[mira_talk] Re: vector clipping

On Sunday 15 March 2009 Jan Paces wrote:
> [...]
> I am using sffinco2mirafiles.tcl according to this line in documentation:
> [...]
> (I found it somewhere, but I am not sure where, I wasn't able to track it
> again - maybe outdated info.)

sff2info was a quick hack of mine which I ditched as soon as Jose had published 
his excellent sff_extract.

> I am curious, why there should be "vector clip" in xml instead od "quality
> clip"? I though information extracted from sff file is mostly about
> quality clipping. Anyway, I shall use sff_extract from now on.

Long story short: although there are fields reserved for sequencing vector 
(well, adaptor) clips in the SFF specification, the 454/Roche tool chain puts 
every clip information as "quality clip" into the SFF. Including adaptor 
clips.

Now, that would not be a problem if MIRA didn't have routines that try to use 
also bad quality sequence data if the situation permits. To do so, it analyses 
sequence that is quality clipped, but never touches sequences sequences under 
sequence vector clip.

Well, as the 454/Roche clips are all filed as "quality clips", hilarity ensues 
(NOT).

Perhaps, one day, we'll see the adaptor clips correctly put into the correct 
fields, but until then it's better to treat everything as sequencing vector 
(adaptor) clip.

Regards,
  Bastien


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