Luis Pedro Coelho

CP.sourceProcessWithStreams with stdin will raise exception if process ends

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I'm not sure if this is a bug or just undocumented behaviour, but the following will raise an exception: CP.sourceProcessWithStreams (proc "false" []) (CC.yieldMany ["Hello", "World"]) CL.consume CL.consume See full...

seperate -> separate

Deadlock when using `$$&` and the upstream uses `throwError`

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When using `$$&` and the upstream conduit throws an exception with `throwError`, we get a deadlock. I can trigger an error of the type `Main.hs: thread blocked indefinitely in an...

Feature request: implement "circular aware" binning

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>It would be great if the user could provide the list of circular contigs to avoid creation of spurious bins. — https://twitter.com/fplazaonate/status/1603366542825119746 > "Circular-aware" binning is a simple but important...

Also, check for errors calling 'prodigal -help'

This is a bit of a meta-issue as this seems to be a oft-reported problem: - https://github.com/BigDataBiology/SemiBin/issues/165 - https://github.com/BigDataBiology/SemiBin/issues/166 (@apcamargo rightfully comments that at least we should try to be...

Trivial patch, but I noticed this while reading. HTH, Luis

Currently, we just distribute `pickle`d scikit-learn objects, which works but is brittle to version changes A more robust approach would solve this

## Summary - fix `read_configuration_file` to handle booleans correctly - add test verifying boolean options read from config files ## Testing - `pytest jug/tests/test_options.py::test_bool_from_config -q` - `pytest -q` *(fails: PermissionError...