Tim O'Donnell
Tim O'Donnell
There's quite a lot of business logic in `VCFOutput` around [here](https://github.com/hammerlab/guacamole/blob/master/src/main/scala/org/hammerlab/guacamole/commands/jointcaller/VCFOutput.scala#L135) where we take `MultiSampleMultiAlleleEvidence` instances and make them into `htsjdk.VariantContext` instances. This makes it non-trivial to support other output...
We currently include clipped (either S or N cigar operator) reads in the pleup at a locus. For RNA-seq this is a performance issue (and arguably a programming gotcha) since...
Not sure if this is already doable as-is, but I have a case now where I'd like to do this, so it'd be good to figure out what the best...
When calling variants at only a subset of loci, it would be great if we could push that into an ADAM predicate to avoid loading the whole dataset. This would...
When we show help for a caller, we should include a description of the algorithm used instead of just the arguments it takes. We should: - add a hook for...
Would it be feasible to add tests that run epidisco locally on a small set of reads and verify that the expected variant calls are made? We generated data like...
These get thrown in a separate thread. They do not seem to affect the results. Possible fix: https://github.com/insanum/gcalcli/issues/237#issuecomment-189591494 Also related: https://github.com/google/oauth2client/issues/414 ``` Traceback (most recent call last): File "/opt/conda/lib/python3.5/site-packages/googleapiclient/discovery_cache/__init__.py", line...
Input should be a csv file with columns: * name * bash command to run * output files to save Run it with something like: ``` ./kubeface-run-commands commands.csv --out-dir /path/to/results...
Kubeface writes a bunch of stuff to the bucket. After a computation has succeeded, we'll usually want to get rid of these. The user should call `client.cleanup()` after their script...