[Bioc-devel] seqlevelsStyle on alternate chromosomes

[Michael Lawrence]

Ok. Could it at least issue a warning when some seqlevels are not mappable?

Thanks,
Michael

On Thu, Dec 17, 2015 at 3:40 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> Hi Michael,
>
> On 12/17/2015 02:45 PM, Michael Lawrence wrote:
>>
>> Seems like seqlevelsStyle<- between e.g. UCSC and NCBI does not work
>> outside of the "standard" chromosomes. Since GRCh38 (NCBI) and hg38
>> (UCSC) are the same assembly, we could probably implement a complete
>> mapping, right?
>
>
> Unfortunately, the seqlevelsStyle() getter and setter were designed
> from the very beginning to handle only the standard chromosomes.
> Changing this is on the TODO list but didn't happen yet because it
> requires a complete refactoring. In the mean time, see
> ?fetchExtendedChromInfoFromUCSC for how to map GRCh38 seqlevels to
> hg38 seqlevels.
>
> H.
>
>>
>> Michael
>>
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>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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>
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