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annotate gene_fraction/src/Alignments.h @ 0:2aad8349d84b draft

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planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
author chrisd
date Sun, 21 Feb 2016 23:20:22 -0500
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2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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1 #ifndef ALIGNMENTS_H
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2 #define ALIGNMENTS_H
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3
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4 #include <string>
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5 #include <vector>
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7 /**
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8 * Stores information about an alignment
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9 */
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10 struct alignment_fields {
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11 std::string QNAME;
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12 int FLAG;
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13 std::string RNAME;
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14 int POS;
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15 int MAPQ;
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16 std::string CIGAR;
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17 std::string RNEXT;
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18 int PNEXT;
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19 int TLEN;
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20 std::string SEQ;
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21 std::string QUAL;
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22 };
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24 /**
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25 * Class for dealing with alignments
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26 */
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27 class Alignments {
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28 public:
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29 /**
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30 * Ctor that initializes alignment
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31 */
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32 Alignments(std::string alignment);
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34 /**
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35 * Stores information about each of the eleven
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36 * required alignment fields
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37 */
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38 void fill_alignment_fields(const std::string &alignment);
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40 std::vector<std::pair<int,char>> cigar();
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42 inline std::string alignment() const { return _alignment; };
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44 inline std::string qname() const { return field.QNAME; };
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45 inline std::string rname() const { return field.RNAME; };
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46 inline std::string cigar() const { return field.CIGAR; };
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47 inline std::string rnext() const { return field.RNEXT; };
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48 inline std::string seq() const { return field.SEQ; };
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49 inline std::string qual() const { return field.QUAL; };
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51 inline int flag() const { return field.FLAG; };
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52 inline int pos() const { return field.POS; };
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53 inline int mapq() const { return field.MAPQ; };
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54 inline int pnext() const { return field.PNEXT; };
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55 inline int tlen() const { return field.TLEN; };
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57 private:
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58 /**
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59 * Returns a pair of cigar operations as (occurrence, operation)
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60 * Ex: 10M5I -> (10, M), (5, I)
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61 */
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62 std::vector<std::pair<int,char>> get_cigar_operations(const std::string &cigar);
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64 std::string _alignment;
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65 alignment_fields field;
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66 };
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68 #endif /* ALIGNMENTS_H */