Move command structure to bdg-utils?

[fnothaft]

The command infrastructure is useful for much more than ADAM, and isn't really specific to genomics. For example, I myself use it in avocado, PacMin, and a few non-genomics projects. I'd like to move it to bdg-utils. At the same point in time, I think we could roll the build information work (see here and here) to the main command (e.g., as a command line argument, -v/--version).

This is similar to how we pulled SparkFunSuite out of ADAM. It's really useful code, but for projects where I don't need to bring ADAM in as a dependency (e.g., the non-omics ones referred to earlier), I'd really prefer not to pull it in.

[tdanford]

As an alternative, move the command structure further up (or down, depending on your orientation) the food chain. I ended up replicating a subset of ADAMMain as a class called QCMain in the qc-metrics repository.

Maybe all the support classes (e.g. ADAMCommandCompanion) can go in bdg-utils, and all the actual Main classes and commands can go in downstream repos?

[fnothaft]

@tdanford

Maybe all the support classes (e.g. ADAMCommandCompanion) can go in bdg-utils, and all the actual Main classes and commands can go in downstream repos?

That'd be my preference as well.

[tdanford]

+1.

[fnothaft]

@tdanford I've opened a PR upstream: bigdatagenomics/utils#30. I'll open a PR against ADAM tomorrow showing what these changes would look like.

[laserson]

+1 to factoring out the common stuff

[fnothaft]

This was closed by #678.