First commit for GA4GH common classes and Picard runner

Cassie, did you have an issue with the ga4gh:// or the dataset in the
hierarchy?


On Thu, Sep 4, 2014 at 3:38 AM, Ilia Tulchinsky <notifications@github.com>
wrote:

> In README.md:
>
> > +Tools for using Picard and GATK with Genomics API.
> > +
> > +- Common classes for getting Reads from GA4GH Genomics API and
> > +exposing them as SAMRecord "Iterable" resource.
> > +
> > +- Ga4GHPicardRunner wrapper around Picard tools that allows for INPUTS into
> > +Picard tools to be ga4gh:// urls.
> > +
> > +Build/Run:
> > +No Maven setup yet, builds and runs in Eclipse.
> > +
> > +Arguments for running:
> > +--client_secrets_filename=<path to client_secrets.json>
> > +-path=<path to Picard tool jars>
> > +-tool=ValidateSamFile.jar
> > +INPUT=ga4gh://www.googleapis.com/genomics/v1beta/reads/16801540936334623823/CLqN8Z3sDRCwgrmdkOXjn_sB/*/
>
> Sure, I can change to
> https://www.googleapis.com/genomics/v1beta/readgroupsets///[range]
> The dataset id is not strictly needed. I wanted to include it because it
> supports the hierarchical notion and I can validate that the readset is
> indeed under that dataset but this might be redundant.
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/googlegenomics/gatk-tools-java/pull/1/files#r17106170>
> .
>