rtrackylayer import bedpe error
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tangming2005 ▴ 190
@tangming2005-6754
Last seen 5 months ago
United States

I am using rtracklayer to import bedpe but had an error:

what's wrong? thanks! There are no empty lines in the file.

cat -A test.bedpe

chr1^I100^I200^Ichr5^I5000^I5100^Ibedpe_example1^I30^I+^I-$

chr9^I1000^I5000^Ichr9^I3000^I3800^Ibedpe_example2^I100^I+^I-$


import("test.bedpe", format="bedpe")

Error in validObject(.Object) : 
  invalid class “GRanges” object: 'seqnames(x)' contains missing values

 

 

rtracklayer • 1.2k views
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@michael-lawrence-3846
Last seen 2.4 years ago
United States

Thanks, fixed in 1.33.1.

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Actually, this might be a real bug. It seems that a seqinfo object somewhere is defined from the first set of chromosomes (chr1 and chr9), so that when it comes to load the second set of GRanges, the chr5 entry ends up being a missing value. I can reproduce the error message in the original post, and I can get it to go away by changing chr5 to chr1.

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good to know you can reproduce the error. Thx.

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Thanks for pointing that out, updated answer.

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