Bashir Sadjad

A fix for this issue can be found [here](https://github.com/GoogleCloudPlatform/openmrs-fhir-analytics/commit/3db04b898533a73bbed4b6961f66d913cb6cb54a).

I think what you are experiencing is a combination of two things. First, during parsing, the `id` is replaced with the `fullUrl` of the bundle entry. Then in json encoding,...

Saman, can you please clarify (or add pointers) on how htsget currently (i.e., before partitioning) integrates with BigQuery output of Variant Transforms?

Isn't [autoscaling](https://cloud.google.com/dataflow/service/dataflow-service-desc#autoscaling) properly handling this? Can you provide links to two dataflow runs for the same set of VCFs where the merge header part has taken significantly longer with more...

A prototype of this idea is implemented in PR #361.

Bumping the priority of this issue because it keeps haunting us. Today, I was trying to reproduce an issue that broke the build ([sample failure](https://travis-ci.org/googlegenomics/gcp-variant-transforms/builds/397027106)) but couldn't do it in...

To correct a wrong conjecture in my previous message: I think the main reason for not upgrading some packages is that they are not needed by the requirements. When doing...

Thanks @smrgit for the note. The main idea here is that when a downstream pipeline needs to use Variant Transforms output, it has the option of both reading from the...

The mismatch variants are also dropped and this needs to be communicated to the user. Also it would be nice to detect the mismatch issue and fail or warn early.

Closing #202 as a duplicate.