Re: [Seqan-dev] SwiftPattern reinit required

[Fabian Buske <f.buske@uq.edu.au>]

Hi Birte,

thanks for fixing the bug. I made another observation that seems 
strange. I run swift on a bunch of sequences (Finder). However, only the 
first sequence will ever get a match.
Looking at you swiftlocal app I see that you call

Pattern<TQGramIndex, Swift<SwiftLocal> > pattern_swift(index_qgram);

in the inner loop. This probably resets something in the object that is 
crucial to the program. I was wondering if it wouldn't make sense to 
"reuse" the already instantiated object and "just" reset what ever 
required? Or is there a special reason to do it this way? I think it 
used to work (with seqan release 1.2). The swiftlocal app currently 
doesn't compile so I couldn't just give it a go and try what happens 
when the line mentioned above is initialized outside the loop.

Cheers,
Fabian

Kehr, Birte wrote:
> Hi Fabian,
>
>   
> > I've updated my local version to the current trunk but I still get a 
> >     
> "Bus error" when running the Waterman Eggert algorithm. In fact the very 
> first of the examples of alignment_local demo causes the problem. I'm 
> working on i686-apple-darwin9-gcc-4.0.1 on a Mac osx.
>   
> > [...]
> > So I take it that it has not been initialized properly.
> >     
>
> Thanks, there was an initialization problem that did not appear under Linux and Windows. It is fixed now.
>
> Cheers, Birte
>
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--
Fabian Buske
Institute for Molecular Bioscience
The University of Queensland 
Brisbane, Qld. 4072 Australia
Phone: (61)-(7)-334-62608