libStatGen Software  1
Main.cpp
1 /*
2  * Copyright (C) 2010 Regents of the University of Michigan
3  *
4  * This program is free software: you can redistribute it and/or modify
5  * it under the terms of the GNU General Public License as published by
6  * the Free Software Foundation, either version 3 of the License, or
7  * (at your option) any later version.
8  *
9  * This program is distributed in the hope that it will be useful,
10  * but WITHOUT ANY WARRANTY; without even the implied warranty of
11  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12  * GNU General Public License for more details.
13  *
14  * You should have received a copy of the GNU General Public License
15  * along with this program. If not, see <http://www.gnu.org/licenses/>.
16  */
17 
18 #include <iostream>
19 #include <string.h>
20 #include <stdlib.h>
21 
22 #include "PrintRefPositions.h"
23 
24 int main(int argc, char ** argv)
25 {
26  std::string inFile = "../../test/testFiles/sortedBam.bam";
27  std::string indexFile = "../../test/testFiles/sortedBam.bam.bai";
28  std::string rname = "1";
29  int startPosition = 1013;
30  int endPosition = 1751;
31  if(argc == 6)
32  {
33  inFile = argv[1];
34  indexFile = argv[2];
35  rname = argv[3];
36  startPosition = atoi(argv[4]);
37  endPosition = atoi(argv[5]);
38  }
39  printRefPositions(inFile, indexFile, rname, startPosition, endPosition);
40  return(0);
41 }
42 
43 
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