[BioC] How to annotate genomic coordinates

[Valerie Obenchain]

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  ;)
>
>