Daniel Cameron
Daniel Cameron
Names such as `failed_body_info_020.vcf` are uninformative and imposes an unnecessary ordering on the test cases. Files should be renamed to be more meaningful (e.g. `failed_body_info_H3_not_flag.vcf`)
1. Haplotype Should this be redefined as a path along a molecule? Description needs cleanup. "Members must share the same reference sequence as adjacent members." is inconsistent with "Sequence references...
In this first wave, we will define the minimal representation needed to encode SVs. High-level design: two sub-components of SV-VRS. The first is a minimal representation that encodes the structural...
"The genotype.count attribute explicitly captures the total count of molecules associated with a genomic locus represented by the Genotype." This definition is problematic when there are genomic rearrangements. For example,...
I've finally manage to run Weaver on COLO829 and the output `SV_CN_PHASE`, `SV_REMOVED`, and `SV_SELECTED` are all empty, and `SNPO_CN_PHASE` and `EACH_REGION` contains all zeros. Looking a bit further I...
I've spent the last two weeks trying to get Weaver to run on COLO829 and I'm still failing. How exactly is a matched normal used by Weaver? I have encountered...
I am attempting to reproduce the Weaver results, but I have been unable to either find the exact data used, nor have I need able to successfully run Weaver. Is...
I have installed weaver from github to ~/weaver and unpacked Weaver_data.tar.gz and Weaver_example.tar.gz to the Weaver_data and Weaver_example sub-directories respectively. I have fixed the broken symlinks in ~/weaver/data I am...
Looking through the source code and specifications document, I've noticed that both compress and decompression spill to disk for large files. This is particularly problematic in the decompression scenario due...
Repo steps: - pull copy of bioconda-recipes - make recipe changes (in my case https://github.com/bioconda/bioconda-recipes/pull/20651) - Install circleci (as root) - Successfully run `docker pull bioconda/bioconda-utils-build-env:latest` - Run `circleci build`...