Sure, "*" makes more sense for strand, given the precedent. On Fri, Oct 16, 2015 at 9:55 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: > On 10/16/2015 09:28 AM, Michael Lawrence wrote: >> >> I kind of wish it would return NA for things like seqnames and strand, >> but yes that would be very useful. > > > Could do this for seqnames() but I'm hesitant to do this for strand(). > If you look at ?strand in BiocGenerics, ‘*’ is used when the exact > strand of the location is unknown, or irrelevant, or when the "feature" > at that location belongs to both strands. A pair with discordant strand > belongs to both strands. Also there is a lot of code around that > assumes strand() never returns NAs. > > > H. > >> >> On Fri, Oct 16, 2015 at 9:15 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: >>> >>> Hi Michael, Martin, >>> >>> On 10/16/2015 06:48 AM, Michael Lawrence wrote: >>>> >>>> >>>> It does seem like starting with the more general data structure is the >>>> better approach, but I couldn't find an easy way to move the paired >>>> subset >>>> of GAlignmentsList to GAlignmentPairs. You mention a coercion, but it's >>>> not >>>> obvious to me, unfortunately. >>>> >>>> Another approach would be a GAlignmentPairs where the unpaired reads >>>> have >>>> "missing" mates. I know GAlignments has no concept of missing, but it >>>> would >>>> get everything into a single data structure that is convenient for >>>> computing on pairs. >>> >>> >>> >>> I could modify readGAlignmentPairs() to have the discordant and/or >>> ambiguous pairs end up in th GAlignmentPairs. The ambiguous pairs >>> could be marked as such thru a metadata col of the object or thru >>> a proper slot. The seqnames() and strand() accessors will return >>> * on discordant pairs. Does that sound reasonable? >>> >>> H. >>> >>> >>>> >>>> On Fri, Oct 16, 2015 at 5:21 AM, Morgan, Martin < >>>> martin.mor...@roswellpark.org> wrote: >>>> >>>>> >>>>> >>>>>> -----Original Message----- >>>>>> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf >>>>>> Of >>>>>> Michael Lawrence >>>>>> Sent: Friday, October 16, 2015 7:41 AM >>>>>> To: bioc-devel@r-project.org >>>>>> Subject: [Bioc-devel] readGAlignmentPairs with discordant strand >>>>>> >>>>>> Now that GAlignmentPairs supports discordant strand between mates, how >>>>>> hard would it be to relax that restriction on readGAlignmentPairs()? >>>>>> >>>>>> Also, would be nice if getDumpedAlignments() returned those dumped by >>>>>> readGAlignmentPairs(). Right now, I'm reading a GAlignments (with the >>>>> >>>>> >>>>> extra >>>>>> >>>>>> >>>>>> mcols) and calling makeGAlignmentPairs(). Not so convenient. >>>>> >>>>> >>>>> >>>>> I'm not sure whether this is relevant to your use case but >>>>> readGAlignmentsList returns a list of paired mates, and if appropriate >>>>> (based on ScanBamParam) list elements with solo travelers. The paired >>>>> portion of the list can be coerced to GAlignmentPairs if the additional >>>>> structure of that class is required. >>>>> >>>>> Martin >>>>> >>>>>> >>>>>> Michael >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> Bioc-devel@r-project.org mailing list >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>>>> >>>>> >>>>> >>>>> This email message may contain legally privileged and/or confidential >>>>> information. If you are not the intended recipient(s), or the employee >>>>> or >>>>> agent responsible for the delivery of this message to the intended >>>>> recipient(s), you are hereby notified that any disclosure, copying, >>>>> distribution, or use of this email message is prohibited. If you have >>>>> received this message in error, please notify the sender immediately by >>>>> e-mail and delete this email message from your computer. Thank you. >>>>> >>>> >>>> [[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 > > > -- > 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
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