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annotate snp_caller/src/Alignment.h @ 0:0fd352f62446 draft default tip

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planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
author chrisd
date Sun, 21 Feb 2016 06:05:24 -0500
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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1 #ifndef ALIGNMENT_H
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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2 #define ALIGNMENT_H
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4 #include <string>
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5 #include <vector>
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6 #include <algorithm>
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8 struct bit_flag {
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9 /* SAM flags in English */
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10 bool read_paired = false;
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11 bool read_mapped_in_proper_pair = false;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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12 bool read_unmapped = false;
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13 bool mate_unmapped = false;
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14 bool read_reverse_strand = false;
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15 bool mate_reverse_strand = false;
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16 bool first_in_pair = false;
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17 bool second_in_pair = false;
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18 };
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20 struct alignment_fields {
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21 std::string QNAME;
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22 int FLAG;
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23 std::string RNAME;
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24 int POS;
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25 std::string MAPQ;
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26 std::string CIGAR;
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27 std::string RNEXT;
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28 int PNEXT;
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29 int TLEN;
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30 std::string SEQ;
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31 std::string QUAL;
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32 };
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34 class Alignment {
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35 public:
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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36 Alignment(std::string alignment);
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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37 void fill_alignment_fields(const std::string &alignment);
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38 void fill_bit_flag(const int &flag);
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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39 bool fill_xa_field(const std::string &alignment);
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40 std::vector<std::pair<int,char> > get_cigar();
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42 inline std::string alignment() const { return _alignment; };
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43 inline std::string qname() const { return field.QNAME; };
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44 inline std::string rname() const { return field.RNAME; };
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45 inline std::string mapq() const { return field.MAPQ; };
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46 inline std::string cigar() const { return field.CIGAR; };
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47 inline std::string seq() const { return field.SEQ; };
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48 inline std::string rnext() const { return field.RNEXT; };
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49 inline int flag() const { return field.FLAG; };
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50 inline int pos() const { return field.POS; };
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51 inline int pnext() const { return field.PNEXT; };
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52 inline int tlen() const { return field.TLEN; };
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54 inline bool read_paired() const { return b_flag.read_paired; };
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55 inline bool read_mapped_in_proper_pair() const { return b_flag.read_mapped_in_proper_pair; };
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56 inline bool read_unmapped() const { return b_flag.read_unmapped; };
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57 inline bool mate_unmapped() const { return b_flag.mate_unmapped; };
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58 inline bool read_reverse_strand() const { return b_flag.read_reverse_strand; }
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59 inline bool mate_reverse_strand() const { return b_flag.mate_reverse_strand; };
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60 inline bool first_in_pair() const { return b_flag.first_in_pair; };
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61 inline bool second_in_pair() const { return b_flag.second_in_pair; };
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63 inline void set_rname(std::string rname) {
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64 field.RNAME = rname;
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65 }
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66 inline void set_cigar(std::string cigar) {
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67 field.CIGAR = cigar;
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68 }
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69 inline void set_pos(int pos) {
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70 field.POS = pos;
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71 }
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73 struct xa_fields {
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74 std::string rname;
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75 std::string cigar;
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76 int pos;
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77 int edit;
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78 };
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80 std::vector<xa_fields> alternate_hits;
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81 private:
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82 std::vector<std::pair<int,char> > get_cigar_operations(const std::string &cigar);
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84 std::string _alignment;
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86 alignment_fields field;
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88 bit_flag b_flag;
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89 };
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91 #endif // ALIGNMENT_H