[ensembl-dev] R59: -stepSize=5 in blat_gfclient.pm

[Hiram Clawson]

Pardon me, you are so correct.  There is no such option to gfClient.
If the ensembl business uses that, it would be incorrect.  It doesn't
make any sense for that argument to gfClient.

--Hiram

volker.weinberger at novartis.com wrote:
> Dear Hiram,
> 
> absolutely and sorry for the typo in the posting.  I meant -stepSize. It's 
> not available in our gfClient.
> 
> stepSize would e.g. be an option for gfServer, but not for gfClient.

> 
> Hiram Clawson <hiram at soe.ucsc.edu> 
> 23.09.2010 18:01
> 
> To
> volker.weinberger at novartis.com
> cc
> dev at ensembl.org
> Subject
> Re: [ensembl-dev] R59: -stepSize=5   in blat_gfclient.pm
> 
> 
> 
> 
> 
> 
> The case on the arguments is important.  It is -stepSize
> 
> See also:  http://www.kentinformatics.com/contact-us.html
> 
> --Hiram
> 
> volker.weinberger at novartis.com wrote:
>> Hi,
>>
>> I'm confused about the option settings for gfClient in 
>> modules/Bio/Tools/Run/Search/blat_gfclient.pm :
>>
>>     "-out=wublast -stepSize=5 -minScore=20"
>>
>> as our internal version of gfClient (from BLAT34) doesn't support the 
>> "-stepsize" option.
>>
>> Do you use a customized version of BLAT or any version other than 34 ?
>>
>> BTW it would be great if the path to the gfClient executable was 
>> configurable in one of the configuration files rather than hard-coded.
>>
>> Best regards,
>>
>> Volker