[Bioc-devel] readGAlignmentPairs with discordant strand

[Hervé Pagès]

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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-- 
Hervé Pagès

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