PyVCF
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jamescasbon
A Variant Call Format reader for Python.
I haven't looked at this branch for a few weeks, and you should bear in mind that I've never used Cython before. I've rebased it and it passes all current...
pip3 install PyVCF (version 0.6.8) will fail when setuptools version is >=58. Instead PyVCF will install version 0.4.3, which fails to run with this error: ImportError: cannot import name 'Reader'...
In [vcf/parser.py](https://github.com/jamescasbon/PyVCF/blob/master/vcf/parser.py) we open `filename` but never close it which is causing Resource warning while using the library. 
Hello, When parsing an input .vcf file with a QUAL value = 0.0, i.e.: `MN908947.3 12739 . T TA 0.0 PASS DP=3.0;DPS=3.0,0.0 GT:GQ 1:0` the float QUAL value is converted...
Hi, After running vcf_reader.fetch() I am getting the following error: ValueError: start (22296796) >= end (22287220) I have checked the gene position file I am using for points where start...
Hi, PyVCF 0.6.8 throws an exception when description field in filter line contains escaped double quote. For example: `##FILTER=
When I try to use the `--output` arg to vcf_filter.py I get this traceback: ``` Traceback (most recent call last): File "/home/coyote/anaconda3/bin/vcf_filter.py", line 168, in if __name__ == '__main__': main()...
VCF uses encodings only if compressed (gzip). I moved the check of Python 3 or later to outside the "if compressed" so it occurs in all cases.
This is in regards to issue "Custom section delimited by ";" and not ":" #325 As it turns out, the issue was not the demilmiter, it was that the VCF...
Hello, Is there an easy way to create a data frame from the records? Something like below? ```py vcf_reader = vcf.Reader(open(somatic, 'r')) lines = [el for el in vcf_reader] df_vcf...
