53 lines
1.2 KiB
C
53 lines
1.2 KiB
C
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/*
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* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
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*
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* This file is part of Bowtie 2.
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*
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* Bowtie 2 is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* Bowtie 2 is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#ifndef BANDED_H_
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#define BANDED_H_
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#include "sse_util.h"
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/**
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* Use SSE instructions to quickly find stretches with lots of matches, then
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* resolve alignments.
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*/
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class BandedSseAligner {
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public:
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void init(
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int *q, // query, maskized
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size_t qi, // query start
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size_t qf, // query end
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int *r, // reference, maskized
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size_t ri, // reference start
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size_t rf) // reference end
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{
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}
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void nextAlignment() {
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}
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protected:
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EList_m128i mat_;
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};
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#endif
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