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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