81 lines
2.3 KiB
C++
81 lines
2.3 KiB
C++
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/*
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* Copyright 2012, 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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#include "aligner_driver.h"
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void AlignerDriverRootSelector::select(
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const Read& q,
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const Read* qo,
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bool nofw,
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bool norc,
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EList<DescentConfig>& confs,
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EList<DescentRoot>& roots)
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{
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// Calculate interval length for both mates
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int interval = rootIval_.f<int>((double)q.length());
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if(qo != NULL) {
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// Boost interval length by 20% for paired-end reads
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interval = (int)(interval * 1.2 + 0.5);
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}
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float pri = 0.0f;
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for(int fwi = 0; fwi < 2; fwi++) {
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bool fw = (fwi == 0);
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if((fw && nofw) || (!fw && norc)) {
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continue;
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}
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// Put down left-to-right roots w/r/t forward and reverse-complement reads
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{
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bool first = true;
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size_t i = 0;
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while(first || (i + landing_ <= q.length())) {
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confs.expand();
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confs.back().cons.init(landing_, consExp_);
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roots.expand();
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roots.back().init(
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i, // offset from 5' end
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true, // left-to-right?
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fw, // fw?
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q.length(), // query length
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pri); // root priority
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i += interval;
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first = false;
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}
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}
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// Put down right-to-left roots w/r/t forward and reverse-complement reads
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{
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bool first = true;
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size_t i = 0;
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while(first || (i + landing_ <= q.length())) {
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confs.expand();
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confs.back().cons.init(landing_, consExp_);
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roots.expand();
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roots.back().init(
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q.length() - i - 1, // offset from 5' end
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false, // left-to-right?
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fw, // fw?
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q.length(), // query length
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pri); // root priority
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i += interval;
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first = false;
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}
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}
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}
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}
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