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nsheff / LOLA

Locus Overlap Analysis: Enrichment of Genomic Ranges
http://code.databio.org/LOLA
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readBed Input Format #19

Closed imk1 closed 6 years ago

imk1 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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

nsheff commented 6 years ago

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