[Bioc-devel] readGAlignmentPairs with discordant strand

[Michael Lawrence]

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

On Fri, Oct 16, 2015 at 9:15 AM, Hervé Pagès <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
>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
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>>
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>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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