Hi Michael, Martin,
On 10/16/2015 06:48 AM, Michael Lawrence wrote:
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.
I could modify readGAlignmentPairs() to have the discordant and/or
ambiguous pairs end up in th GAlignmentPairs. The ambiguous pairs
could be marked as such thru a metadata col of the object or thru
a proper slot. The seqnames() and strand() accessors will return
* on discordant pairs. Does that sound reasonable?
H.
On Fri, Oct 16, 2015 at 5:21 AM, Morgan, Martin <
martin.mor...@roswellpark.org> wrote:
-----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
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