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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 <algorithm></span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#include<vector></span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#include<fstream></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 "alignment.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="comment">/* Substitution Matrix</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"></span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> A T G C N</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">A 1 -1 -1 -1 0</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">T -1 1 -1 -1 0</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">G -1 -1 1 -1 0</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">C -1 -1 -1 1 0</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">N 0 0 0 0 0</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">*/</span></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> <span class="keywordtype">int</span> get_sub_score(<span class="keywordtype">char</span> a, <span class="keywordtype">char</span> b){</div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  <span class="keywordtype">int</span> i,j;</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  <span class="keywordflow">switch</span>(a){</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  <span class="keywordflow">case</span> <span class="charliteral">'A'</span>:</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  i = 0;</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  <span class="keywordflow">case</span> <span class="charliteral">'T'</span>:</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  i = 1;</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  <span class="keywordflow">case</span> <span class="charliteral">'G'</span>:</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  i = 2;</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keywordflow">case</span> <span class="charliteral">'C'</span>:</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  i = 3;</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordflow">case</span> <span class="charliteral">'N'</span>:</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  i = 4;</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keywordflow">break</span>;</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">switch</span>(b){</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keywordflow">case</span> <span class="charliteral">'A'</span>:</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  j = 0;</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordflow">case</span> <span class="charliteral">'T'</span>:</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  j = 1;</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> <span class="charliteral">'G'</span>:</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  j = 2;</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> <span class="charliteral">'C'</span>:</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  j = 3;</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> <span class="charliteral">'N'</span>:</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  i = 4;</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>  }</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keywordflow">return</span> substitution[i][j];</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> }</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> </div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="keywordtype">int</span> get_gap_penalty(<span class="keywordtype">int</span> k, <span class="keywordtype">char</span> a){</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keywordflow">if</span>(a == <span class="charliteral">'N'</span>) <span class="comment">// Allow for i7 and i5 indexesto be specified as NNNNNNNN</span></div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordflow">return</span> k * gap_open; <span class="comment">// Linear Gap Penalty</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> </div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="keywordtype">void</span> print_matrix(<span class="keywordtype">int</span> h[][max_adapter_size], <span class="keywordtype">int</span> r, <span class="keywordtype">int</span> c, std::string read, std::string adap){</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i =0; i< r;i++){</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keywordflow">if</span>(i == 0){</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  std::cout << <span class="stringliteral">" "</span>;</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> k =0; k < c-1; k++) std::cout << adap[k] << <span class="stringliteral">" "</span>;</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  std::cout << <span class="stringliteral">"\n"</span>;</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  }</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> j = 0; j < c;j++){</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="keywordflow">if</span>(j == 0 && i > 0){</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordflow">if</span>(i -1 < read.length())</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  std::cout << read[i-1] << <span class="stringliteral">" "</span>;</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  }</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keywordflow">if</span>(i == 0 && j == 0)</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  std::cout << <span class="stringliteral">" "</span> << <span class="stringliteral">" "</span>;</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  std::cout << h[i][j] << <span class="stringliteral">" "</span>;</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  }</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  std::cout << <span class="stringliteral">"\n"</span>;</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  }</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> </div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> <span class="comment">// Return Value 1 - Diag, 2->Right, 3->Down, 0-> 0</span></div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> <span class="keywordtype">int</span>* get_score_cell(<span class="keywordtype">int</span> h[][max_adapter_size], <span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j, std::string read, std::string adap){</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordtype">int</span> s[] = {0,0,0};</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keywordtype">int</span> *tmp = <span class="keyword">new</span> <span class="keywordtype">int</span>[2];</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  tmp[0] = 0;</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  tmp[1] = 0;</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  s[0] = h[i-1][j-1] + get_sub_score(read[i-1], adap[j-1]);</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  s[1] = h[i-1][j] - get_gap_penalty(1, adap[j-1]);</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  s[2] = h[i][j-1] - get_gap_penalty(1, read[i-1]);</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordtype">int</span> max = (s[0]>=s[1]) ? s[0] : s[1];</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  max = (max>=s[2]) ? max : s[2];</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  max = (max > 0) ? max : 0;</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  tmp[0] = max;</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keywordflow">if</span>(max == s[0]){</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  tmp[1] = 1;</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span>(max == s[1]){</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  tmp[1] = 3;</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span>(max == s[2]){</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  tmp[1] = 2;</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="keywordflow">return</span> tmp;</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> </div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span> <span class="keywordtype">void</span> print_alignment(<span class="keywordtype">char</span> a[2][max_read_size], <span class="keywordtype">int</span> n){</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  std::cout << <span class="stringliteral">"Alignment: "</span> << std::endl << std::endl;</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> j =0;j<2;j++){</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordflow">if</span>(j == 0)</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  std::cout << <span class="stringliteral">"Read: "</span>;</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span>(j == 1)</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  std::cout << <span class="stringliteral">"Adap: "</span>;</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = n -1; i >= 0;i--){</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  std::cout << a[j][i] << <span class="stringliteral">" "</span>;</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  }</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  std::cout << std::endl;</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  }</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span> }</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span> <span class="keywordtype">int</span>* align_seqs(std::string read, std::string adap){</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordtype">int</span> h[max_read_size][max_adapter_size],</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  t[max_read_size][max_adapter_size],</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  m = read.length() + 1,</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  n=adap.length()+ 1,</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  max_i = 0,</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  max_j = 0,</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  max_v = -1,</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  max_score,</div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  *rt = <span class="keyword">new</span> <span class="keywordtype">int</span>[2],</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  *tmp = <span class="keyword">new</span> <span class="keywordtype">int</span>[2];</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  rt[0] = -1;</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  rt[1] = read.length();</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="comment">// Initialize first column to 0</span></div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 0; i < n; i++) h[0][i] = 0;</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="comment">// Initialize first row to 0</span></div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 0; i < m; i++) h[i][0] = 0;</div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="comment">// print_matrix(h, m, n, read, adap);</span></div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 1; i < m; i++){</div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> j = 1; j < n; j++){</div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  tmp = get_score_cell(h, i, j, read, adap);</div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  h[i][j] = *tmp;</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  t[i][j] = *(tmp+1);</div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="keywordflow">if</span>(*tmp >= max_v){</div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  max_i = i;</div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  max_j = j;</div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  max_v = *tmp;</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  }</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  }</div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  }</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  max_score = max_v;</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="comment">// if(max_i != read.length()) // Ensure alignment to end of read.</span></div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="comment">// return rt;</span></div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="comment">// std::cout << "Score: " << max_v << " ";</span></div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="comment">// print_matrix(h, m, n, read, adap);</span></div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="comment">// print_matrix(t, m, n, read, adap);</span></div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="comment">// Traceback</span></div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="keywordtype">int</span> _t, _l, _d, _align_n = 0;</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordtype">char</span> _align[2][max_read_size];</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="comment">// 1 - Diag, 2->Right, 3->Down</span></div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="keywordflow">while</span>(max_v != 0){</div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  _d = h[max_i-1][max_j-1];</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  _l = h[max_i][max_j-1];</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  _t = h[max_i-1][max_j];</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="keywordflow">switch</span>(t[max_i][max_j]){</div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordflow">case</span> 1:</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  max_v = _d;</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  max_i = max_i -1;</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  max_j = max_j - 1;</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  _align[0][_align_n] = read[max_i];</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  _align[1][_align_n] = adap[max_j];</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  _align_n++;</div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordflow">case</span> 2:</div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  max_v = _l;</div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  max_j = max_j - 1;</div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  _align[0][_align_n] = <span class="charliteral">'-'</span>;</div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  _align[1][_align_n] = adap[max_j];</div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  _align_n++;</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> 3:</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  max_v = _t;</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  max_i = max_i - 1;</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  _align[0][_align_n] = read[max_i];</div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  _align[1][_align_n] = <span class="charliteral">'-'</span>;</div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  _align_n++;</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  <span class="keywordflow">case</span> 0:</div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  max_v = 0;</div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  }</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>  rt[1] = max_i;</div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  print_alignment(_align, _align_n);</div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <span class="keywordflow">if</span>(max_score <= ((_align_n - 2) * unit_score) - get_gap_penalty(2, <span class="charliteral">'A'</span>) || max_j != 0) <span class="comment">// If alignment does not start at beginning of adapter</span></div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="keywordflow">return</span> rt;</div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  rt[0] = max_score;</div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <span class="comment">// print_alignment(_align, _align_n);</span></div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <span class="keywordflow">return</span> rt;</div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span> }</div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span> </div><div class="line"><a name="l00201"></a><span class="lineno"> 201</span> <span class="comment">// int find_adapters_contaminants(std::istream &cin, std::string adp_cntms_file){</span></div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span> <span class="comment">// std::vector<std::string> adp = read_adapters_from_fasta(adp_cntms_file, "Read1");</span></div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span> <span class="comment">// std::string line, bases, qual, b;</span></div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span> <span class="comment">// int ctr = 0, score, *t = new int[2];</span></div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span> <span class="comment">// while (std::getline(cin, line)){</span></div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span> <span class="comment">// if(ctr % 400000 == 0)</span></div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span> <span class="comment">// std::cout << "Processed " << (ctr/4) << " reads ..." << std::endl;</span></div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span> <span class="comment">// if(ctr % 2 == 0){</span></div><div class="line"><a name="l00209"></a><span class="lineno"> 209</span> <span class="comment">// ctr++;</span></div><div class="line"><a name="l00210"></a><span class="lineno"> 210</span> <span class="comment">// continue;</span></div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span> <span class="comment">// }</span></div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span> <span class="comment">// if((ctr+1) % 2 == 0 && (ctr + 1) % 4 == 0 ){</span></div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span> <span class="comment">// qual = line;</span></div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span> <span class="comment">// // std::cout << bases << std::endl;</span></div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span> <span class="comment">// // std::cout << qual << std::endl;</span></div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span> <span class="comment">// score = -1;</span></div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span> <span class="comment">// for(std::vector<std::string>::iterator it = adp.begin(); it != adp.end() && score == -1; ++it) {</span></div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span> <span class="comment">// b = ((*it).length() > bases.length()) ? bases : bases.substr(bases.length() - (*it).length(), (*it).length());</span></div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span> <span class="comment">// t = align_seqs(b, *it);</span></div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span> <span class="comment">// score = *t;</span></div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span> <span class="comment">// if(score != -1)</span></div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span> <span class="comment">// std::cout << "Trimmed: " << bases.substr(0, bases.length() - *(t+1)) << std::endl;</span></div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span> <span class="comment">// }</span></div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span> <span class="comment">// } else {</span></div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span> <span class="comment">// bases = line;</span></div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span> <span class="comment">// }</span></div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span> <span class="comment">// ctr++;</span></div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span> <span class="comment">// }</span></div><div class="line"><a name="l00229"></a><span class="lineno"> 229</span> <span class="comment">// return 0;</span></div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span> <span class="comment">// }</span></div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span> </div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span> <span class="comment">// int main(int argc, char* argv[]){</span></div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span> <span class="comment">// std::string adp = "../data/adapters/NexteraPR.fa";</span></div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span> <span class="comment">// // clock_t begin = clock();</span></div><div class="line"><a name="l00235"></a><span class="lineno"> 235</span> <span class="comment">// find_adapters_contaminants(std::cin, adp);</span></div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span> <span class="comment">// // clock_t end = clock();</span></div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span> <span class="comment">// // double elapsed_secs = double(end - begin) / CLOCKS_PER_SEC;</span></div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span> <span class="comment">// // std::cout << "Time Taken: " << elapsed_secs << std::endl;</span></div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span> <span class="comment">// return 0;</span></div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span> <span class="comment">// }</span></div></div><!-- fragment --></div><!-- contents -->
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