Bede Constantinides

Hi there, 1. Hostile offers equal or higher retention of bacterial reads than other host read removal approaches with the default index (`human-t2t-hla`), but using `human-t2t-hla-argos985` can slightly improve this...

No problem :) 1. Correct 2. Ideally yes. If enabled, trimming would reduce the number of human reads removed by Hostile. 3. I am not sure what is common practice...

Hey Sam, thanks for opening this. Agree it would be nice to have. When I get time I'll investigate whether it's straightforward and how much it improves performance. Can imagine...

Hey Sam, Sorry for delay. I've just had a look and am deciding whether to implement it. Streaming the reads through the Python interpreter adds some overhead, but not as...

This will be released in v2.0.0 soon

Released in 2.0.0

Thanks @ddooley ! I'm encountering this issue with LinkML 1.5.0 installed with Python 3.11 (conda) on MacOS 12.6, running under Rosetta (x86_64) on Apple silicon. ``` % linkml-convert --version linkml-convert,...

Thanks so much @cmungall ! I had tried something along these lines already which triggered further errors – perhaps you can suggest where I was failing? `developers` now reads as...

Thank you all so much! Working great, and I'm cracking on with integrating LinkML into our project 🙏

Thank you all for helping so much here. I got a solution working well until LinkML `1.5.3`, given [this model](https://github.com/pha4ge/primer-schemes/blob/056e8f537e70a8400fdad43c29fb2e2c6ba8cb47/schema/primer_scheme.yml) and [these data](https://github.com/pha4ge/primer-schemes/blob/056e8f537e70a8400fdad43c29fb2e2c6ba8cb47/sars-cov-2/midnight/v1/info.yml): With LinkML `1.5.2`: _Works as expected without...