[Bioc-devel] seqlevelsStyle on alternate chromosomes

[Hervé Pagès]

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

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