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Pysam UnicodeDecodeError when loading with tabixed VCF #139
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Interesting, what is your locale setting? |
Hi @holtgrewe !! $ locale
LANG=en_US.UTF-8
LANGUAGE=en_US:en
LC_CTYPE="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=en_US.UTF-8 |
Any other idea about the issue @holtgrewe?? |
It looks like that you have non-ASCII unicode in your VCF file and pysam is stumbling over this... |
Hm, I don't remember why I was using pysam in favour of pytabix. I don't know whether that is more robust... Hm, one could try to replace the tabix part of pysam with pytabix in vcfpy... |
Description
When I fetch variants by contig ID I get the following
UnicodeDecodeError
demosntrating some issues when parsing the tabix file. Maybe the issue comes frompysam
, but I would like to know if you have had previous reports based on this issue.What I Did
Traceback Error
The text was updated successfully, but these errors were encountered: