[ensembl-dev] Bugs in gtf2vep.pl script

Will McLaren wm2 at ebi.ac.uk
Thu Nov 8 15:57:06 GMT 2012


Hi Duarte,

Thanks for the suggestions.

The @ARGV thing slipped through the net! I've fixed that on the CVS tree,
but using a slightly different change to the one you suggest.

There is nothing in GetOptions that requires you specify --dir or
--cache_region_size; GetOptions will only fail if you provide an invalid
option, for example providing a string to --db_version instead of an
integer.

cache_region_size is not mentioned at all because it is not an option you
should be changing unless you really really know what you are doing - it is
there mainly to assist me in development.

Thanks again

Will McLaren
Ensembl Variation


On 8 November 2012 15:24, Duarte Molha <Duarte.Molha at ogt.co.uk> wrote:

> Dear Developers****
>
> ** **
>
> I had a play around with the new gtf2vep script and came across a few bugs
> and incomplete help.****
>
> ** **
>
> I have made some improvements on the help usage information and corrected
> the bugs on line 29 , 30 and 34****
>
> ** **
>
> Briefly, the first issue I encountered is that I believe the
> “cache_region_size” and the “dir” arguments are suppose to be optional
> since they are assigned default values on lines 46 and 49****
>
> They are set to be required so the script does not pass the GetOptions
> step if you do not provide them. ****
>
> Also the  “cache_region_size” wasn’t even mentioned in the usage
> information so I added it.****
>
> ** **
>
> In line 34 the if statement:****
>
> if(defined($config->{help}) || !@ARGV) ****
>
> would always fail because on a correctly input command line, after the
> GetOptions step the @ARGV variable should be empty. So the expression for a
> valid syntax would always return true and the script would not continue. *
> ***
>
> I corrected it to:****
>
> if(defined($config->{help}) || @ARGV) ****
>
> ** **
>
> I also took the liberty to indicate in the help session what arguments a
> really required and what arguments are optional.****
>
> ** **
>
> I hope you agree with the changes.****
>
> ** **
>
> Best regards****
>
> ** **
>
> Duarte Molha****
>
> ** **
>
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