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jamescasbon / PyVCF

A Variant Call Format reader for Python.
http://pyvcf.readthedocs.org/en/latest/index.html
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===> PyVCF3 <<=== #335

Open dridk opened 2 years ago

dridk commented 2 years ago

PYVCF3 is available here : https://pypi.org/project/PyVCF3/

As the project is not maintained anymore, but very used... I suggest to make a fork and rename the project as "PyVCF2" on pypi. We will finally be able merge the pull requests. Who's motivated?

dridk commented 2 years ago

I suggest to start from the last critical fix

https://github.com/ousamg/pyvcf.git@v0.6.9

dridk commented 2 years ago

I did one here named "PyVCF3" . Those one works on python3 only :

https://pypi.org/project/PyVCF3/1.0.0/

I m going to merge some pull request right now.

iamh2o commented 2 years ago

I'll start using that and have some fixes I can prob add. This has been abandoned a long time, but still one of the better VCF parsers. Thanks for rescuing it.

dridk commented 2 years ago

No problem ! I already merge some pull request and did some improvement

pkMyt1 commented 2 years ago

@dridk Thank you. I don't work with vcf files that often and just found the bug in the original version. Unfortunately, maintaining repos is a drudge.

gdurif commented 2 years ago

Thank you very much @dridk

Could you open the issues on your repository? I encounter #337 even with PyVCF3 (edit: the problem was the VCF file and not pyvcf)

dridk commented 2 years ago

you can rate the project to make it known by other

mbhall88 commented 2 years ago

Could you open the issues on your repository?

Agreed, this would be very handy.

I've also created a recipe on bioconda for pyvcf3 https://github.com/bioconda/bioconda-recipes/pull/34505

dridk commented 2 years ago

I just open the issues page on pyvcf3 ! It was disabled, sorry...
https://github.com/dridk/PyVCF3/issues/1