Nicole Deflaux

https://github.com/googlegenomics/dataflow-java/blob/master/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java https://github.com/googlegenomics/dataflow-java/blob/master/src/main/java/com/google/cloud/genomics/dataflow/pipelines/DeleteVariants.java

Fix all sphinx warnings

1

or silence those that are "okay". Then newly introduced issues will be easier to identify and fix.

Add a topic for loading annotations.

1

It should live underneath http://googlegenomics.readthedocs.org/en/latest/use_cases/load_data/index.html

Instead, use [Application Default Credentials](http://googlecloudplatform.blogspot.com/2015/07/Easier-Auth-for-Google-Cloud-APIs-Introducing-the-Application-Default-Credentials-feature.html) ``` --------------------------------------------------------------------------- ImportError Traceback (most recent call last) in () 1 from httplib2 import Http ----> 2 from oauth2client.gce import AppAssertionCredentials 3 credentials = AppAssertionCredentials(...

[WriteBAMTransform](https://github.com/googlegenomics/dataflow-java/blob/master/src/main/java/com/google/cloud/genomics/dataflow/writers/bam/WriteBAMTransform.java) used by [ShardedBAMWriting](https://github.com/googlegenomics/dataflow-java/blob/master/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java) assumes that it receives reads in order. Add a group by and a sort operation so that input reads can be read from multiple BAM shards...

When the genomic region we want to examine is divided into shards, we use a STRICT shard boundary to remove duplicate data that would occur at the end of the...

https://github.com/googlegenomics/dataflow-java/blob/master/src/main/java/com/google/cloud/genomics/dataflow/utils/AnnotationUtils.java has no Dataflow dependencies. Move it and any other code with no Dataflow dependencies down into utils-java.

Update code to use Dataflow's new support for custom sources

1

We [manually create data shards](https://github.com/googlegenomics/utils-java/blob/master/src/main/java/com/google/cloud/genomics/utils/ShardUtils.java#L32) right now via `--references` (or `--allReferences`) and `--basesPerShard` from [ShardOptions](https://github.com/googlegenomics/dataflow-java/blob/master/src/main/java/com/google/cloud/genomics/dataflow/utils/ShardOptions.java). Updating to custom sources will allow the data shards to be not only createed but...