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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#include<iostream></span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#include<fstream></span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#include<sstream></span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#include<vector></span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#include<algorithm></span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#include<string></span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#include<regex></span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor">#include<cmath></span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor">#include<htslib/kfunc.h></span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#include "htslib/kfunc.h"</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> </div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor">#include "allele_functions.h"</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> </div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="keyword">const</span> <span class="keywordtype">char</span> gap=<span class="charliteral">'N'</span>;</div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="keyword">const</span> <span class="keywordtype">float</span> sig_level = 0.01;</div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> std::vector<allele>::iterator get_ref_allele(std::vector<allele> &ad, <span class="keywordtype">char</span> ref){</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  <span class="keywordflow">for</span>(std::vector<allele>::iterator it = ad.begin(); it != ad.end(); ++it) {</div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  <span class="keywordflow">if</span>(it->nuc[0] == ref)</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  <span class="keywordflow">return</span> it;</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  }</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  <span class="comment">// print_allele_depths(ad);</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  <span class="keywordflow">return</span> ad.end();</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="keywordtype">int</span> call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min_qual, <span class="keywordtype">double</span> min_threshold){</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  std::string line, cell, bases, qualities, region;</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  std::ofstream fout(out_file+<span class="stringliteral">".tsv"</span>);</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  fout << <span class="stringliteral">"REGION\tPOS\tREF\tALT\tAD\tRAD\tDP\tFREQ\tQUAL\tPVAL\tPASS"</span><<std::endl;</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keywordtype">int</span> ctr = 0, pos = 0, mdepth = 0;</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keywordtype">double</span> pval_left, pval_right, pval_twotailed, freq, err;</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  std::stringstream lineStream;</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordtype">char</span> ref;</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  std::vector<allele> ad;</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  std::vector<allele>::iterator ref_it;</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keywordflow">while</span> (std::getline(cin, line)){</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  lineStream << line;</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  ctr = 0;</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="keywordflow">while</span>(std::getline(lineStream,cell,<span class="charliteral">'\t'</span>)){</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keywordflow">switch</span>(ctr){</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordflow">case</span> 0:</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  region = cell;</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordflow">case</span> 1:</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  pos = stoi(cell);</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordflow">case</span> 2:</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  ref = cell[0];</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keywordflow">case</span> 3:</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  mdepth = stoi(cell);</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keywordflow">case</span> 4:</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  bases = cell;</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordflow">case</span> 5:</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  qualities = cell;</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordflow">case</span> 6:</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  }</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  ctr++;</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  }</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  ad = update_allele_depth(ref, bases, qualities, min_qual);</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keywordflow">if</span>(ad.size() == 0){</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  lineStream.clear();</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  }</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  ref_it = get_ref_allele(ad, ref);</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="comment">// Get ungapped coverage</span></div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  mdepth = 0;</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordflow">for</span>(std::vector<allele>::iterator it = ad.begin(); it != ad.end(); ++it) {</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordflow">if</span>(it->nuc[0]==<span class="charliteral">'*'</span> || it->nuc[0] == <span class="charliteral">'+'</span> || it->nuc[0] == <span class="charliteral">'-'</span>)</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  mdepth += it->depth;</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  }</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordflow">for</span>(std::vector<allele>::iterator it = ad.begin(); it != ad.end(); ++it) {</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordflow">if</span>((*it == *ref_it) || it->nuc[0]==<span class="charliteral">'*'</span>)</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  freq = it->depth/(double)mdepth;</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordflow">if</span>(freq < min_threshold)</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  fout << region << <span class="stringliteral">"\t"</span>;</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  fout << pos << <span class="stringliteral">"\t"</span>;</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  fout << ref << <span class="stringliteral">"\t"</span>;</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  fout << it->nuc << <span class="stringliteral">"\t"</span>;</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  fout << it->depth << <span class="stringliteral">"\t"</span>;</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  fout << it->reverse << <span class="stringliteral">"\t"</span>;</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  fout << mdepth << <span class="stringliteral">"\t"</span>;</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  fout << freq << <span class="stringliteral">"\t"</span>;</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  fout << (uint16_t)it->mean_qual << <span class="stringliteral">"\t"</span>;</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="comment">/*</span></div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> <span class="comment"> | Var | Ref |</span></div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> <span class="comment"> Exp | Error | Err free |</span></div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span> <span class="comment"> Obs | AD | RD |</span></div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span> <span class="comment"> */</span></div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  err = pow(10, ( -1 * (it->mean_qual)/10));</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  kt_fisher_exact((err * mdepth), (1-err) * mdepth, it->depth, ref_it->depth, &pval_left, &pval_right, &pval_twotailed);</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  fout << pval_left << <span class="stringliteral">"\t"</span>;</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="keywordflow">if</span>(pval_left <= sig_level){</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  fout << <span class="stringliteral">"TRUE"</span>;</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  fout << <span class="stringliteral">"FALSE"</span>;</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  }</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  fout << std::endl;</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  }</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  lineStream.clear();</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  }</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  fout.close();</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span> }</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span> </div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span> <span class="comment">// int main_old(int argc, char* argv[]) {</span></div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span> <span class="comment">// std::string line, cell;</span></div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span> <span class="comment">// std::string out_file = argv[1];</span></div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span> <span class="comment">// uint8_t min_qual = 20;</span></div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span> <span class="comment">// if(argc > 2)</span></div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span> <span class="comment">// min_qual = atoi(argv[2]);</span></div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> <span class="comment">// std::cout << "Min Qual: " << (uint16_t)min_qual << std::endl;</span></div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span> <span class="comment">// std::ofstream fout(out_file+".tsv");</span></div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span> <span class="comment">// fout << "POS\tREF\tALT\tAD\tRAD\tDP\tQUAL"<<std::endl;</span></div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span> <span class="comment">// int ctr = 0, pos = 0, mdepth = 0;</span></div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span> <span class="comment">// std::stringstream lineStream;</span></div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="comment">// char ref;</span></div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span> <span class="comment">// std::string bases;</span></div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span> <span class="comment">// std::string qualities;</span></div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> <span class="comment">// std::vector<allele> ad;</span></div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span> <span class="comment">// while (std::getline(std::cin, line)){</span></div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span> <span class="comment">// lineStream << line;</span></div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span> <span class="comment">// ctr = 0;</span></div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span> <span class="comment">// while(std::getline(lineStream,cell,'\t')){</span></div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span> <span class="comment">// switch(ctr){</span></div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span> <span class="comment">// case 0:</span></div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span> <span class="comment">// break;</span></div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span> <span class="comment">// case 1:</span></div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span> <span class="comment">// pos = stoi(cell);</span></div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span> <span class="comment">// break;</span></div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span> <span class="comment">// case 2:</span></div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span> <span class="comment">// ref = cell[0];</span></div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span> <span class="comment">// break;</span></div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span> <span class="comment">// case 3:</span></div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span> <span class="comment">// mdepth = stoi(cell);</span></div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span> <span class="comment">// break;</span></div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span> <span class="comment">// case 4:</span></div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span> <span class="comment">// bases = cell;</span></div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span> <span class="comment">// break;</span></div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span> <span class="comment">// case 5:</span></div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span> <span class="comment">// qualities = cell;</span></div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span> <span class="comment">// break;</span></div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span> <span class="comment">// case 6:</span></div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span> <span class="comment">// break;</span></div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span> <span class="comment">// }</span></div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span> <span class="comment">// ctr++;</span></div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span> <span class="comment">// }</span></div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span> <span class="comment">// ad = update_allele_depth(ref, bases, qualities, min_qual);</span></div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span> <span class="comment">// for(std::vector<allele>::iterator it = ad.begin(); it != ad.end(); ++it) {</span></div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span> <span class="comment">// if((it->nuc[0] == ref && it->nuc.length() == 1) || it->nuc[0]=='*')</span></div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span> <span class="comment">// continue;</span></div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span> <span class="comment">// fout << pos << "\t";</span></div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span> <span class="comment">// fout << ref << "\t";</span></div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span> <span class="comment">// fout << it->nuc << "\t";</span></div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span> <span class="comment">// fout << it->depth << "\t";</span></div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span> <span class="comment">// fout << it->reverse << "\t";</span></div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span> <span class="comment">// fout << mdepth << "\t";</span></div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span> <span class="comment">// fout << (uint16_t)it->mean_qual << std::endl;</span></div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span> <span class="comment">// }</span></div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span> <span class="comment">// lineStream.clear();</span></div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span> <span class="comment">// }</span></div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span> <span class="comment">// fout.close();</span></div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span> <span class="comment">// return 0;</span></div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span> <span class="comment">// }</span></div></div><!-- fragment --></div><!-- contents -->
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