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. 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
