[BioC] query and subject hits in findOverlaps through different space names

[Robert Castelo]

thanks Michael for fixing this quickly, one minor detail, i've noticed 
that the version
number of the IRanges code i've checked out with the fix from the svn 
repository is
1.5.76 which is the same that showed up in the sessionInfo() below 
reporting the bug.
maybe it is ok like this, but just wanted to point it out in case that 
it should be different
for the automagic update.packages() thingy.

cheers,
robert.


On 4/13/10 5:13 PM, Michael Lawrence wrote:
> Yes this has been fixed.
>
> On Tue, Apr 13, 2010 at 7:24 AM, James W. MacDonald
> <jmacdon at med.umich.edu>wrote:
>
>    
>> Has this been fixed in svn?
>>
>> Michael Lawrence wrote:
>>
>>      
>>> On Tue, Apr 13, 2010 at 2:38 AM, Robert Castelo<robert.castelo at upf.edu
>>>        
>>>> wrote:
>>>>          
>>>   dear list and, particularly, IRanges developers,
>>>        
>>>> i've noticed a change shown below in the functionality of the
>>>> findOverlap function from the IRanges package from the current BioC
>>>> release version 2.10 to the current BioC devel (about to become release)
>>>> version 2.11 (i've checked-out the latest IRanges version at the svn
>>>> repository).
>>>>
>>>> this change seems to alter the way in which findOverlaps() return the
>>>> hits. in the current release findOverlaps() was returning the index of
>>>> the hits with respect to the entire RangedData object while in the
>>>> current devel version it does it with respect to the corresponding
>>>> space. is this an intended change or is it a bug? (i was happier with
>>>> the behavior of the release..)
>>>>
>>>>
>>>>   It's a bug. Dimensions got switched around in RangesMatching, which
>>>>          
>>> confused
>>> RangesMatchingList. It's been broken since 2/26/10, in case anyone wants
>>> to
>>> re-run their scripts.
>>>
>>> Thanks a lot for catching this,
>>>
>>> Michael
>>>
>>>
>>>   thanks!
>>>        
>>>> robert.
>>>>
>>>> =========================current release 2.10==================
>>>> suppressPackageStartupMessages(library(IRanges))
>>>>
>>>> x<- RangedData(IRanges(start=c(1,6), end=c(5,10)),
>>>>                        space=c("chr1","chr2"))
>>>> x
>>>> RangedData with 2 rows and 0 value columns across 2 spaces
>>>>        space    ranges |
>>>>   <character>  <IRanges>  |
>>>> 1        chr1   [1,  5] |
>>>> 2        chr2   [6, 10] |
>>>>
>>>> y<- RangedData(IRanges(start=8, end=10),
>>>>                        space="chr2")
>>>> y
>>>> RangedData with 1 row and 0 value columns across 1 space
>>>>        space    ranges |
>>>>   <character>  <IRanges>  |
>>>> 1        chr2   [8, 10] |
>>>>
>>>> as.matrix(findOverlaps(x, y))
>>>>     query subject
>>>> [1,]     2       1
>>>> sessionInfo()
>>>> R version 2.10.1 (2009-12-14)
>>>> x86_64-unknown-linux-gnu
>>>>
>>>> locale:
>>>> [1] C
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods
>>>> base
>>>>
>>>> other attached packages:
>>>> [1] IRanges_1.4.14
>>>> ===============================================================
>>>>
>>>> ========================current devel 2.11=====================
>>>> suppressPackageStartupMessages(library(IRanges))
>>>>
>>>> x<- RangedData(IRanges(start=c(1,6), end=c(5,10)),
>>>>                        space=c("chr1","chr2"))
>>>> x
>>>> RangedData with 2 rows and 0 value columns across 2 spaces
>>>>        space    ranges |
>>>>   <character>  <IRanges>  |
>>>> 1        chr1   [1,  5] |
>>>> 2        chr2   [6, 10] |
>>>> y<- RangedData(IRanges(start=8, end=10),
>>>>                        space="chr2")
>>>> y
>>>> RangedData with 1 row and 0 value columns across 1 space
>>>>        space    ranges |
>>>>   <character>  <IRanges>  |
>>>> 1        chr2   [8, 10] |
>>>> as.matrix(findOverlaps(x, y))
>>>>     query subject
>>>> [1,]     1       1
>>>> R version 2.11.0 Under development (unstable) (2010-02-25 r51180)
>>>> x86_64-unknown-linux-gnu
>>>>
>>>> locale:
>>>> [1] C
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods
>>>> base
>>>>
>>>> other attached packages:
>>>> [1] IRanges_1.5.76
>>>>
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>>>>
>>>>          
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>>>
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>>>        
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> University of Michigan
>> Department of Human Genetics
>> 5912 Buhl
>> 1241 E. Catherine St.
>> Ann Arbor MI 48109-5618
>> 734-615-7826
>> **********************************************************
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>>      
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