Nathan Roach

Hello, I'm a little confused about some of the info in the poreplex log file. I'm running poreplex with the --basecall flag, but in the log file I'm getting a...

Adding options to log metadata about lockfile in comments in the lockfile

13

Hello! thank you for making conda-lock, it's a great tool. This PR would add the ability to specify extra comment lines into the lockfile as well as info about git...

Hello, I've been using your implementation of DBSCAN, and noticed that its been outputting clusters smaller than the minimum size I specified at initialization. The relevant section of code I've...

Hello, Seems that TALON's logic fails with python installations >= 3.8. When running on the test data provided with your distribution with the commands provided the program fails with the...

Locking fails when pypi package depends on package being installed via conda

8

Hello, I'm attempting to lock the following environment. ``` name: example channels: - conda-forge - bioconda - default dependencies: - pybedlite=0.0.2 - pip: - fgpyo==0.0.3 ``` The dependencies are, simplified,...

Tool-chain version of clippy not being honored

2

Would seem our tool-chain file setup is not working, as it seems like the CI in PR #22 is failing in an untouched section due to a clippy lint added...

Feature/ samtools typehinted wrappers

1

Closes: https://github.com/fulcrumgenomics/fgpyo/issues/22 EDIT: This is the first 4 type hinted wrappers around pysam dispatch functions. ~~A lot more to do but I wanted to start with the functions most important...

Create methods and type stubs on pysam htslib C extension calls

4

It is often helpful to use `pysam` bindings to htslib functions a la ```python import pysam pysam.sort(myfile, "-o", my_output) ``` etc. `mypy` will complain when attempting to use these functions...

See: https://github.com/conda-incubator/conda-lock/issues/236 Recommendation from conda-lock people is we add fgpyo to conda-forge. Easy enough.