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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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warning in STDERR about non-numeric argument in de-novo cluster identification/analysis phase #22

Closed shahsam closed 9 years ago

shahsam commented 9 years ago

Occasional warning about non-numeric arguments comes up in STDERR while running ShortStack v 3.0: "Argument "19C1" isn't numeric in addition (+) at ./ShortStack line 3982" The characters (19C1) following "Argument" in above warning varies from file to file.

MikeAxtell commented 9 years ago

This occurs when a potential mature miRNA alignment has one or more mismatches to the reference genome. This is rare in our testing so far but will probably occur in experimental settings with a polymorphic or poor-quality reference assembly. Should be a quick fix...

MikeAxtell commented 9 years ago

I should add that the bug is potentially serious in those cases since such miRNAs can't be discovered.

MikeAxtell commented 9 years ago

Actually probably wasn't that serious. It looks like it would only be affecting the text-based display of discovered MIRNA loci.

Anyway, try commit eb3e3eb... in which I think the bug is fixed. Please let me know if that fixed it.

shahsam commented 9 years ago

thanks, I am checking now.

shahsam commented 9 years ago

I finished the run with the new commit for the same file, no warnings anymore. Thanks!

MikeAxtell commented 9 years ago

OK, this bugfix will make it into the next release, which will be 3.1