[Bioc-devel] Build error in released version

[Hervé Pagès]

Hi Julie,

On 07/05/2016 01:03 PM, Zhu, Lihua (Julie) wrote:
> Dear Herve,
>
> Thank you so much for the detailed explanation and quick fix!
>
> When fusion occurs, the 2 alignments in a pair could be on different
> chromosomes. Not sure what is the best way to handle this situation. If
> set seqnames to *, then the mapping location is lost.

The exact mapping location is stored in the GAligmentPairs object and
will be preserved when the user coerces to GRangesList, either with
grglist(.) or as(. , "GRangesList"). I was thinking in using * only
when coercing to GRanges, either with granges(.) or as(. , "GRanges").

> Maybe set seqnames
> to one of the chromosome, and have a mcol seqname2? Indicating chromosome
> fusion?

There is really no good way to represent features that span multiple
chromosomes with a GRanges object. These features are better represented
with a GRangesList object. That's really what GRangesList objects are
for.

So after giving it a 2nd thought, I'm tempted to either (a) just let
coercion of GAligmentPairs to GRanges fail (with an informative error
message) when some pairs span more than 1 chromosome, or (b) drop
these pairs with a warning, or (c) add an extra argument to granges()
to let the user decide between (a) and (b).

Hopefully that makes sense.

H.

>
> Best,
>
> Julie
>
>
>
>
>
>
> On 7/4/16 12:28 AM, "Hervé Pagès" <hpages at fredhutch.org> wrote:
>
>> Hi Julie,
>>
>> The GAlignmentPairs container didn't support discordant strand until
>> BioC 3.4 (current devel). In the current release (and in previous
>> versions of BioC) strand discordance was not supported. I recently
>> fixed a bug in the released version of GenomicAlignments where the
>> strand() getter was returning an incorrect strand for pairs with
>> discordant strand, instead of raising an error. This fix is what
>> breaks the GUIDEseq vignette which creates and manipulates a
>> GAlignmentPairs object with discordant strand.
>>
>> I just changed this again (in GenomicAlignments 1.8.4) so the
>> strand() getter now returns * instead of raising an error in case
>> of discordant strand (this is actually what strand() does in devel
>> where strand discordance is now fully supported). That seems to
>> fix GUIDEseq's vignette.
>>
>> I guess there was no solid reason for not supporting strand discordance.
>> It was just a matter of deciding how the various GAlignmentPairs getters
>> and extractors should handle this. Having strand() or granges() return
>> * is probably the natural thing to do.
>>
>> A more complicated situation, which is also much less common, is
>> chromosome discordance i.e. when the 2 alignments in a pair are on
>> different chromosomes. Not clear what seqnames() or granges() should
>> do in that case. Maybe return/set the seqname to * but that means
>> introducing * as a special seqlevel. Still need to think about the
>> implications of this.
>>
>> Cheers,
>> H.
>>
>> On 07/01/2016 02:23 PM, Zhu, Lihua (Julie) wrote:
>>> Hi,
>>>
>>> I just noticed that the released version of GUIDEseq failed at build
>>> stage, which did not occur previously and I did not make any change to
>>> the release version.
>>>
>>> The error points to the GAlignmentPairs container. Is this an intended
>>> change and should I modify my code to accommodate the change? If yes,
>>> what is the rational to enforce the rule that
>>>
>>> GAlignmentPairs container supports pairs where the 2 alignments are on
>>> opposite strands of the same  chromosome?
>>>
>>> Thanks for your help!
>>>
>>> Error in .local(x, ...) :
>>>     For some pairs in 'x', the 2 alignments are not on opposite strands.
>>> Cannot
>>>     associate a strand to them. Note that the GAlignmentPairs container
>>> only
>>>     supports pairs where the 2 alignments are on opposite strands of the
>>> same
>>>     chromosome at the moment.
>>>
>>> Best regards,
>>>
>>> Julie
>>>
>>> 	[[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