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

[volker.weinberger at novartis.com]

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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