[mira_talk] Re: 454 trimming, sff_extract and SFF to traceinfo.xml
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 6 Jan 2011 21:46:18 +0100
On Mittwoch 05 Januar 2011 Peter wrote:
> What puzzles me is why using sff_extract on a typical SFF file (with
> "quality" clipping points but not adapter clipping points) produces a
> traceinfo.xml file with vector trimming entries and NOT quality
> clipping. Is this just a practical solution to the fact that SFF files
> from Roche seem to just have a single value for quality+adapter
> clipping so this be simply mapped to separate quality+vector clipping
> values?
It is a practical solution, yes: it prevents accidents happening should people
ever use -DP:ure=yes on 454 data without having thought things through,
because MIRA would then try to expand also into adaptor areas (which it then
does not know of as they are not marked as adaptors).
> If these two types of information were in the traceinfo.xml
> file given to MIRA would it take advantage of this distinction?
Yes, but then you really need a good adaptor search to add those values to the
XML file. I have the feeling that this is not trivial. But if done right, you
would probably be able to just use the vector clippings and drop the quality
clippings altogether as -CL:pec is pretty good at finding usable base ranges.
B.
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