[Bioc-devel] readGAlignmentPairs with discordant strand

[Hervé Pagès]

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, 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]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
>>>>
>>>> This email message may contain legally privileged and/or confidential
>>>> information.  If you are not the intended recipient(s), or the employee
>>>> or
>>>> agent responsible for the delivery of this message to the intended
>>>> recipient(s), you are hereby notified that any disclosure, copying,
>>>> distribution, or use of this email message is prohibited.  If you have
>>>> received this message in error, please notify the sender immediately by
>>>> e-mail and delete this email message from your computer. Thank you.
>>>>
>>>
>>>          [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>> --
>> Hervé Pagès
>>
>> 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

-- 
Hervé Pagès

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