GoogleGenomics

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Add a method to reset the OAuth token.

7

Something like the following, but package-internal and tested to ensure 1. `getReads\Variants()` return the "you need to authenticate" error until authentication is performed 2. the oauth flow is triggered by...

deflaux

For example, variant data with no values for `quality` or `filter` cause the converters to fail.

deflaux

The variant converters currently have trouble with multi-allelic data and non-variant segments. We can work around this by filtering and reshaping the data before sending it to the converters (example...

deflaux

Document steps for new package releases

4

After #28 is complete, let's be sure to document the exact steps for a new release much like we have for [utils-java](https://github.com/googlegenomics/utils-java#making-a-new-release) For example, click on the RStudio "check" button...

deflaux

genome reference assembly extraction from variants/reads objects?

4

One of the handy defaults in Bioconductor GRanges/VRanges objects is a slot for the genome (reference assembly) of each chromosome (should all be the same for any sane object, of...

ttriche

coding style

19

There are some competing style guides for R. Let's decide upon which one to follow or some combination of both and make sure the R package version of the client...

deflaux

similar to the java client library, we should use some kind of exponential backoff for all API calls that fail with a >= 500 http error

cassiedoll

Example code motivating seqlevelsStyle() patch

1

Per #15 and ensuing blahblah, here's the unvarnished code. If it breaks, you get to keep the pieces. :-) ``` R library(GoogleGenomics) ## ## may need to do this interactively:...

ttriche