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chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R
http://bcbio.wordpress.com
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Documentation + email notifications + misc fixes #28

Closed brainstorm closed 13 years ago

brainstorm commented 13 years ago

The barcode has a failing test, I left it that way because I cannot understand why it does not return the sequence with the removed barcode (returns the seq+bc_seq instead) :_S

Thanks Brad !

chapmanb commented 13 years ago

Roman; Thanks for all the work on these parts. The only file that I'm worried about is illumina_finished_msg.py. I recently abstacted out some the code in search_for_new, which looks like it has snuck back in:

https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/illumina_finished_msg.py#L63

Is the main change in this function, the addition of this logbook context?

with logbook.Processor(lambda record: record.extra.setitem('run', os.path.basename(dname))):

Would it be possible to add in your changes to the latest illumina_finished_msg.py on your branch? Then I could pull the full request without needing to cherry pick. Thanks again.

brainstorm commented 13 years ago

Ok, integrated your RTA-related changes & reopening pull request...