[Bioc-devel] Missing seqinfo method for BamFileList?

[Martin Morgan]

Hi Ryan --

I implemented your suggestion in Rsamtools 1.17.8; it's a little weird to come 
up with such a synthetic Seqinfo, but I think the usual use case will be that 
the bam files are actually identical with respect to their seqinfo. And it's 
better than the previous behavior.

Thanks for the suggestion,

Martin

On 04/25/2014 03:58 PM, Ryan C. Thompson wrote:
> Hi all,
>
> I noticed that the seqinfo works on BamFile objects, but not on BamFileList
> objects. For BamFileList, it does not throw an error, but rather uses the
> inherited method for "List", which does not return a useful result for
> BamFileList. I suggest the following implementation of a useful seqinfo function
> for BamFileList, along with some code demonstrating the problem:
>
> fl <- BamFile(system.file("extdata", "ex1.bam", package="Rsamtools",
> mustWork=TRUE))
> # This works.
> seqinfo(fl)
>
> fll <- BamFileList(fl, fl)
> ## This works, but it uses the generic for "List" which gives a useless result.
> seqinfo(fll)
>
> ## Now add a method
> setMethod("seqinfo", signature=list(x="BamFileList"), function (x)
> {
>      Reduce(merge, lapply(x, seqinfo))
> }
> )
>
> ## Now this returns a good result
> seqinfo(fll)
> ## So does this
> seqlengths(fll)
>
>
>
> -Ryan Thompson
>
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