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, "Hervé Pagès" <hpa...@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]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > >-- >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: hpa...@fredhutch.org >Phone: (206) 667-5791 >Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
