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annotate snp_caller/src/alignment_util.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_UTIL_H
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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2 #define ALIGNMENT_UTIL_H
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4 #include "int_util.h"
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6 #include <string>
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7 #include <vector>
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9 #include <boost/algorithm/string.hpp>
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11 #define READ_PAIRED 1
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12 #define PROPER_PAIR 2
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13 #define READ_UNMAPPED 4
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14 #define MATE_UNMAPPED 8
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16 std::vector<std::string> split_alignment(std::string &alignment) {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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17 std::vector<std::string> parts;
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18 boost::trim_if(alignment, boost::is_any_of("\t "));
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19 boost::split(parts, alignment, boost::is_any_of("\t "), boost::token_compress_on);
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20 return parts;
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21 }
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23 bool is_good_se_flag(const int &flag) {
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24 if( (flag & READ_UNMAPPED) > 0) {
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25 return false;
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26 }
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27 else {
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28 return true;
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29 }
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30 }
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32 bool is_good_pe_flag(const int &flag) {
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33 if( (flag & READ_UNMAPPED) > 0 || (flag & MATE_UNMAPPED) > 0 ||
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34 (flag & READ_PAIRED) == 0 || (flag & PROPER_PAIR == 0) ) {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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35 return false;
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36 }
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37 else {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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38 return true;
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39 }
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40 }
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42 bool is_good_rname(const std::string &rname) {
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43 return rname.compare("*") != 0;
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44 }
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46 bool is_good_pos(const int &pos) {
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47 return pos > 0;
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48 }
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50 bool is_good_pnext(const int &pnext) {
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51 return pnext > 0;
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52 }
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54 bool is_good_cigar(const std::string &cigar) {
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55 return cigar.compare("*") != 0;
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56 }
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58 bool is_good_seq(const std::string &seq) {
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59 return seq.compare("*") != 0;
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60 }
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61
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62 bool is_alignment_unique(const std::string &alignment) {
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63 if(alignment.find("XT:A:U") != std::string::npos) {
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64 return true;
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65 }
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66 else {
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67 return false;
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68 }
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69 }
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70
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71 /*bool is_good_alignment(std::string &alignment) {
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72 std::vector<std::string> alignment_parts;
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73
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74 alignment_parts = split_alignment(alignment);
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75
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76 if(!(fields_are_good(alignment_parts)))
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77 return false;
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78 else
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79 return true;
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80 }*/
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81
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82 bool se_fields_are_good(std::string &alignment, bool best) {
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83 std::vector<std::string> parts = split_alignment(alignment);
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84 int flag = s_to_i(parts[1]);
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85 int pos = s_to_i(parts[3]);
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86
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87 std::string rname = parts[2];
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88 std::string cigar = parts[5];
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89 std::string seq = parts[9];
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90
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91 if(!(is_good_se_flag(flag))) return false;
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92 if(!(is_good_pos(pos))) return false;
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93 if(!(is_good_rname(rname))) return false;
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94 if(!(is_good_cigar(cigar))) return false;
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95 if(!(is_good_seq(seq))) return false;
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96 if(best) {
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97 if(!(is_alignment_unique(alignment))) {
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98 return false;
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99 }
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100 }
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101
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102 return true;
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103 }
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104
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105 bool pe_fields_are_good(std::string &alignment, bool best) {
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106 std::vector<std::string> parts = split_alignment(alignment);
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107 int flag = s_to_i(parts[1]);
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108 int pos = s_to_i(parts[3]);
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109 int pnext = s_to_i(parts[7]);
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110
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111 std::string rname = parts[2];
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112 std::string cigar = parts[5];
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113 std::string seq = parts[9];
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114
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115 if(!(is_good_pe_flag(flag))) return false;
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116 if(!(is_good_pos(pos))) return false;
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117 if(!(is_good_rname(rname))) return false;
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118 if(!(is_good_cigar(cigar))) return false;
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119 if(!(is_good_pnext(pnext))) return false;
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120 if(!(is_good_seq(seq))) return false;
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121 if(best) {
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122 if(!(is_alignment_unique(alignment))) {
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123 return false;
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124 }
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125 }
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126
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127 return true;
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128 }
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129
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130 #endif // ALIGNMENT_UTIL_H