to do than to substitute it with
the one the distribution ships. Is anybody close to upstream on this
list to have a look?

With regards,

Liubov

[1] https://github.com/brentp/cyvcf2/issues/89#issuecomment-406354822