Error:"the supplied start/end lead to a negative width" in AnnotatePeaksFromGTF about sierra

[davhum]

Hi Amisios,

You are correct assuming issue was due to peak being positioned near end of chromosome. Annotation functions scan sequence up and downstream, and in this case the default offsets resulted in functions attempting to get sequence from outside chromosome boundaries. Error should not occur any more, but note peak entry will remain in final output. Instead a warning message is now displayed to identify problematic entries.

Thanks for providing a working example where code fell over. Made it easier to debug.

Let us know if you continue to have problems.

Cheers,
Dave

[amisios]

No time to test atm, but I will close the issue.