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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
139 stars 53 forks source link

Handle reads on stdin #49

Closed bwlang closed 6 years ago

bwlang commented 6 years ago

re #48

@brentp What do you think of this approach? If you like it, i'll do some more testing to be sure things work with files too.

Maybe you want to add an option to nopen to support this?

bwlang commented 6 years ago

This is working well on novaseq datasets for me. Now that I've added a test for this I'm removing the WIP.
@brentp: let me know if you have suggestions to improve this

bwlang commented 6 years ago

@brentp added chain.from_iterable and addressed your other comment. let me know what you think.

bwlang commented 6 years ago

@brentp - i've been using this in production for a while now, any remaining concerns?

brentp commented 6 years ago

thanks.