On 10/13/2014 07:45 AM, Michael Lawrence wrote:
But the behavior has changed for this case:
merge(Seqinfo("chr1"), Seqinfo())
Before it was "each has seqlevels not in the other" but now it is "these
two sets are disjoint". Subtle difference, but I think it's important?
What has changed is that now we get the warning for the edge-case where
one of the 2 Seqinfo objects is empty. In that particular case the
warning is arguably not useful so I just removed it.
H.
On Sun, Oct 12, 2014 at 11:46 PM, Hervé Pagès <hpa...@fhcrc.org
<mailto:hpa...@fhcrc.org>> wrote:
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
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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