Tim O'Donnell
Tim O'Donnell
My most common operation in the ketrew UI is to look at the logs for the most recently failing node. Currently that takes quite a few clicks to drill down...
The variables `weights` and `biases` were switched earlier to `weights_and_biases` but two lines using the old variables were left in place. This PR fixes that
Would be nice to maintain order. Could be an option, or just always inherit from `OrderedDict`.
I find I need an immutable mapping fairly often. Would it be reasonable to add an `attrdict.FrozenAttrDict` class that supports `__hash__`?
Some classes could use some more explanation: - GenotypeFilter.scala - need a file-level header comment describing high-level idea - PileupFilter.scala - need file-level header comment. These filters seem to be...
I had mistakenly thought that no one tried calling copy number variants on exome seq due to amplification and capture biases, but apparently the original varscan2 paper found they could...
The joint caller should optionally output a csv file that gives for pairs A, B of variants (both germline and somatic) at each sample: - total number of fragments (i.e....
Some filters we should probably have (going by artifacts I've observed in real data) - Strand bias - Variants reads mostly start or end at the same place - Variants...
Once we have the phasing information collected in #389 , besides just writing it out we can also use it to make better calls Somatic variants should all be "consistent"...