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Main.cpp
/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include <iostream>
#include <string.h>
#include <stdlib.h>
#include "PrintRefPositions.h"
int main(int argc, char ** argv)
{
std::string inFile = "../../test/testFiles/sortedBam.bam";
std::string indexFile = "../../test/testFiles/sortedBam.bam.bai";
std::string rname = "1";
int startPosition = 1013;
int endPosition = 1751;
if(argc == 6)
{
inFile = argv[1];
indexFile = argv[2];
rname = argv[3];
startPosition = atoi(argv[4]);
endPosition = atoi(argv[5]);
}
printRefPositions(inFile, indexFile, rname, startPosition, endPosition);
return(0);
}