Tim O'Donnell

Looks like we can get around these errors with: ``` SamReaderFactory.setDefaultValidationStringency(ValidationStringency.LENIENT) ``` So this ticket is much lower priority. We should focus on getting a good somatic test case (both...

I think it should be possible to get at the clipped reads in a pileup if you want to, but after dealing with RNA a bit in Guacamole I think...

I think the right compromise may be to have the convenience functions on the `Pileup` class (`depth`, `positiveDepth`, `alleleElements`) exclude clipped reads, but not go the more extreme route and...

Awesome! Since we can't release TCGA data, we probably can't put it in the unit tests per se, but having these test cases easily runnable will be very helpful.

related: https://github.com/hammerlab/guacamole/issues/106

another nit: if you give an incorrect argument, the error is reported on stdout, not stderr

Also 3 WGS BAMs here, 1 normal and 2 tumors, for which it would be great to get mutect/strelka calls: https://console.cloud.google.com/storage/browser/variant-calling-benchmarks-data/aocs/?project=pici-1286 And Arun's DREAM data: https://console.cloud.google.com/storage/browser/dream-challenge/?project=pici-1286 On Mon, Aug 8,...

We should also cleanup broadcasts

It's limited to google cloud, since it only supports google cloud storage buckets and not an AWS storage service like S3. The [bucket interface](https://github.com/hammerlab/kubeface/blob/master/kubeface/bucket_storage.py) code is simple though, and if...

Awesome. Yep, that's right. The uploads and downloads are used to pass input and output data to and from tasks. I updated the README for the project to hopefully give...