[mira_talk] Re: miraSearchESTSNPs

On Freitag 29 Mai 2009 hegemon78@xxxxxxxxxxxxxx wrote:
> >> 2. Is there any way to force program to do outputs in GAP4 format for
> >> step 1 and step 2?
> >Putting -OUT:org=yes in the me_step*.par file does not work?
>
> no, but in log is:
> ...454 type data present, switching off GAP4DA type output results
> (you *DO NOT* want millions of files in a directory, really)...

Ah, I remember. Yes, that's a fool guard I had built in when 454 came into the 
game and gap4 directories regularly had half a million or millions of entries 
... which lets filesystems get exteremely slow and system admins despair when 
running overnight backups.

Do you have a compelling reason *not* to use the CAF files which are written by 
default? If yes I could remove it, but please note that CAFs can be 
transformed into a gap4 database via the "caf2gap" command (from the Sanger 
Centre) or to a gap4 directory with the "convert_project" command (from the 
MIRA package).

Regards,
  Bastien


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