Hi Michael,
On 10/17/2015 12:01 PM, Michael Lawrence wrote:
Cool, thanks. So does it make sense to have that as the coercion from
GAlignmentsList to GAlignmentPairs? I can add it, if it seems
reasonable. I'm kind of torn on whether a coercion should discard records.
Right, the coercion won't return an object parallel to the input but you
don't have much choice. You could emit a warning to mitigate this.
2 more things:
1) We should refrain from propagating discordant pairs for now. Even
though the GAlignmentPairs container can store them, the API is not
ready. It will be easy to propagate them later. For now, the coercion
method could emit the same kind of warning emitted by
readGAlignmentPairs() about the discordant pairs being dropped.
2) You might want to propagate pairs with
mate_status %in% c("mated", "ambiguous")
instead of "mated" pairs only.
Thanks,
H.
On Sat, Oct 17, 2015 at 8:37 AM, Morgan, Martin
<martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>>
wrote:
Val and I discussed this a bit, with the resolution that calling the
GAlignmentPairs() constructor on the first and the second element of
the GAlignmentsList was the 'easiest' way to go.
ga = unlist(gal[mcols(gal)$mate_status == "mated"])
GAlignmentPairs(ga[c(TRUE, FALSE)], ga[c(FALSE, TRUE)])
(completely speculative code). If I understand correctly, there's a
check in for discordant pairs in readGAlignmentPairs, but not in
GAlignmentPairs itself; could be mistaken though...
Martin
________________________________________
From: Michael Lawrence [lawrence.mich...@gene.com
<mailto:lawrence.mich...@gene.com>]
Sent: Saturday, October 17, 2015 9:48 AM
To: Hervé Pagès
Cc: Michael Lawrence; Morgan, Martin; bioc-devel@r-project.org
<mailto:bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] readGAlignmentPairs with discordant strand
This might have been lost in this thread. If there is an easy way to
coerce a GAlignmentsList where all(lengths(x) == 2) to a
GAlignmentPairs, please let me know. Otherwise, I'll add a coerce
method. Debating whether it should discard elements of length != 2,
or if it should fail.
On Fri, Oct 16, 2015 at 9:58 AM, Michael Lawrence <micha...@gene.com
<mailto:micha...@gene.com><mailto:micha...@gene.com
<mailto:micha...@gene.com>>> wrote:
Sure, "*" makes more sense for strand, given the precedent.
On Fri, Oct 16, 2015 at 9:55 AM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org><mailto:hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>>> wrote:
> 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 <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org><mailto:hpa...@fredhutch.org
<mailto:hpa...@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.mor...@roswellpark.org
<mailto:martin.mor...@roswellpark.org><mailto:martin.mor...@roswellpark.org
<mailto:martin.mor...@roswellpark.org>>> wrote:
>>>>
>>>>>
>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org
<mailto:bioc-devel-boun...@r-project.org><mailto:bioc-devel-boun...@r-project.org
<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
<mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org
<mailto: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
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel@r-project.org
<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org
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>>>>>
>>>>>
>>>>>
>>>>>
>>>>> This email message may contain legally privileged and/or confidential
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>>>>> or
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>>>>
>>>> [[alternative HTML version deleted]]
>>>>
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>>>
>>> --
>>> 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: hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org><mailto:hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>>
>>> Phone: (206) 667-5791
<tel:%28206%29%20667-5791><tel:%28206%29%20667-5791>
>>> Fax: (206) 667-1319
<tel:%28206%29%20667-1319><tel:%28206%29%20667-1319>
>
>
> --
> 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: hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org><mailto:hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>>
> Phone: (206) 667-5791
<tel:%28206%29%20667-5791><tel:%28206%29%20667-5791>
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This email message may contain legally privileged and/or
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is prohibited. If you have received this message in error, please
notify the sender immediately by e-mail and delete this email
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--
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: hpa...@fredhutch.org
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