[Bioc-devel] readGAlignmentPairs with discordant strand
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
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