[BioC] How to annotate genomic coordinates
Valerie Obenchain
vobencha at fhcrc.org
Tue Nov 13 21:21:04 CET 2012
Hi Jose,
Thanks for reporting the bug. You should not have to remove circular
chromosomes yourself, it should be done automatically. I've also reduced
the number of warnings (re: circular sequences) to one vs multiple.
Fixes are in devel, 1.5.13 and release 1.4.4 which will be available via
biocLite() Wednesday ~9am PST or in svn immediately.
Valerie
>
> PD. I almost forgot it, but I also had to filter ChrM related features
> because otherwise I got the following error:
>
> *Error in .findOverlaps.circle(circle.length, seqselect(q_ranges, q_idx), :
> overlap type "within" is not yet supported for circular sequence chrM
> In addition: Warning messages:
> 1: In .setActiveSubjectSeq(query, subject) :
> circular sequence(s) in query 'chrM' ignored
> 2: In .setActiveSubjectSeq(query, subject) :
> circular sequence(s) in query 'chrM' ignored
> 3: In .setActiveSubjectSeq(query, subject) :
> circular sequence(s) in query 'chrM' ignored
> 4: In .setActiveSubjectSeq(query, subject) :
> circular sequence(s) in query 'chrM' ignored
> 5: In .setActiveSubjectSeq(query, subject) :
> circular sequence(s) in query 'chrM' ignored*
>
> Hope this may be of interest for someone sometime in the future ;)
>
>
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