Tom White

VCFFileReader can't read BCF files with IDX fields in the header

5

IDX fields have been allowed since BCF v 2.2 (see end of http://samtools.github.io/hts-specs/VCFv4.3.pdf). The file ex2.uncompressed.bcf in the htsjdk source has IDX fields and cannot be parsed by VCFFileReader, see:...

Wish: build images in the cloud

6

This would help reduce friction when getting started since there would be no need to install docker, and it would avoid a large upload (multi-GB potentially). Is this something that...

NumPy version compatibility

2

It's not clear what version of NumPy each cyvcf2 release was built against, which can cause issues with binary compatibility. For example, when running cyvcf2 0.30.16 with NumPy 1.22.4 I...

Run wheel build more regularly

1

Perhaps on a weekly schedule (to check it hasn't broken)?

This still happens with 0.30.9, and it was happening with 0.30.4 before too: ``` Python 3.8.11 (default, Jul 5 2021, 19:22:52) [GCC 9.3.0] on linux Type "help", "copyright", "credits" or...

Return missing values mask for Integer INFO/FORMAT fields

2

Missing values for Integer INFO/FORMAT fields are represented by the minimum int32 value (-2147483648, or `np.iinfo(np.int32).min`). It would be nice if a mask array could be retrieved that didn't rely...

Support boolean indexing with a COO sparse matrix

9

While investigating https://github.com/theislab/scanpy/issues/921 I ran into the following limitation when using a boolean array as an index. This is the expected behaviour for regular NumPy: ```python >>> import numpy as...

Deprecate the covid-19-uk-data repo

9

I would like to deprecate this repo and encourage consumers to move to official upstream data sources. I'd like to stop updates in a month's time (1 August 2020). When...

Pillar 2 includes as many as 90% of new cases (https://twitter.com/jburnmurdoch/status/1277961740697796620) so it's misleading to publish England UTLA numbers as if they are the complete picture. This has been discussed...