[BioC] Rsamtools Error: vector of negative length

[Martin Morgan]

On 11/09/2010 05:22 AM, Christoph Bartenhagen wrote:
> Hello everyone,
> 
> I am experiencing a strange error, while reading (large) BAM-files (>
> 2GB) in R with the function scanBam() in the Rsamtools package.
> It stops saying "negative length vectors are not allowed".
> 
> I think my BAM-file is ok, because I can read it in small chunks like
> reads on positive strand first, then reads on the negative strand (using
> ScanBamParam). This might be a more general Error in R because it seems
> to occur in very different R programs.
> 
> Has anyone experienced this error?
> I would really appreciate any ideas how to fix this problem or
> concerning the reason for this error (I don't really understand what a
> "negative length vector" is).

Hi Christoph --

This is an integer overflow when the (accumulated) underlying DNA or
quality strings are too long. But I think this has been addressed and so
your sessionInfo() and a reproducible example (or at least the explicit
command that triggers the problem) would help.

Martin

> 
> Thanks in advance
> Christoph
> 
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