Eric Talevich

Equality of floating point numbers can be a little dangerous because of machine precision. Not sure whether we're safe here, but for maximum mathematical validity, how about testing that the...

Yes, this would be nice to have under Bio.Phylo and would fit well alongside TreeConstructor.

Yes, this fix makes sense to me. My original implementation was not well tested, but this one looks good. Thanks!

I think we're waiting on a unit test before merging this. The test could be: 1. Set the random seed to a fixed value, e.g. 1 2. Create a distance...

Further info on how to prepare a VCF for BAF calculation and LOH detection: * https://cnvkit.readthedocs.io/en/stable/baf.html * https://cnvkit.readthedocs.io/en/stable/fileformats.html#vcf As @tskir notes in #616 , the documentation could stand to be...

I haven't tried those options myself but the names look like they would do what CNVkit needs, i.e. keep the germline SNP sites in the output VCF.

It's not an option for VCF. But it is an option for BED format: `cnvkit.py export bed --show all`. Will that format work for your pipeline?

It would be best to get the bait/target coordinates or the name of capture kit the provider used, if you can. With the kit name alone you could get the...

Hi guys, I'm happy to help with testing CNVkit and/or tweaking the test suite to play better with argparse2cwl. You can skip wrapping anything marked "deprecated" (e.g. `loh`, `genome2access`), those...

I've released a new minor version of CNVkit that drops the deprecated parts and introduces a few new options. I think the current CWL wrappers in Anton's repo should still...