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readBed Input Format #19

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imk1 opened this issue Jul 4, 2017 · 3 comments
Closed

readBed Input Format #19

imk1 opened this issue Jul 4, 2017 · 3 comments

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@imk1
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imk1 commented Jul 4, 2017

The current input format for readBed requires that the strand be +, -, or *. The standard bed format uses . instead of * when the strand is unknown (https://genome.ucsc.edu/FAQ/FAQformat.html#format1). It would be great if readBed could be modified so that unknown strands can be . or *. Thank you!
@nsheff
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nsheff commented Jul 5, 2017

In the most recent version, readBed should accept anything that is not + or - and consider that unknown -- so * or . should be the same. have you tried the latest version from github (which hasn't been put into bioconductor yet)? I think it should work...

@imk1
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imk1 commented Jul 6, 2017

I was using the version in bioconductor. Thanks for the suggestion!

@nsheff
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nsheff commented Aug 24, 2017

Just letting you know, I've pushed this change now into the dev version of bioconductor (it should build in a few days).

@nsheff nsheff closed this as completed Aug 24, 2017
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@nsheff @imk1