[BioC] Rsamtools Error: vector of negative length

Christoph Bartenhagen Christoph.Bartenhagen at ukmuenster.de
Tue Nov 9 14:22:19 CET 2010


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).

Thanks in advance
Christoph



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