Glenn Hickey
Glenn Hickey
I started getting an error when importing files after upgrading cactus docker images to ubuntu 22.04: I was able to fix it by *not* installing `toil[all]` (using just `toil[aws]` instead)...
Command being run: ``` cactus ./js ./examples/evolverMammals.txt out.hal --root mr ``` If toil is installed with `pip install toil[aws]==5.6.0`, the running time is **78**s. If toil is installed with `pip...
I've been running jobs with AWS autoscale for the first time in a bit and it seems when Cactus fails, the jobstore is left in an unusable state. For example,...
This changes a (very rare) assertion failure into a (cryptic) message, allowing HG005 to be run on the CHM13-based year-1 HPRC graph. This is probably not the idea fix, but...
An unmapped read pair `cat up.gaf`: ``` SRR835033.100738 95 * * * * * * * * * 0 SRR835033.100738 95 * * * * * * * * *...
This would be a field like `AT` but containing the "stable coordinate" version, ie its range in the original input contig sequence.
Each site is converted independently. In the event of multiple traversals through a site for a given haplotype it just chooses one (I think) and uses it. If there are...
To reproduce: ``` wget http://public.gi.ucsc.edu/~hickey/chrOther.clip.gfa.gaffixed.vg vg validate chrOther.clip.gfa.gaffixed.vg graph: valid vg mod -O ./chrOther.clip.gfa.gaffixed.vg | vg validate - graph invalid: missing edge between 53612th step (296702:1) and 53613th step (296702:1)...
This has annoyed me a few times. I've never bothered to fix but am posting here to remember. I think the safest thing is to just stop using xg's `from_gfa`,...
Hello, I'm experimenting with adding abPOA as an option within [cactus](https://github.com/ComparativeGenomicsToolkit/cactus) ([manuscript](https://www.biorxiv.org/content/10.1101/730531v1)). Thanks for making a great tool -- it's amazingly fast. I was wondering if there's a way to...