Eric Talevich

This doesn't appear to alter any existing Biopython components beyond the trivial change to setup.py -- so it's a fairly safe merge. All of this works without explicit parent-child relationships,...

@gabeng I'm aiming for one this week, while I have some time off.

Folks, CNVkit 0.9.11 is released. Enjoy!

Yep, freshly rolled: https://github.com/etal/cnvkit/releases/tag/v0.9.11

This is a new one to me, looks like a static check on the conda packaging failed: * https://dev.azure.com/bioconda/bioconda-recipes/_build/results?buildId=56108&view=logs&j=eb1ca712-fec5-5d93-deb0-40983fe61f2f&t=22a463be-d34e-5e0b-a210-c6720f3b9b60&l=32 Error message: > ERROR: recipes/cnvkit/meta.yaml:0: missing_run_exports: Recipe should have a run_exports...

Here's a possible fix for the conda recipe: https://github.com/etal/cnvkit/pull/880 I have no idea how to test whether this patch will fix the build for bioconda.

I haven't encountered this myself. Not sure what's happening, but the "All samples were removed" message could be spurious, e.g. there's some other error reading the input and GISTIC2 handles...

There are a [couple ways](https://stackoverflow.com/questions/44659851/unicodedecodeerror-utf-8-codec-cant-decode-byte-0x8b-in-position-1-invalid) this could have happened: * CNVkit's FASTA reader doesn't appear to automatically handle gzipped input. So, the input should be uncompressed, as you had it....

+1 for pandas or dask. There are partial implementations of these in [scikit-allel](https://github.com/cggh/scikit-allel/), for reference. Here's [another approach](https://github.com/etal/cnvkit/blob/master/cnvlib/tabio/vcfio.py) that assumes the 1 or 2 samples of interest are known up...

In P03-TD.cnr, is the weight column empty, or does it have some empty cells along with numeric values?