[Bioc-devel] readGAlignmentPairs with discordant strand

[Morgan, Martin]

> -----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
> 
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