[GenABEL-dev] bug_in_OmicABEL_reshuffle_fixed

[L.C. Karssen]

Thanks Содбо, good work!

I've got a similar feature request/bug report for ProbABEL, do you know
what the effect of going from unsigned int to int64 will be on memory
usage? In the case of ProbABEL it is mostly about the counters for SNPs
and samples/IDs, so my guess is that it wouldn't be much of an increase
(only a few extra bits for those counters); all the allelic
dosages/probabilities are stored as doubles, so that won't change.

Of course going from unsigned int to in64 will mean people can load more
data at the same time, but in my opinion it is their responsibility to
have enough free memory (if they don't have that ProbABEL will fail with
an allocation error).


Thanks,

Lennart.

On 01-07-13 09:51, Содбо Шарапов wrote:
> Dear all!
> I fixed bug in OmicABEL_reshuffle.
> This bug was only for big data. The reason is, that for big output data
> value of tile_coordinate is higher, than max(int).
> For example: for data with 1080 ids and 122756 SNPs
> max(tile_coordinate)=1080(ids) * 122756(SNPs) * 8 (sizeof(double)) * 5
> (columns:beta_1,se_1,beta_SNP,se_SNP, etc) =  5 303 059 200
> max(int) = 2 147 483 647
> max(unsigned int) = 4 294 967 295
> This values is lower than max(tile_coordinate). That's why
> tile_coordinates for a half of data were incorrect and senseless.
> So, the solution of this problem is change type of variabels for
> tile_coordinates: I select int64_t instead of int.
> max (int64_t)= 9,223,372,036,854,775,808. I think this is enough!=)
> Now, "reshuffle" works with big data correctly. Compilation for Linux
> and Windows was succesful.
> -- 
> ___________________________________
> _
> _With best regards
> 
> Sodbo Zh. Sharapov
> Phone:  +79831347688
> Email:    sharapovsodbo at gmail.com <mailto:sharapovsodbo at gmail.com>
>              sharapov at bionet.nsc.ru <mailto:sharapov at bionet.nsc.ru>
> Skype:   sharapovsodbo
> 
> 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

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