i was able to trigger this error by supplying a snp id with more than 126
characters (BUFFERSIZE of the
read_uncertain.c source).

check for a record that has a very long string, perhaps because whitespace
was accidentally eliminated in
generating the impute2 output.


On Thu, Jan 23, 2014 at 12:08 PM, francesca casalino <
francy.casalino@gmail.com> wrote:

> Hi all,
> I am trying to read a file called "chr1.gen" that contains imputation
> posterior probabilities (3 values per SNP) and SNP names in the second
> column, and I am trying to use the snpStats function "read.impute", but
> when I try to read the whole file:
>
> x=read.impute("chr1.gen"))
>
> I get the following error message:
>
> Error in read.impute("chr.gen") :
> input field exceeds buffer length
>
> However the data seems to load when I set a limit for the number of SNPs:
>
>  x=read.impute("chr1.gen",nsnp=200)
>
> Does anyone know what this error means? Is it expecting maybe a subset of
> the file, or is this an R issue? I could not find any examples of this on
> the web, so if you have encountered this error before please let me know.
>
> Thank you
>
> -fra
>
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