[Bioc-devel] Build error in released version

Hervé Pagès hpages at fredhutch.org
Mon Jul 4 06:28:38 CEST 2016

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. Cannot
>    associate a strand to them. Note that the GAlignmentPairs container only
>    supports pairs where the 2 alignments are on opposite strands of the same
>    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
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