Hi Andreas,
On Mon, 17 Dec 2018 at 20:25, Andreas Tille <[email protected]> wrote:
> On Mon, Dec 17, 2018 at 06:00:59PM +0100, Liubov Chuprikova wrote:
> > > Could someone please have a look?
> >
> > I have started to investigate this: the fail is related to recent
> upstream
> > changes [1] and [2]. I have no time to look deeper into this right now,
> > maybe at the end of the week,
>
> That's perfect.
>
I've just uploaded a patch that adds hts to the libraries in setup.py.
Tests started
to pass, but one of them failed:
cyvcf2.tests.test_reader.test_set_format_int ... [W::vcf_parse] Contig '7'
is not defined in the header. (Quick workaround: index the file with tabix.)
/<<PKGBUILDDIR>>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:581:
FutureWarning: Conversion of the second argument of issubdtype from `int`
to `np.signedinteger` is deprecated. In future, it will be treated as
`np.int64 == np.dtype(int).type`.
v.set_format("PI", np.array([5, 1], dtype=np.int))
/<<PKGBUILDDIR>>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:584:
FutureWarning: Conversion of the second argument of issubdtype from `int`
to `np.signedinteger` is deprecated. In future, it will be treated as
`np.int64 == np.dtype(int).type`.
v.set_format("PI", np.array([855, 11], dtype=np.int64))
python2.7: vcf.c:3496: bcf_update_format: Assertion `!fmt->p_free' failed.
Aborted
I remember that we already experienced the same error with previous version
of cyvcf2. I'll take a look at this later.
__
Liubov
