In biscuit pileup, a misspelling of Description as 'Desccription' in the output VCF header raises an error when parsing with pyVCF. I managed to fix this by directly editing the output VCF myself, but felt it was worth pointing out.
Here is the error raised:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.5/site-packages/vcf/parser.py", line 300, in __init__
self._parse_metainfo()
File "/usr/local/lib/python3.5/site-packages/vcf/parser.py", line 326, in _parse_metainfo
key, val = parser.read_filter(line)
File "/usr/local/lib/python3.5/site-packages/vcf/parser.py", line 143, in read_filter
"One of the FILTER lines is malformed: %s" % filter_string)
SyntaxError: One of the FILTER lines is malformed: ##FILTER=<ID=PASS,Desccription="All filters passed">
In
biscuit pileup
, a misspelling of Description as 'Desccription' in the output VCF header raises an error when parsing with pyVCF. I managed to fix this by directly editing the output VCF myself, but felt it was worth pointing out.Here is the error raised:
And here is the putative cause: https://github.com/zwdzwd/biscuit/blob/7680b8e28954053bc79297abc3bc983b86a31b44/src/pileup.c#L1379
Thank you for this great tool otherwise!