Hi Michael,
On 10/12/2014 02:02 PM, Michael Lawrence wrote:
This recently became a warning, and I am not sure why. Yes, in the overlap
case, that might be something to worry about. But a perfectly reasonable
use case of merge,Seqinfo is to merge two disjoint sets of seqlevels. Now
we're forced to use suppressWarnings() for that.
For that use case, nothing has changed, we've always had a warning and
we still have it.
With BioC 2.14:
> merge(Seqinfo("chr1"), Seqinfo("chr2"))
Seqinfo of length 2
seqnames seqlengths isCircular genome
chr1 NA NA <NA>
chr2 NA NA <NA>
Warning message:
In .Seqinfo.mergexy(x, y) :
Each of the 2 combined objects has sequence levels not in the other:
- in 'x': chr1
- in 'y': chr2
Make sure to always combine/compare objects based on the same reference
genome (use suppressWarnings() to suppress this warning).
With BioC 3.0:
> merge(Seqinfo("chr1"), Seqinfo("chr2"))
Seqinfo object with 2 sequences from an unspecified genome; no
seqlengths:
seqnames seqlengths isCircular genome
chr1 NA NA <NA>
chr2 NA NA <NA>
Warning message:
In .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
It's just that the warning is different. The intention was to make
the new warning more to the point.
H.
Michael
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Hervé Pagès
Program in Computational Biology
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