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