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brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
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Overriding hardcoded -B values is possible from command line #92

Open edawson opened 4 months ago

edawson commented 4 months ago

Hi @brentp ,

While testing this, I noticed that it's possible to pass -B <N> at the command line and override the -B 2 value set in bwa-meth.py. Is this intended behavior to allow users to override -B, or should it always be fixed to -B 2 for things to properly function?

Thanks, Eric

brentp commented 4 months ago

Hi Eric, I don't really remember why that's there, but is it a problem to allow a user to set it? I guess it could mess up other thresholds if other penalties/scores are not modified?

edawson commented 4 months ago

I don't know enough about the flag to know for sure; just wanted to clarify the intended behavior. I think it's even possible to pass -B multiple times and override the user override.

It might be clearer to add -B to the argparse arguments with a default of 2 and a single int value as input?

brentp commented 4 months ago

is there a "not" missing from your original issue? I don't see how it's possible to set -B: https://github.com/brentp/bwa-meth/blob/master/bwameth.py#L358-L361

are you asking to make that available? I'd rather not unless you have compelling reason especially since bwa-meth has been unchanged for so long.