Ryan Williams

magic-rdds_2.11 versions [have been live](http://search.maven.org/#search%7Cgav%7C1%7Cg%3A%22org.hammerlab%22%20AND%20a%3A%22magic-rdds_2.11%22) for several weeks so I don't think we have any remaining blockers here; #594 fixed some issues as well.

Spark recently made a change to broadcast serialized `Task`s to executors, IIRC. I guess the significance of this is that it can happen much more quickly, e.g. using torrent-broadcast methods...

Hi @ankushreddy! If you are calling variants on a BAM that is already MD-tagged, then you shouldn't need to pass in a reference. Per @arahuja's work on #376, the `--reference-fasta`...

I was able to run the joint-caller on this data successfully from a recent HEAD (08dcc6ca7f896056194df5cac85687bc834e7863) three times today with varying numbers of executors: 10, 20, and dynamic (52-369, per...

ADAM has recently added functionality for "easily" writing single-file VCFs and SAMs/BAMs; could be useful here, or just useful for us to mimic. https://github.com/bigdatagenomics/adam/pull/689

Thanks for the PR @jstjohn! One of @timodonnell, @arahuja, or I will have a look this week. Any interest in a quick call to discuss your interest in Guacamole? Shoot...

> The solution to this is either to copy the args over to vals when they are referenced in a Spark serialized closure, or else copy all of the args...

otomh I don't have a strong desire to switch to SBT and stop supporting Maven. supporting both also seems reasonable but I also don't have a strong desire to make...

Hey @ankushreddy `HEAD` of ADAM has different schemas than guacamole expects; we depend on [ADAM 0.18.1](https://github.com/hammerlab/guacamole/blob/6e6681e846289666a8b5e29439e93b640acf5a7d/pom.xml#L19) and they've been doing big refactorings recently. If you can try those steps again...

Your NPE is coming from [this line](https://github.com/bigdatagenomics/adam/blob/adam-parent_2.10-0.18.1/adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala#L268); some contig is `null`. I'm not sure why that would happen, at a glance.