[mira_talk] Re: bug

Hi Bastien,
the bug is reproducable. It occures when I use the option --min_left_clip=11. 
If it's helpful I can send you the sff.
cheers
Burkhard

Bastien Chevreux schrieb:

On Dienstag 05 Mai 2009 Burkhard Steuernagel wrote:

Hi Laurent,
did you use the sff_extract third party script? I had exactly the same
error for some of my SFFs and it turned out that the sff_extract script
produced wrong data.
Once upon a time there was the command
sffinfo mysff.sff |sffinfo2mirafiles.tcl -project mysff
and applying this on the same sff worked good.
Yikes! This is something I'd actually like to hear earlier. sff_extract is actually quite good and as long 454/Roche does not offer the possibility to split paired-end reads of a SFF, it's the only possibility I know to get these sequences out of the container.
Actually, there has been some work don on sff_extract and I'm waiting for Jorge to put it up on his web site. 

Burkhard, can you please have a look at
    http://www.chevreux.org/tmp/mira_3rdparty_05-05-2009.tar.bz2
and tell whether the version contained within still produces wrong results for you? 

If yes, I'd need to wield a debugger and go out on a hunt.

Regards,
  Bastien




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