cyvcf2

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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...

tomwhite

Run wheel build more regularly

1

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

tomwhite

Can't install from source

5

I've been trying to install cyvcf2 from the source. But i end up with the following error. I'm on MacOS Monterey v12.1 and i have a M1 chip (dunno if...

dprat

Windows 11 Installing Issue

6

I cannot install somehow cyvcf2. I upgraded to python 3.9.x and also updated visual studio. ``` Running setup.py install for cyvcf2 ... error error: subprocess-exited-with-error × Running setup.py install for...

genewater

Vulnerable shared libraries might make cyvcf2 vulnerable. Can you help upgrade to patch versions?

3

Hi, @brentp , @tomwhite , I'd like to report a vulnerability issue in **cyvcf2_0.30.15**. ### Dependency Graph between Python and Shared Libraries  ### Issue Description As shown in the...

MikeWazoWski123

Issue querying db's made with latest cyvcf2

5

Hi @brentp, I've come across a weird issue. I've updated one of our bcbio installations, resulting in an environment with the latest vcf2db + cyvcf2=0.30.14. When I try to query...

matthdsm

modify VCF header

1

Hello, I would like to know if it is possible to modify the header of a vcf. Functions "add_info_to_header" and "update" allow to add a new INFO line to the...

aude-darracq

Copy header from one VCF to another

1

My use case is that I'm writing a VCF merge tool. For that reason, I want the output VCF to have the union of all input VCF headers (INFO and...

multimeric

libhts image not found

1

Hi. I'm having this error on python 3.7 in osx el capitan `Traceback (most recent call last): File "/Volumes/Data1/pycli/pycli/vcf/test_cyvcf.py", line 1, in from cyvcf2 import VCF File "/Users/proton/anaconda3/envs/pgx/lib/python3.7/site-packages/cyvcf2/__init__.py", line 1,...

chadapohn

undefined symbol: SHA256 during test

12

Hi, The installation of cyvcf2 is successful. I followed the steps below for installation and everything was success. When I did a test of install I get the undefined symbol:...

rajkump