search

harrispopgen / mushi

[mu]tation [s]pectrum [h]istory [i]nference
https://harrispopgen.github.io/mushi/
MIT License
24 stars 5 forks source link

Tiny bug in pipeline #61

Closed terhorst closed 3 years ago

terhorst commented 4 years ago

Hi there,

I encountered a small bug when running your 1kg pipeline. The offending line is:

https://github.com/harrispopgen/mushi/blob/a20069339ecb8c730bddb4939b252f0fd63820ce/1KG/SConstruct#L83-L84

When I run this command, it produces an empty .bed file, resulting in a fatal error soon after. I believe the issue is that egrep on my machine defaults to POSIX regexps, which don't match tabs as \t. I fixed it by switching to PCRE via grep -P. (I suspect this is the default behavior of egrep on whatever your development platform is.) I'm on a recent version of Ubuntu. Cheers,

Jonathan

wsdewitt commented 4 years ago

Hi 😃, thanks for bringing this to our attention! We're planning several revisions of our pipeline in the near future, so we'll be sure to include this fix.