Ryan Williams
Ryan Williams
@jstjohn [discussed hitting some issues](https://github.com/hammerlab/guacamole/issues/386#issuecomment-198755271) running on the "case 2" data [here](http://txcrb.org/data.html#registration). I'm downloading the data now to attempt to reproduce.
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...
I recently removed Scalariform due to conflicts between it, my personal preferences, and (most importantly) IntelliJ that I wasn't able to resolve. In #435, #436, and #437, some questions have...
(summarizing @arahuja on the subject) **Simple Version** When many SNVs are found close together, consider dropping them under the assumption that something may have been wrong with the reads there....
I typically see more than a minute of reference-broadcasting at the beginning of apps before the first stage starts; we should be able to do something more efficient there.
As we run guacamole on more inputs, we have config blocks like [this](https://github.com/hammerlab/variant-calling-benchmarks/blob/07c8f43c5536a8d8dc2534f0fa871f64243912e0/benchmarks/pt189/benchmark.json) in [variant-calling-benchmarks](https://github.com/hammerlab/variant-calling-benchmarks) (VCB). Some of those JSON blocks correspond directly to structures that exist in Guacamole, e.g....
Spark's log4j wrapper is already used in a few places for e.g. logging warnings, and we should fold our logging into that infrastructure, where we currently have [a tiny homegrown...
Currently points to https://github.com/hammerlab/epidisco/blob/master/docs, probably should at least point to https://github.com/hammerlab/epidisco/blob/master/docs/running-on-coclobas.md directly, and perhaps directly to https://github.com/hammerlab/secotrec if that's the new recommended doc.
Having just started to work on pileup.js, I'm trying to understand the best workflows to use. Some snags I've hit that imply questions about whether there are better ways: -...