I kind of wish it would return NA for things like seqnames and strand, but yes that would be very useful.
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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
