This was my doing. I guess merge,Seqinfo,Seqinfo does not support different
orderings? Would help to see the actual error message and stack trace. Any
advice Herve?

Michael


On Sun, Nov 3, 2013 at 6:55 AM, Julian Gehring <julian.gehring@embl.de>wrote:

> Hi Valerie and Herve,
>
> When providing a 'Seqinfo' object as the 'genome' argument to 'readVcf',
> would it be possible to not have the requirement of the VCF header and the
> seqinfo object to have the same ordering?  As the moment
> (VariantAnnotation_1.8.2), the import will fail if this is not the case.
>  However, this requires the user to know the ordering of the seqnames in
> the VCF file beforehand.  In the ideal case, the readVcf function could
> reorder the seqnames in the way as provided by the 'genome' argument.
>
>
> Best wishes
> Julian
>
>
> On 09/28/2013 12:57 AM, Hervé Pagès wrote:
>
>> Hi Julian,
>>
>> With the latest devel version of GenomicRanges (1.13.48, should become
>> available via biocLite() in the next 24 hours or so), setting the
>> seqinfo of a big VCF object should be much faster but your mileage
>> may vary. Let us know if you still find it slow enough to justify a
>> mechanism for letting the user specify the seqinfo upfront when using
>> readVcf() (e.g. the 'genome' arg could be renamed 'seqinfo' and accept
>> everything it supports now plus a Seqinfo object).
>>
>> Cheers,
>> H.
>>
>> On 09/24/2013 10:00 AM, Julian Gehring wrote:
>>
>>> Hi Valerie,
>>>
>>>  Thanks for clarifying. No, there is not currently a way to do this.
>>>>
>>>> The 'seqinfo' on the rowData(vcf) should not be difficult to change. Can
>>>> you provide more detail as to (1) why you are changing it (did readVcf()
>>>> import something incorrectly or ?) and (2) what operations on the
>>>> 'seqinfo' are taking a long time.
>>>>
>>>
>>> 'readVcf' did everything in a correct way.  I needed to add the
>>> information about the genome, circularity, and seqlengths based on
>>> external annotitation, since it is not part of the VCF file.
>>>
>>> I can't tell you at the moment where 'seqinfo <-' spends most of its
>>> time.  I'll profile it and get back to you.
>>>
>>> Thank your for your quick answer and your help!
>>>
>>> Best wishes
>>> Julian
>>>
>>>
>>>  Thanks.
>>>> Valerie
>>>>
>>>>
>>>>> Best wishes
>>>>> Julian
>>>>>
>>>>>
>>>>> On 09/24/2013 06:31 PM, Valerie Obenchain wrote:
>>>>>
>>>>>> Hi Julian,
>>>>>>
>>>>>> On 09/24/2013 02:29 AM, Julian Gehring wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Is there a direct way to specifiy the 'seqinfo' of a genome for the
>>>>>>> import of a VCF file using 'readVcf'?
>>>>>>>
>>>>>>
>>>>>> I think the question is how to read in a subset of
>>>>>> chromosomes/positions
>>>>>> from a vcf file without an accompanying tabix index. You can't.
>>>>>> readVcf() requires an index when subsets are defined by
>>>>>> chromosome/position. However you can read in subsets defined by INFO
>>>>>> and/or GENO fields without an index.
>>>>>>
>>>>>> Approaches:
>>>>>> (1) create index with ?indexTabix and specify 'which' in ScanVcfParam
>>>>>> (2) use ?filterVcf to write out a new file of records of interest
>>>>>>
>>>>>>  I'm aware that one can change it
>>>>>>> with the 'seqinfo' method afterwards, but for large VCF files this
>>>>>>> can
>>>>>>> take a significant amount of time.
>>>>>>>
>>>>>>
>>>>>> What operation is taking along time? Subsetting the VCF object by
>>>>>> chromosome?
>>>>>>
>>>>>> Valerie
>>>>>>
>>>>>>
>>>>>>> An alternative would be to sneak it in by the 'which' arguments, such
>>>>>>> as:
>>>>>>>
>>>>>>> readVcf(file, genome, ScanVcfParam(which = as(seq_info, "GRanges")))
>>>>>>>
>>>>>>> but this requires the file to be indexed beforehand.
>>>>>>>
>>>>>>> Best wishes
>>>>>>> Julian
>>>>>>>
>>>>>>>
>>>>>>
>>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.
> science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

