Committed in -central changeset 146d0f4c29de

Thanks much Jim,
J.

On Aug 22, 2012, at 4:09 PM, Jim Johnson wrote:

> The VCF format ( 
> http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
>  )
> specifies "." to represent missing values.
> 
> lib/galaxy/visualization/tracks/data_providers.py  throws an float conversion 
> error when the qual field of  a vcf file has the missing value:  "."
> 
> This can be remedied with the following patch,  trackster handles the "None"  
> value when displaying the variant.
> 
> diff -r eb542e228a0f lib/galaxy/visualization/tracks/data_providers.py
> --- a/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:56:49 
> 2012 -0500
> +++ b/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:58:46 
> 2012 -0500
> @@ -634,7 +634,7 @@
>                             # TODO? VCF does not have strand, so default to 
> positive.
>                             "+",
>                             new_seq,
> -                            float( feature[5] ) ]
> +                            None if feature[5] == '.' else float( feature[5] 
> ) ]
>                 rval.append(payload)
> 
>         return { 'data': rval, 'message': message }
> 


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