Upgrade to Scala 2.11

[ryan-williams]

Eventually we should do this; collecting notes about how/when here.

• should we have a transition period where we support both?
• or should we switch over in one go (once we're sure things work on 2.11)?

Based on only high-level knowledge of the ramifications, I'm in favor of the latter.

Some context / notes:

• 2.10 has been EoL'd for ~18mos.
• Of our dependencies, ADAM and Spark support Scala 2.11; if any don't that's worth finding out because it also probably means they're unmaintained.
• Spark currently debating dropping Java 7 / Scala 2.10 in upcoming Spark 2.0 release.
• @arahuja or @timodonnell mentioned that case-class boxing might be better in 2.11, as well as whatever else was added to scala in the last ~18mos :)

[arahuja]

Also, a fan of the latter. Tried this in #433 but ran into some dependency issues (run time class not found errors),but I think I had just needed Spark compiled for the right scala version though and didn't test further

[ryan-williams]

Cool, gtk! Also the impending move to Java 8 seems like a nudge toward Scala 2.11, as I've heard that Java 8 interactions with Scala 2.10 are possibly wonky.

[arahuja]

@ryan-williams Have you given this a shot? I tried just changing the config and an error I got was

Error:(132, 47) diverging implicit expansion for type org.hammerlab.guacamole.reference.Position => Comparable[org.hammerlab.guacamole.reference.Position]
starting with method orderingToOrdered in object Ordered
      ReferenceRegion(contigName, start, end) <- rdd                                        ^

Seems to have to do with the val ordering defined in the Position companion object, but not sure how to proceed.

I'm guessing we will also need to handle hammerlab/magic-rdds#23 first?

[ryan-williams]

I tried this once a little while ago; one issue I remember is that it was unclear whether Zinc / incremental compilation works in Scala 2.11? This may be happening on bigdatagenomics/adam#1142 atm too.

I think you're right about magic-rdds 2.11 support. I will start working on that soon, was thinking of that as a test-bed for how that process might work in guac anyway.

[ryan-williams]

magic-rdds_2.11 versions have been live for several weeks so I don't think we have any remaining blockers here; #594 fixed some issues as well.