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

Hiram Clawson hiram at soe.ucsc.edu
Thu Sep 23 17:01:25 BST 2010

The case on the arguments is important.  It is -stepSize

See also:  http://www.kentinformatics.com/contact-us.html


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

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