[Bioc-devel] readGAlignmentPairs with discordant strand

On 10/16/2015 09:28 AM, Michael Lawrence wrote:

I kind of wish it would return NA for things like seqnames and strand,
but yes that would be very useful.

Could do this for seqnames() but I'm hesitant to do this for strand().
If you look at ?strand in BiocGenerics, ?*? is used when the exact
strand of the location is unknown, or irrelevant, or when the "feature"
at that location belongs to both strands. A pair with discordant strand
belongs to both strands. Also there is a lot of code around that
assumes strand() never returns NAs.


H.

On Fri, Oct 16, 2015 at 9:15 AM, Herv? Pag?s <hpages at fredhutch.org> wrote:

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.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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--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319