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1 /*****************************************************************************
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2 bedGraphFile.cpp
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3
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4 (c) 2010 - Assaf Gordon
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5 Hall Laboratory
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6 Department of Biochemistry and Molecular Genetics
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7 University of Virginia
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8 aaronquinlan@gmail.com
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9
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10 Licenced under the GNU General Public License 2.0 license.
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11 ******************************************************************************/
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12 #include "bedGraphFile.h"
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13 #include <sstream>
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14
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15 // Constructor
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16 BedGraphFile::BedGraphFile(string &_file) :
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17 bedGraphFile(_file),
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18 _bedGraphStream(NULL)
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19 {}
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20
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21
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22 // Destructor
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23 BedGraphFile::~BedGraphFile() {
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24 Close();
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25 }
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26
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27
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28 // Open the BEDGRAPH file
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29 void BedGraphFile::Open() {
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30 if (bedGraphFile == "stdin" || bedGraphFile == "-") {
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31 _bedGraphStream = &cin;
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32 }
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33 else {
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34 _bedGraphStream = new ifstream(bedGraphFile.c_str(), ios::in);
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35
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36 if (isGzipFile(_bedGraphStream) == true) {
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37 delete _bedGraphStream;
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38 _bedGraphStream = new igzstream(bedGraphFile.c_str(), ios::in);
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39 }
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40 // can we open the file?
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41 if ( !(_bedGraphStream->good()) ) {
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42 cerr << "Error: The requested bed file (" << bedGraphFile << ") could not be opened. Exiting!" << endl;
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43 exit (1);
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44 }
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45 }
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46 }
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47
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48
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49 // Close the BEDGRAPH file
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50 void BedGraphFile::Close() {
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51 if (bedGraphFile != "stdin" && bedGraphFile != "-") {
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52 if (_bedGraphStream) {
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53 delete _bedGraphStream;
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54 _bedGraphStream = NULL ;
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55 }
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56 }
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57 }
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58
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