49 lines
1.4 KiB
C
49 lines
1.4 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 SEARCH_GLOBALS_H_
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#define SEARCH_GLOBALS_H_
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#include <stdint.h>
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// declared in ebwt_search.cpp
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extern bool gColor;
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extern bool gColorExEnds;
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extern bool gReportOverhangs;
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extern bool gColorSeq;
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extern bool gColorEdit;
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extern bool gColorQual;
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extern bool gNoMaqRound;
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extern bool gStrandFix;
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extern bool gRangeMode;
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extern int gVerbose;
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extern int gQuiet;
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extern bool gNofw;
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extern bool gNorc;
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extern bool gMate1fw;
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extern bool gMate2fw;
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extern int gMinInsert;
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extern int gMaxInsert;
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extern int gTrim5;
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extern int gTrim3;
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extern int gGapBarrier;
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extern int gAllowRedundant;
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#endif /* SEARCH_GLOBALS_H_ */
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