[Bioc-devel] readGAlignmentPairs with discordant strand

[Michael Lawrence]

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.Morgan at roswellpark.org> wrote:

>
>
> > -----Original Message-----
> > From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf Of
> > Michael Lawrence
> > Sent: Friday, October 16, 2015 7:41 AM
> > To: bioc-devel at 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]]
> >
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