Open tedil opened 1 year ago
Can you use single quotes and let me know if the error persists:
slivar expr --info='INFO.some_integer >= 2' -v slivar-example.vcf
I think your shell might be interpreting before it gets to slivar.
Yes, I thought that is what was happening, too, but it happens with both single and double quotes, and both with bash and zsh.
Oh, I see, you can't use --info=...
just use `--info '...'
so:
slivar expr --info 'INFO.some_integer >= 2' -v slivar-example.vcf
Ah, I see, that indeed solves the issue!
The CLI help explicitly states --info='...'
. If that is not intended, the help page should reflect that (and error on incorrect usage).
Indeed it does. That's a PITA. It's from the argument parser that I'm using.
Given an invocation of slivar such as
slivar expr --info="INFO.some_integer >= 2" -v slivar-example.vcf
, a syntax error occurs:However, replacing
>=
with>
works as expected (same for<=
and<
).slivar version: 0.2.7 71af7d12881ae0590c6d2a97ef2b282cc93fe7c6
(installed via bioconda)I have attached a small VCF file which can be used to reproduce this problem: slivar-example.vcf.txt