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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#include<string></span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#include<vector></span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#include<algorithm></span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#include<iostream></span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> </div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#include "allele_functions.h"</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> </div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="keywordtype">void</span> print_allele_depths(std::vector<allele> ad){</div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span>  std::cout << <span class="stringliteral">"AD Size: "</span> << ad.size() << <span class="stringliteral">" "</span> << std::endl;</div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span>  <span class="keywordflow">for</span>(std::vector<allele>::iterator it = ad.begin(); it != ad.end(); ++it) {</div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span>  std::cout << <span class="stringliteral">"Nuc: "</span> << it->nuc << std::endl;;</div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  std::cout << <span class="stringliteral">"Depth: "</span> << it->depth << std::endl;</div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  std::cout << <span class="stringliteral">"Reverse: "</span> << it->reverse <<std::endl;</div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span>  std::cout << <span class="stringliteral">"Qual: "</span> << (uint16_t) it->mean_qual << std::endl;</div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  std::cout << <span class="stringliteral">"Beg: "</span> << it->beg << std::endl;</div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  std::cout << <span class="stringliteral">"End: "</span> << it->end << std::endl;</div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  }</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> }</div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> </div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="keywordtype">int</span> check_allele_exists(std::string n, std::vector<allele> ad){</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  <span class="keywordflow">for</span>(std::vector<allele>::iterator it = ad.begin(); it != ad.end(); ++it) {</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  <span class="keywordflow">if</span>(it->nuc.compare(n) == 0){</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  <span class="keywordflow">return</span> it - ad.begin();</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  }</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  }</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> }</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> </div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="keywordtype">int</span> find_ref_in_allele(std::vector<allele> ad, <span class="keywordtype">char</span> ref){</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  std::string ref_s(1, ref);</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  std::vector<allele>::iterator it = ad.begin();</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="keywordflow">while</span>(it < ad.end()){</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordflow">if</span>(it->nuc.compare(ref_s) == 0)</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keywordflow">return</span> (it - ad.begin());</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  it++;</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  }</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> }</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> std::vector<allele> update_allele_depth(<span class="keywordtype">char</span> ref,std::string bases, std::string qualities, uint8_t min_qual){</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  std::vector<allele> ad;</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  std::string indel;</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keywordtype">int</span> i = 0, n =0, j = 0, q_ind = 0;</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordtype">bool</span> beg, end;</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  uint8_t q;</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keywordtype">float</span> num = 0, den = 0;</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordflow">while</span> (i < bases.length()){</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  beg = <span class="keyword">false</span>;</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  end = <span class="keyword">false</span>;</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keywordflow">if</span>(bases[i] == <span class="charliteral">'^'</span>){</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  i += 2; <span class="comment">// Skip mapping quality as well (i+1) - 33</span></div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  }</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keywordflow">if</span>(bases[i] == <span class="charliteral">'$'</span>){</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  i++;</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  }</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  q = qualities[q_ind] - 33;</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  std::string b;</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <a class="code" href="structallele.html">allele</a> tmp;</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keywordtype">bool</span> forward= <span class="keyword">true</span>;</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keywordflow">switch</span>(bases[i]){</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keywordflow">case</span> <span class="charliteral">'.'</span>:</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  b = ref;</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  end = (bases[i+1] == <span class="charliteral">'$'</span>);</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  beg = (bases[i+1] == <span class="charliteral">'^'</span>);</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keywordflow">case</span> <span class="charliteral">','</span>:</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  b = ref;</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  forward = <span class="keyword">false</span>;</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  end = (bases[i+1] == <span class="charliteral">'$'</span>);</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  beg = (bases[i+1] == <span class="charliteral">'^'</span>);</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordflow">case</span> <span class="charliteral">'*'</span>:</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  b = bases[i];</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordflow">case</span> <span class="charliteral">'+'</span>: <span class="keywordflow">case</span> <span class="charliteral">'-'</span>:</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  j = i+1;</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordflow">while</span>(isdigit(bases[j])){</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  j++;</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  }</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  j = j - (i+1);</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  n = stoi(bases.substr(i+1, j));</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  indel = bases.substr(i+1+j, n);</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  transform(indel.begin(), indel.end(), indel.begin(),::toupper);</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  b = bases[i] + indel; <span class="comment">// + for Insertion and - for Deletion</span></div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  i += n + j;</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordflow">if</span>(indel[0]>=97 && indel[0] <= 122)</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  forward=<span class="keyword">false</span>;</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  q = min_qual; <span class="comment">// For insertions and deletion ust use minimum quality.</span></div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordflow">default</span>:</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keywordtype">int</span> asc_val = bases[i];</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keywordflow">if</span>(asc_val >= 65 && asc_val <= 90){</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  b = bases[i];</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span>(bases[i]>=97 && bases[i]<=122){</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  b = bases[i] - (<span class="charliteral">'a'</span> - <span class="charliteral">'A'</span>);</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  forward = <span class="keyword">false</span>;</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  }</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  end = (bases[i+1] == <span class="charliteral">'$'</span>);</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  beg = (bases[i+1] == <span class="charliteral">'^'</span>);</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  }</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keywordtype">int</span> ind = check_allele_exists(b, ad);</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordflow">if</span>(q >= min_qual){</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keywordflow">if</span> (ind==-1){</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  tmp.nuc = b;</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  tmp.depth = 1;</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  tmp.tmp_mean_qual = q;</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordflow">if</span>(!forward)</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  tmp.reverse = 1;</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  tmp.reverse = 0;</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordflow">if</span>(beg)</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  tmp.beg = 1;</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  tmp.beg = 0;</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="keywordflow">if</span>(end)</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  tmp.end = 1;</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  tmp.end = 0;</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  ad.push_back(tmp);</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  ad.at(ind).tmp_mean_qual = (ad.at(ind).tmp_mean_qual * ad.at(ind).depth + q)/(ad.at(ind).depth + 1);</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  ad.at(ind).depth += 1;</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordflow">if</span>(beg)</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  ad.at(ind).beg += 1;</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordflow">if</span>(end)</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  ad.at(ind).end += 1;</div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordflow">if</span>(!forward)</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  ad.at(ind).reverse += 1;</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  }</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  }</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  i++;</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordflow">if</span>(b[0] !=<span class="charliteral">'+'</span> && b[0]!=<span class="charliteral">'-'</span>)</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  q_ind++;</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  }</div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keywordflow">for</span>(std::vector<allele>::iterator it = ad.begin(); it!=ad.end(); ++it){</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  it->mean_qual = (uint8_t) it->tmp_mean_qual;</div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  }</div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keywordflow">if</span>(ad.size() > 0)</div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  std::sort(ad.begin(), ad.end());</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordflow">return</span> ad;</div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span> }</div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span> <span class="keywordtype">int</span> get_index(<span class="keywordtype">char</span> a){</div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="keywordflow">switch</span>(a){</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordflow">case</span><span class="charliteral">'Y'</span>:</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  a = 0;</div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="keywordflow">case</span><span class="charliteral">'R'</span>:</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  a = 1;</div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordflow">case</span><span class="charliteral">'W'</span>:</div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  a = 2;</div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="keywordflow">case</span><span class="charliteral">'S'</span>:</div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  a = 3;</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="keywordflow">case</span><span class="charliteral">'K'</span>:</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  a = 4;</div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="keywordflow">case</span><span class="charliteral">'M'</span>:</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  a = 5;</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordflow">case</span><span class="charliteral">'A'</span>:</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  a = 6;</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="keywordflow">case</span><span class="charliteral">'T'</span>:</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  a = 7;</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <span class="keywordflow">case</span><span class="charliteral">'G'</span>:</div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  a = 8;</div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <span class="keywordflow">case</span><span class="charliteral">'C'</span>:</div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  a = 9;</div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keywordflow">case</span><span class="charliteral">'D'</span>:</div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  a = 10;</div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="keywordflow">case</span><span class="charliteral">'V'</span>:</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  a = 11;</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keywordflow">case</span><span class="charliteral">'H'</span>:</div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  a = 12;</div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <span class="keywordflow">case</span><span class="charliteral">'B'</span>:</div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  a = 13;</div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordflow">default</span>:</div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  a = -1;</div><div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  }</div><div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="keywordflow">return</span> (<span class="keywordtype">int</span>) a;</div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span> }</div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span> </div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span> <span class="comment">// Modified gt2iupac from bcftools.h. Expanded iupac matrix to include all ambigious nucleotides(added Y, R, W, S, K, M, A, T, G, C, D, V, H, B) - https://github.com/samtools/bcftools/blob/b0376dff1ed70603c9490802f37883b9009215d2/bcftools.h#L48</span></div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span> <span class="comment">/*</span></div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span> <span class="comment">Expanded IUPAC matrix:</span></div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span> <span class="comment"></span></div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span> <span class="comment">Y N H B B H H Y B Y N N H B</span></div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span> <span class="comment">N R D V D V R D R V D V N N</span></div><div class="line"><a name="l00201"></a><span class="lineno"> 201</span> <span class="comment">H D W N D H W W D H D N H N</span></div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span> <span class="comment">B V N S B V V B S S N V N B</span></div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span> <span class="comment">B D D B K N D K K B D N N B</span></div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span> <span class="comment">H V H V N M M H V M N V H N</span></div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span> <span class="comment">H R W V D M A W R M D V H N</span></div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span> <span class="comment">Y D W B K H W T K Y D N H B</span></div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span> <span class="comment">B R D S K V R K G S D V N B</span></div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span> <span class="comment">Y V H S B M M Y S C N V H B</span></div><div class="line"><a name="l00209"></a><span class="lineno"> 209</span> <span class="comment">N D D N D N D D D N D N N N</span></div><div class="line"><a name="l00210"></a><span class="lineno"> 210</span> <span class="comment">N V N V N V V N V V N V N N</span></div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span> <span class="comment">H N H N N H H H N H N N H N</span></div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span> <span class="comment">B N N B B N N B B B N N N B</span></div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span> <span class="comment"></span></div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span> <span class="comment"> */</span></div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span> <span class="keywordtype">char</span> gt2iupac(<span class="keywordtype">char</span> a, <span class="keywordtype">char</span> b){</div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  <span class="keywordflow">if</span>(a == <span class="charliteral">'*'</span> || b == <span class="charliteral">'*'</span>)</div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <span class="keywordflow">return</span> <span class="charliteral">'N'</span>;</div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> iupac[14][14] = {</div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  {<span class="charliteral">'Y'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'Y'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'Y'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'B'</span>},</div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  {<span class="charliteral">'N'</span>, <span class="charliteral">'R'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'R'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'R'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>},</div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  {<span class="charliteral">'H'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'W'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'W'</span>, <span class="charliteral">'W'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'N'</span>},</div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  {<span class="charliteral">'B'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'S'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'S'</span>, <span class="charliteral">'S'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'B'</span>},</div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  {<span class="charliteral">'B'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'K'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'K'</span>, <span class="charliteral">'K'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'B'</span>},</div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  {<span class="charliteral">'H'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'M'</span>, <span class="charliteral">'M'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'M'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'N'</span>},</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  {<span class="charliteral">'H'</span>, <span class="charliteral">'R'</span>, <span class="charliteral">'W'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'M'</span>, <span class="charliteral">'A'</span>, <span class="charliteral">'W'</span>, <span class="charliteral">'R'</span>, <span class="charliteral">'M'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'N'</span>},</div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  {<span class="charliteral">'Y'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'W'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'K'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'W'</span>, <span class="charliteral">'T'</span>, <span class="charliteral">'K'</span>, <span class="charliteral">'Y'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'B'</span>},</div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  {<span class="charliteral">'B'</span>, <span class="charliteral">'R'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'S'</span>, <span class="charliteral">'K'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'R'</span>, <span class="charliteral">'K'</span>, <span class="charliteral">'G'</span>, <span class="charliteral">'S'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'B'</span>},</div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  {<span class="charliteral">'Y'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'S'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'M'</span>, <span class="charliteral">'M'</span>, <span class="charliteral">'Y'</span>, <span class="charliteral">'S'</span>, <span class="charliteral">'C'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'B'</span>},</div><div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  {<span class="charliteral">'N'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'D'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>},</div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  {<span class="charliteral">'N'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'V'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>},</div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  {<span class="charliteral">'H'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'H'</span>, <span class="charliteral">'N'</span>},</div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  {<span class="charliteral">'B'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'B'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'B'</span>}</div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  };</div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <span class="keywordflow">if</span> ( a>=<span class="charliteral">'a'</span> ) a -= <span class="charliteral">'a'</span> - <span class="charliteral">'A'</span>;</div><div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="keywordflow">if</span> ( b>=<span class="charliteral">'a'</span> ) b -= <span class="charliteral">'a'</span> - <span class="charliteral">'A'</span>;</div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="keywordtype">int</span> _a, _b;</div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  _a = get_index(a);</div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  _b = get_index(b);</div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="keywordflow">if</span>(_a == -1 || _b == -1)</div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="keywordflow">return</span> <span class="charliteral">'N'</span>;</div><div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="keywordflow">return</span> iupac[_a][_b];</div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span> }</div><div class="ttc" id="structallele_html"><div class="ttname"><a href="structallele.html">allele</a></div><div class="ttdef"><b>Definition:</b> <a href="allele__functions_8h_source.html#l00007">allele_functions.h:7</a></div></div>
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