Simon Coetzee

Could you please share the objects that you are using, as an .rda file, and I'll load them up and see where the problem is arising in the code.

I think I've figured it out. The code as it exists relies upon the motif rows being in the specific order A, C, G, T, and your example matrix was...

is it possible that you have a palindromic motif with hits on both the + and - strands in your results, with the same providerID and providerName? I'm trying to...

I think this should work now with the most updated version available.

I believe the problem here is that the interval in your bed file is 5000bp representing the SNV. So for example your first entry should be something like `chr3 31882397...

Perhaps if you give me an example of the bed file with this variant in it, and the species, I can take a look and see where things are going...

I'm not sure what the nature of your error is, you can try running it with SerialParam() and maybe get a better error message. However the first thing I would...

Hi, sorry you're having trouble - can you please share the five variants you're testing with?

I think this bug got fixed in the most recent update here on github, should be going out to bioc soon.

Hi, does the index of the vcf file exist?