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databio / bedboss

Python pipeline for processing BED files for BEDbase
https://docs.bedbase.org
BSD 2-Clause "Simplified" License
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Should we standardize bed files? #62

Open khoroshevskyi opened 6 months ago

khoroshevskyi commented 6 months ago

While I wanted to create bigbed file I got error: image

Should we standardize bedfiles? Or what should we do in this case?

Related file: https://bedbase.org/bed/ba3e096f7ed69774a9bba86b5036e761

nsheff commented 6 months ago

This will become easier when the sequence collections standard is finished. I need another month or so of work on that before we can solve this. Can you just ignore them for a few weeks and then revisit when that project is a bit more mature?

donaldcampbelljr commented 5 months ago

Another thing to consider, discovered during #60, is that some bed files have utf-16 encodings not utf-8. Should we attempt to convert them to utf8? What are the consequences of doing that?