Angie Hinrichs

Yeah, you're right. It makes the page output a lot bigger but doesn't really slow us down. OK, I will make it just spew out the table and details for...

Sorry about that and thanks for the report! Taking a look...

The requested subtree size (5000) being greater than the number of samples in the current tree (3741) is causing a SEGV in usher-sampled. @yceh I will send a test case....

Thanks to @yceh for the quick fix! You can peg it to 5000 again @corneliusroemer. 😄

Since both fasta sequence placement and name lookup have been sped up, can we close this now? 😄

I believe this is fixed on dev.usher.bio now - CV.2 and XBB.1.5 are good for testing this. Also a cluster in XBC.2 that has a (probably false) reversion on 23019...

Thanks @ivan-aksamentov! I will give both a try. I see v3 can be run without a dataset if --input-ref is provided, great. 🚀

pblat is separate from kent / UCSC. @galt was pointing out that it exists, but is not the same as blat or UCSC Genome Browser utils despite having a similar...

There are a few codons that are translated differently by mitochondria: https://en.wikipedia.org/wiki/Human_mitochondrial_genetics#Genetic_code_variants so the wrapper would need a bit more code to deal with those.

Thanks for pointing out the discrepancy @wtporter, I will look into it.