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1 #ifndef INPUT_FILE_PARSER_HPP
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2 #define INPUT_FILE_PARSER_HPP
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3
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4 #include <string>
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5 #include <vector>
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6 #include <map>
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7 #include "genomicInterval.hpp"
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8
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9 typedef vector<Interval *> IntervalsType;
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10 typedef map<string, IntervalsType *> SortedIntervalsTypes;
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11 typedef map<string, unsigned int> CounterType;
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12 typedef pair<Interval *, unsigned int> NumberIntervalType;
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13
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14 static bool operator<(const NumberIntervalType &i1, const NumberIntervalType &i2) {
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15 if (i1.first < i2.first) return true;
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16 return ((i1.first == i2.first) && (i1.second < i2.second));
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17 }
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18
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19 class InputFileParser {
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20
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21 private:
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22 SortedIntervalsTypes sortedIntervals;
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23 CounterType counter;
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24
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25 void addToList(GenomicInterval &genomicInterval);
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26 void writeTmpFile(string &chromosome);
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27 void syncFiles();
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28 string getTmpName(const string &chromosome, unsigned int i);
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29 string getTmpName(const string &chromosome);
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30 void merge();
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31 void merge(const string &chromosome, ofstream &outputFile);
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32
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33 public:
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34 string inputFileName;
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35 string outputFileName;
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36 string outputFilePrefix;
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37
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38 InputFileParser(string inputFileName, string outputFileName);
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39
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40 void parse();
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41
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42 };
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43
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44 #endif
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45
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