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Commas are valid separators for BED12 #10

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arq5x opened this issue Jan 10, 2022 · 2 comments
Open

Commas are valid separators for BED12 #10

arq5x opened this issue Jan 10, 2022 · 2 comments

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@arq5x
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arq5x commented Jan 10, 2022

Columns 9, 11, and 12 can and typically do have commas.
https://bedtools.readthedocs.io/en/latest/content/general-usage.html

@brwnj
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brwnj commented Jan 10, 2022

a comma is not a valid field separator ([ \t]+) and is only allowed to be used within a field, so unsure what you're trying to point out.

having the commas can throw off the auto-detection of the actual delimiter so I may have to double check fields 1-3 for whitespace when comma is found.

@arq5x
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arq5x commented Jan 10, 2022

Got it, yes commas would be disallowed in columns 1-3,6,10

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