[BioC] findOverlaps error

Hervé Pagès hpages at fhcrc.org
Mon Jun 3 08:44:06 CEST 2013

Hi Reema,

On 06/01/2013 07:46 AM, Reema Singh wrote:
> Dear all,
> I am getting error when i try to read .bam files. The problem is that i
> don't understand what does not it mean and what I do to solve it. here's
> the error.
> "
> Error in queryHits(findOverlaps(query, subject, maxgap = maxgap, minoverlap
> = minoverlap,  :
>    error in evaluating the argument 'x' in selecting a method for function
> 'queryHits': Error in (function (classes, fdef, mtable)  :
>    unable to find an inherited method for function ‘findOverlaps’ for
> signature ‘"list", "GappedAlignments"’
> "

In addition to showing us the error, could you also show us the code
that produces it please? I'm surprised you get this error when trying
to read .bam files since AFAIK reading .bam files with the standard
tools (i.e. readGappedAlignments or readGappedAlignmentPairs) doesn't
involve calls to findOverlaps().


> I would appreciate any help.
> Regards
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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