Rearrange code.

[deflaux]

Pipeline-specific functions were pushed down a package level and one reusable function was moved out of an obsolete 'grpc' package level.

@iliat please take a look at the new organization and let me know if any of the BAM stuff should be grouped differently.

https://github.com/deflaux/dataflow-java/tree/rearrange/src/main/java/com/google/cloud/genomics/dataflow/functions

https://github.com/deflaux/dataflow-java/tree/rearrange/src/main/java/com/google/cloud/genomics/dataflow/utils

https://github.com/deflaux/dataflow-java/tree/rearrange/src/main/java/com/google/cloud/genomics/dataflow/writers/bam

[coveralls]

Coverage remained the same at 20.263% when pulling efdf35f on deflaux:rearrange into 7d25de2 on googlegenomics:master.

[pgrosu]

I would use more general terms such as analysis, validation or qc to group a larger set of classes under. It would be hard for folks to remember transmissionprob as package names, as in Java either they have the whole name in CamelCase, or is only one common word that is truncated, or has the whole package name as an acronym.

The Java class hierarchy provides a nice idea of how to structure an API:

https://docs.oracle.com/javase/8/docs/api/java/lang/package-tree.html

https://docs.oracle.com/javase/8/docs/api/java/util/package-tree.html

Hope it helps,
~p

[iliat]

LGTM for BAM, Thanks !

[coveralls]

Coverage remained the same at 20.263% when pulling 8b06610 on deflaux:rearrange into 7d25de2 on googlegenomics:master.

[coveralls]

Coverage remained the same at 20.263% when pulling 1b92fb6 on deflaux:rearrange into 7d25de2 on googlegenomics:master.

[pgrosu]

The fixes look nice - thanks Nicole :)

[coveralls]

Coverage remained the same at 20.263% when pulling 0134a4f on deflaux:rearrange into 7d25de2 on googlegenomics:master.