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Handle or report differing chromosome labels #8

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

Handle or report differing chromosome labels #8

arq5x opened this issue Jan 10, 2022 · 2 comments

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@arq5x
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arq5x commented Jan 10, 2022

The UCSC files that bedqc uses internally use the "chr1" convention. User files may not.
@brwnj
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brwnj commented Jan 10, 2022

users are allowed "chr1" or "1". do you have a better example that breaks it?

@arq5x
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arq5x commented Jan 10, 2022

some bed files use "Chr1", "Chrom1", etc. Might be good to just report a distinct list of chroms in the file, along with the naming schemes that are expected as part of the base report.

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@arq5x @brwnj