PyVCF
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jamescasbon
A Variant Call Format reader for Python.
The latest git tag is ``v0.6.0`` and is missing ``v0.6.1`` though ``v0.6.8`` as listed on https://pypi.org/project/PyVCF/#history
On all the releases to date, including 0.6.8, the README is treated as plain text on PyPI: https://pypi.org/project/PyVCF/0.6.8/ This is likely because it fails validation as a standalone RST file...
The first bullet list was wrongly preceded by a double colon meaning it was rendered as a literal block. Separately all the bullet lists were needlessly indented, which on GitHub...
If the number of values in the FORMAT column is different from the number of values in the sample columns, the parser crashes. Testcase ``` import io import vcf #...
In a VCF file created by the GATK pipeline, there can be various statistics in the INFO field that have a value of `nul`. See the attached example VCF. For...
Not sure if this is a bug or a misunderstanding on my part. Consider these example VCF records: ``` #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 chrom...
Hi, I am using pyvcf in a program to handle VCF files from SV callers. For the program MELT, I observed some strange behaviour. I can apply various filters while...
