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/*
* Copyright 2011, Ben Langmead <blangmea@jhsph.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef SEARCH_GLOBALS_H_
#define SEARCH_GLOBALS_H_
#include <stdint.h>
// declared in ebwt_search.cpp
extern bool gColor;
extern bool gColorExEnds;
extern bool gReportOverhangs;
extern bool gColorSeq;
extern bool gColorEdit;
extern bool gColorQual;
extern bool gNoMaqRound;
extern bool gStrandFix;
extern bool gRangeMode;
extern int gVerbose;
extern int gQuiet;
extern bool gNofw;
extern bool gNorc;
extern bool gMate1fw;
extern bool gMate2fw;
extern int gMinInsert;
extern int gMaxInsert;
extern int gTrim5;
extern int gTrim3;
extern int gGapBarrier;
extern int gAllowRedundant;
#endif /* SEARCH_GLOBALS_H_ */
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