[mira_talk] Re: smalt doc additions
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 5 Mar 2011 16:42:55 +0100
On Saturday 05 March 2011 16:17:43 Martin Mokrejs wrote:
> I haven't tested this for vector screening (large matches) but for 30nt
> adaptor smalt always crashed on my 32bit linux
Switch to 64 bit. There is nowadays no compelling reason for 64 bit.
Especially not in the area of sequence assembly.
> Hope you clarified that in the docs if one has to ask smalt to produce
> ssaha2-like format or if mira can use some other ... ;-)
Yup.
> [SSAHA2/SMALT]
> What will happen when the match regions are partially overlapping? Will
> their union be used, or the intersection?
Union. Not prgramatically done, but simply because the same routines are
called once for the SSAHA2 file and once for SMALT. Which is a union in effect.
And of course, as in every clipping: rightmost leftlip and leftmost rightclip
will win.
> What if there is no overlap between the two methods?
Well, union still :-)
But please do not built upon this behaviour ... I might very well remove it in
the future when consolidating the code.
> Yeah, the section in the docs about adapter
> clipping is also unclear,
What there?
B.
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