[GenABEL-dev] [genabel-Bugs][5658] Missing genetic data cannot be coded as NA or N as mentioned in the manual

[Yury Aulchenko]

Agree, fix the manual :)

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Sent from mobile device, please excuse possible typos

> On 28 Apr 2014, at 05:47, <genabel-bugs at r-forge.r-project.org> wrote:
> 
> Bugs item #5658, was opened at 2014-04-28 00:46 by Lennart Karssen
> You can respond by visiting: 
> https://r-forge.r-project.org/tracker/?func=detail&atid=2058&aid=5658&group_id=505
> 
> Status: Open
> Priority: 3
> Submitted By: Lennart Karssen (lckarssen)
> Assigned to: Nobody (None)
> Summary: Missing genetic data cannot be coded as NA or N as mentioned in the manual 
> Resolution: Accepted As Bug
> Operating System: All
> Severity: normal
> Hardware: All
> Version: PA v0.4.3
> Component: ProbABEL
> URL: http://forum.genabel.org/viewtopic.php?f=10&t=871
> 
> 
> Initial Comment:
> Thanks to user jal on the forum for reporting this bug. From his post:
> 
> There are missing genotypes in my dosage file, while missing values were coded as "NA". My palogist run is aborted with error message:
>    Reading genotype data... No digits were found while reading genetic data (individual 5, position 1)
> where "individual 5, position 1" is the location where the first missing value "NA" appears. The ProbABEL manual says missing value can be coded as "NA", "NaN" or "N", but seems "NA" and "N" do not work in my case.
> 
> 
> We use the standard C function strtod() to convert the genetic data from text to numbers. I did a quick check and strtod() only accepts "NaN", "NAN", "nan", no "NA" or "N". My guess is that the 'nan' variations are the only ones defined for floating point numbers (IEEE 754). 
> 
> We should decided whether we want to change the manual or change to code. Changning the manual has my preference, because changing the code would make reading data slower. 
> 
> 
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> You can respond by visiting: 
> https://r-forge.r-project.org/tracker/?func=detail&atid=2058&aid=5658&group_id=505