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dcgerard / updog

Flexible Genotyping of Polyploids using Next Generation Sequencing Data
https://dcgerard.github.io/updog/
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export_vcf function is not working #28

Closed huw143 closed 10 months ago

huw143 commented 10 months ago

Hi friends,

Just let you know that export_vcf function in Updog is not working.

Before running this function, I loaded the R packages :

library("updog") library("VariantAnnotation") library("GenomicRanges") library("S4Vectors") library("IRanges")

Then run the export_vcf,

export_vcf(obj = mout, filename = "./multidog_fit.vcf") Error in export_vcf(obj = mout, filename = "./multidog_fit.vcf") : could not find function "export_vcf"

Please see the above for error.

Would you help me fix this issue?

Thanks for developing and maintaining this amazing package, which is really helpful in my research!

Best wishes,

Tiger

dcgerard commented 10 months ago

Hey @huw143,

Sorry for the late response, and thanks for trying out {updog}!

Right now, export_vcf() is not an exported function. You can try it out with updog:::export_vcf(), but it's experimental, so I make no guarantees on its correctness. I have a student working on it this semester, trying out corner cases, and so hopefully it will be ready for prime time in the next few months.

Cheers, David

huw143 commented 10 months ago

Thank you David for your reply, I really appreciated it. Good to know this, hope everything is going well with your research.

Cheers,

Tiger