Adding containsRefName to SequenceDictionary

[tdanford]

(A little update, I'm separating this out and filing it as a separate pull request from a larger request which will follow from us here at GenomeBridge later this week.)

Added containsRefName to SequenceDictionary, allowing us to check whether a SequenceDictionary object contains a particular sequence.

SequenceDictionary recordNames keys should be Strings (they had been Avro Utf8 objects, which was messing up lookups into the map itself from Strings).

[tdanford]

Not sure why the merge build didn't finish...?

[carlyeks]

Looks like the build is stuck: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/29/console

[tdanford]

@massie or @fnothaft -- are you guys able to help?

[AmplabJenkins]

One or more automated tests failed
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/29/

[fnothaft]

Sorry for the slow reply—I just killed the build and am letting it rerun. If it hangs a second time, I'll look into this more deeply. I presume that the unit tests ran OK on your side?

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/30/

[fnothaft]

Yep—looks like it was some small hiccup...

[tdanford]

Yeah, it's only a small change (2-3 lines, plus a test) and all the tests finished fine on our side -- as it appears they did on yours too. Like I said, this is a small, separable thing which is preparatory to larger changes later.

[fnothaft]

Yeah—odd little hiccup! I think the PR builder may run on spot instances, so it is possible that the spot instance was revoked mid build? Don't quote me on that though.

Anywho! Thanks for the change! I've merged it, and am looking forward to seeing what comes next!

[tdanford]

Thanks, Frank!