> -----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. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
