[BioC] Bug (?) in IRanges::findOverlaps(self, ignoreSelf=TRUE, ignoreRedundat=TRUE)

[Steve Lianoglou]

One more : sorry for the spam:

On Wed, May 12, 2010 at 3:54 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
>
> On Wed, May 12, 2010 at 3:35 PM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
>> Hi,
>>
>> I think I've found a corner case in the findOverlaps function when you are:
>>
>> (i) omitting the subject arg
>> (ii) both ignoreSelf and ignoreRedundant areTRUE
>> (iii) and only 1 overlap should be returned(?) <-- not sure about this one
>
> I think adding a judicious ",drop=FALSE]" in line112
> IntervalTree-utils.R (rev 46808) would solve the problem, ie:
>
> mat <- mat[!duplicated(norm_mat),,drop=FALSE]

I guess doing the same on line 108 might be prudent as well.

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact