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Re: [Seqan-dev] SwiftPattern reinit required

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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
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