Brent Pedersen

@bemichel could you check the latest commit (tagged to v0.3.6) and make sure it works for you? If so, I'll release to pypi.

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...

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...

can you make this opt-in, so that the default is 1, meaning it has no effect and only do any extra work if the value is < 1? also, please...

what's with the MC and MP tags?

I guess that's fine. I would prefer not to set CHROM and POS to bad values, just leave the originals and set the flag.

I don't think I want to set POS and CHROM. Can you filter on the flag, rather than on the mapping?

it seems that you have no alignments. Can you show the first few and last few lines of your fastqs and the full stderr of the bwameth run?

yes. care to make a PR?

I no longer even have access to an LSF system so I can't be much help. perhaps your job is finishing before the polling starts? The `poll` function might need...