[Bioc-devel] Build error in released version

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Tue Jul 5 22:03:52 CEST 2016

Dear Herve,

Thank you so much for the detailed explanation and quick fix!

When fusion occurs, the 2 alignments in a pair could be on different
chromosomes. Not sure what is the best way to handle this situation. If
set seqnames to *, then the mapping location is lost. Maybe set seqnames
to one of the chromosome, and have a mcol seqname2? Indicating chromosome




On 7/4/16 12:28 AM, "Hervé Pagès" <hpages at fredhutch.org> wrote:

>Hi Julie,
>The GAlignmentPairs container didn't support discordant strand until
>BioC 3.4 (current devel). In the current release (and in previous
>versions of BioC) strand discordance was not supported. I recently
>fixed a bug in the released version of GenomicAlignments where the
>strand() getter was returning an incorrect strand for pairs with
>discordant strand, instead of raising an error. This fix is what
>breaks the GUIDEseq vignette which creates and manipulates a
>GAlignmentPairs object with discordant strand.
>I just changed this again (in GenomicAlignments 1.8.4) so the
>strand() getter now returns * instead of raising an error in case
>of discordant strand (this is actually what strand() does in devel
>where strand discordance is now fully supported). That seems to
>fix GUIDEseq's vignette.
>I guess there was no solid reason for not supporting strand discordance.
>It was just a matter of deciding how the various GAlignmentPairs getters
>and extractors should handle this. Having strand() or granges() return
>* is probably the natural thing to do.
>A more complicated situation, which is also much less common, is
>chromosome discordance i.e. when the 2 alignments in a pair are on
>different chromosomes. Not clear what seqnames() or granges() should
>do in that case. Maybe return/set the seqname to * but that means
>introducing * as a special seqlevel. Still need to think about the
>implications of this.
>On 07/01/2016 02:23 PM, Zhu, Lihua (Julie) wrote:
>> Hi,
>> I just noticed that the released version of GUIDEseq failed at build
>>stage, which did not occur previously and I did not make any change to
>>the release version.
>> The error points to the GAlignmentPairs container. Is this an intended
>>change and should I modify my code to accommodate the change? If yes,
>>what is the rational to enforce the rule that
>> GAlignmentPairs container supports pairs where the 2 alignments are on
>>opposite strands of the same  chromosome?
>> Thanks for your help!
>> Error in .local(x, ...) :
>>    For some pairs in 'x', the 2 alignments are not on opposite strands.
>>    associate a strand to them. Note that the GAlignmentPairs container
>>    supports pairs where the 2 alignments are on opposite strands of the
>>    chromosome at the moment.
>> Best regards,
>> Julie
>> 	[[alternative HTML version deleted]]
>> _______________________________________________
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>Hervé Pagès
>Program in Computational Biology
>Division of Public Health Sciences
>Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N, M1-B514
>P.O. Box 19024
>Seattle, WA 98109-1024
>E-mail: hpages at fredhutch.org
>Phone:  (206) 667-5791
>Fax:    (206) 667-1319

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