[Bioc-devel] Build error in released version
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 fusion? Best, Julie
On 7/4/16 12:28 AM, "Herv? Pag?s" <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. Cheers, H. 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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-- Herv? Pag?s 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