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to_bigwig: wrong format for chromsizes #168

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rusch-emma opened this issue Aug 18, 2023 · 2 comments
Open

to_bigwig: wrong format for chromsizes #168

rusch-emma opened this issue Aug 18, 2023 · 2 comments

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@rusch-emma
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Hi!
I ran into an issue today with the to_bigwig function and it turned out it was the way I provided chromsizes. The two issues were that chromsizes wasn't indexed by "chrom" and that I included a "name" column which I was used to from other open2c tools such as cooltools (termed "viewFrames", I think?) and which would cause the function to fail with error messages like invalid unsigned integer: "chr2L" which were not very clear to me.

I think it would be helpful if (1) there were clearer error messages describing these mistakes and (2) more flexibility in the data formats provided and/or a more consistent data format to use such as viewFrames.

Thanks!

@gfudenberg
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sorry for the delay in addressing this-- if you have a minimal example onhand (e.g. defining a dataframe & chromsizes), that would be helpful!

@gfudenberg
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@rusch-emma -- just going through old issues now, if this is no longer an issue we can close!

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