[Bioc-devel] readGAlignmentPairs with discordant strand

-----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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