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Bioconductor / GoogleGenomics

[DEPRECATED] An R package for Google Genomics API queries.
Apache License 2.0
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variantsToVRanges loses sample/call information #52

Closed vjcitn closed 7 years ago

vjcitn commented 7 years ago

VRanges can manage all the information on samples and calls, but the current function just acquires one record per variant. Is this function/package still in development?

ttriche commented 7 years ago

(waits to see what the answer is, ponders patching this since VRanges has turned out to be very handy for capture sequencing results and clonality modeling)

--t

On Tue, Jan 17, 2017 at 9:24 AM, Vince Carey notifications@github.com wrote:

VRanges can manage all the information on samples and calls, but the current function just acquires one record per variant. Is this function/package still in development?

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vjcitn commented 7 years ago

Thanks Tim -- Let's be in touch before writing any code as there are some issues to think about regarding when to acquire the detailed data -- working directly with the JSON response or elaborating the current getVariants code ...

siddharthab commented 7 years ago

Hello Vince,

Thank you for your query. This package has not been updated in a while, mostly due to personal time considerations on my part, but we do intend to keep supporting it.

If you have a patch you would like me to review, I will be very grateful. Please read https://github.com/Bioconductor/GoogleGenomics/blob/master/CONTRIBUTING.rst before you start working on the patch.

Else, I will be happy to work on your suggestion in my next set of updates.

siddharthab commented 7 years ago

This has been fixed by contributions from Vincent Carey and his team in pull requests #54 and #55. The changes are also available in the bioc-devel repository.