Michael Lazear

I can reproduce this as well. I have attached lldb backtrace below ``` (lldb) thread backtrace * thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0) * frame...

Unfortunately I have another bug to add here: ``` $ percolator -Y -Q perpxml.pepXML PRM/results.sage.pin Protein decoy-preix used is rev_ All files have been read Percolator version 3.06.0, Build Date...

First problem I reproduced with the example Timo provided. Second example has decoys - let me try and generate an example on data I can share.

Which parquet format are you using?

Gotcha - I'm working on a separate parquet-based format and will probably add a reader at some point. I don't think I will support the Compomics version (which doesn't have...

I like the idea, and have been working on some adjacent stuff. It would be very nice to have SMILES-based modifications, since that could enable better LFQ (given that modifications...

Hi David, This absolutely aligns with my vision - I developed a [very basic pyO3 wrapper](https://github.com/lazear/sage-pyo3/tree/master) at some point, but it has fallen into disrepair and is very out of...

What about putting pysage-connector & the pysage bindings in the same repo? I think that might make sense from a CI/automated release/maintenance perspective - and it also allows for pysage-connector...

Sounds good - I will get an org set up. In the mean time, go ahead and submit a PR whenever you are ready!

I appreciate the PR! Unfortunately relying on an external library to be installed on the system is a non-starter. Not requiring any external dependencies (e.g. having a fully portable binary)...