[Bioc-devel] warning when merging disjoint sets of seqlevels

[Hervé Pagès]

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 <hpages at fhcrc.org
> <mailto:hpages at 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
>
>                  [[alternative HTML version deleted]]
>
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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: hpages at fhcrc.org <mailto:hpages at fhcrc.org>
>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
>

-- 
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: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319