Commit c0c18d7c authored by RomainFeron's avatar RomainFeron
Browse files

Finished first major doc update

parent b5ff6582
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<p>Implements the <a class="el" href="classSignif.html" title="Implements the &quot;signif&quot; analysis. ">Signif</a> class.
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<a href="signif_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span>&#160;<span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span>&#160;<span class="comment">* Copyright (C) 2020 Romain Feron</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span>&#160;<span class="comment">* This file is part of RADSex.</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span>&#160;<span class="comment">* RADSex is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span>&#160;<span class="comment">* it under the terms of the GNU General Public License as published by</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span>&#160;<span class="comment">* the Free Software Foundation, either version 3 of the License, or</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span>&#160;<span class="comment">* (at your option) any later version.</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span>&#160;<span class="comment">* RADSex is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span>&#160;<span class="comment">* but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span>&#160;<span class="comment">* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span>&#160;<span class="comment">* GNU General Public License for more details.</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span>&#160;<span class="comment">* You should have received a copy of the GNU General Public License</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span>&#160;<span class="comment">* along with RADSex. If not, see &lt;https://www.gnu.org/licenses/&gt;.</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span>&#160;<span class="comment">*/</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span>&#160;</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="signif_8h.html">signif.h</a>&quot;</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>&#160;</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>&#160;</div><div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="classSignif.html#ac06a653925053d81985a36dcf6e96ad2"> 27</a></span>&#160;<span class="keywordtype">void</span> <a class="code" href="classSignif.html#ac06a653925053d81985a36dcf6e96ad2">Signif::process_marker</a>(<a class="code" href="classMarker.html">Marker</a>&amp; marker) {</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>&#160;</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>&#160; 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<span class="comment">// First pass: filter markers with non-corrected p &lt; 0.05</span></div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>&#160; <span class="keywordflow">if</span> (static_cast&lt;float&gt;(marker.<a class="code" href="classMarker.html#ae4685d12aeaed673dc151a561af85db6">p</a>) &lt; this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a7a0aec37ff8b323f8924da94d0bc0d4d">signif_threshold</a>) this-&gt;<a class="code" href="classSignif.html#a2a256d1c80dc918b0c4f9453b0552d0f">results</a>.<a class="code" href="structSignifResults.html#a5f27129d21aac037b5926eef1f3c18be">candidate_markers</a>.push_back(marker);</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>&#160;</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>&#160; }</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>&#160;</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>&#160;}</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>&#160;</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>&#160;</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>&#160;</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>&#160;</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>&#160;</div><div class="line"><a name="l00046"></a><span class="lineno"><a class="line" href="classSignif.html#ac64b0e21aed03d3ef10ff1a0f1cea654"> 46</a></span>&#160;<span class="keywordtype">void</span> <a class="code" href="classSignif.html#ac64b0e21aed03d3ef10ff1a0f1cea654">Signif::generate_output</a>() {</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>&#160;</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>&#160; std::ofstream output_file = <a class="code" href="utils_8h.html#ab33b713fe0754a5f7729a22cedc0fa9b">open_output</a>(this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a9cb286258590de65042051e194654fdc">output_file_path</a>);</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>&#160;</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>&#160; <span class="keywordflow">if</span> (not this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a5da0bb1f08576f6646881a1e4f8b7c25">output_fasta</a>) output_file &lt;&lt; <a class="code" href="utils_8h.html#ac5169aeb75bd397c83c20b965cfdbfc6">print_list</a>(this-&gt;<a class="code" href="classAnalysis.html#a3b9bc8b0dcc0ecea11d3a12969397ba7">markers_table</a>.<a class="code" href="classMarkersTable.html#a355de34437483f69d063ebae100a8089">header</a>.<a class="code" href="classHeader.html#a3e5bb0f13d849e5635a0731f13ae58fd">header</a>, <span class="stringliteral">&quot;\t&quot;</span>) &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>&#160;</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>&#160; <span class="keywordflow">if</span> (not this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a44b25c08718abd5476d0ee3eb2a1cec9">disable_correction</a>) this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a7a0aec37ff8b323f8924da94d0bc0d4d">signif_threshold</a> /= this-&gt;<a class="code" href="classSignif.html#a2a256d1c80dc918b0c4f9453b0552d0f">results</a>.<a class="code" href="structSignifResults.html#aef081481be06826327d186e3a287e627">n_markers</a>; <span class="comment">// Bonferroni correction: divide threshold by number of tests</span></div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>&#160;</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>&#160; <span class="comment">// Second pass: filter markers with threshold corrected p &lt; 0.05</span></div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>&#160; <span class="keywordflow">for</span> (<span class="keyword">auto</span> marker: this-&gt;<a class="code" href="classSignif.html#a2a256d1c80dc918b0c4f9453b0552d0f">results</a>.<a class="code" href="structSignifResults.html#a5f27129d21aac037b5926eef1f3c18be">candidate_markers</a>) {</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>&#160;</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>&#160; <span class="keywordflow">if</span> (static_cast&lt;float&gt;(marker.p) &lt; this-&gt;parameters.signif_threshold) {</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>&#160;</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>&#160; this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a5da0bb1f08576f6646881a1e4f8b7c25">output_fasta</a> ? marker.output_as_fasta(output_file, this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#ab362fca31d273c139ca30abdf9d2966e">min_depth</a>) : marker.output_as_table(output_file);</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>&#160;</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>&#160; }</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>&#160;</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>&#160; }</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>&#160;</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>&#160; output_file.close();</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>&#160;</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>&#160;}</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>&#160;</div><div class="ttc" id="structSignifResults_html_aef081481be06826327d186e3a287e627"><div class="ttname"><a href="structSignifResults.html#aef081481be06826327d186e3a287e627">SignifResults::n_markers</a></div><div class="ttdeci">uint64_t n_markers</div><div class="ttdoc">Number of markers present in at least one individual with depth higher than min_depth (for Bonferroni...</div><div class="ttdef"><b>Definition:</b> <a href="signif_8h_source.html#l00046">signif.h:46</a></div></div>
<div class="ttc" id="structParameters_html_aebb77195a9b4edb3f37df32bec3d9eba"><div class="ttname"><a href="structParameters.html#aebb77195a9b4edb3f37df32bec3d9eba">Parameters::group2</a></div><div class="ttdeci">std::string group2</div><div class="ttdoc">Name of the secondfirst group for analysis comparing two groups. </div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00050">parameters.h:50</a></div></div>
<div class="ttc" id="structSignifResults_html_a5f27129d21aac037b5926eef1f3c18be"><div class="ttname"><a href="structSignifResults.html#a5f27129d21aac037b5926eef1f3c18be">SignifResults::candidate_markers</a></div><div class="ttdeci">std::vector&lt; Marker &gt; candidate_markers</div><div class="ttdoc">Vector of markers significantly associated with groups before Bonferroni correction. </div><div class="ttdef"><b>Definition:</b> <a href="signif_8h_source.html#l00045">signif.h:45</a></div></div>
<div class="ttc" id="classMarker_html"><div class="ttname"><a href="classMarker.html">Marker</a></div><div class="ttdoc">Marker class. </div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00037">marker.h:37</a></div></div>
<div class="ttc" id="classAnalysis_html_a964cb61cb6b983aefe7fb2f272d1a330"><div class="ttname"><a href="classAnalysis.html#a964cb61cb6b983aefe7fb2f272d1a330">Analysis::popmap</a></div><div class="ttdeci">Popmap popmap</div><div class="ttdoc">Popmap instance storing group for each individual. </div><div class="ttdef"><b>Definition:</b> <a href="analysis_8h_source.html#l00059">analysis.h:59</a></div></div>
<div class="ttc" id="classSignif_html_a2a256d1c80dc918b0c4f9453b0552d0f"><div class="ttname"><a href="classSignif.html#a2a256d1c80dc918b0c4f9453b0552d0f">Signif::results</a></div><div class="ttdeci">SignifResults results</div><div class="ttdoc">SignifResults instance to store markers significantly associated with groups before Bonferroni correc...</div><div class="ttdef"><b>Definition:</b> <a href="signif_8h_source.html#l00108">signif.h:108</a></div></div>
<div class="ttc" id="structParameters_html_a44b25c08718abd5476d0ee3eb2a1cec9"><div class="ttname"><a href="structParameters.html#a44b25c08718abd5476d0ee3eb2a1cec9">Parameters::disable_correction</a></div><div class="ttdeci">bool disable_correction</div><div class="ttdoc">If true, Bonferroni correction will NOT be applied when estimating significance of association with g...</div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00056">parameters.h:56</a></div></div>
<div class="ttc" id="classSignif_html_ac64b0e21aed03d3ef10ff1a0f1cea654"><div class="ttname"><a href="classSignif.html#ac64b0e21aed03d3ef10ff1a0f1cea654">Signif::generate_output</a></div><div class="ttdeci">void generate_output()</div><div class="ttdoc">Generate the output file. </div><div class="ttdef"><b>Definition:</b> <a href="signif_8cpp_source.html#l00046">signif.cpp:46</a></div></div>
<div class="ttc" id="signif_8h_html"><div class="ttname"><a href="signif_8h.html">signif.h</a></div><div class="ttdoc">Defines the Signif class implementing the &quot;signif&quot; analysis. </div></div>
<div class="ttc" id="classMarker_html_a3dbbb17e3bd5a194b879d983714b04b2"><div class="ttname"><a href="classMarker.html#a3dbbb17e3bd5a194b879d983714b04b2">Marker::n_individuals</a></div><div class="ttdeci">uint n_individuals</div><div class="ttdoc">Total number of individuals in which the marker is present. </div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00045">marker.h:45</a></div></div>
<div class="ttc" id="classAnalysis_html_a3b9bc8b0dcc0ecea11d3a12969397ba7"><div class="ttname"><a href="classAnalysis.html#a3b9bc8b0dcc0ecea11d3a12969397ba7">Analysis::markers_table</a></div><div class="ttdeci">MarkersTable markers_table</div><div class="ttdoc">Markers table instance implementing the markers table parser and markers queue. </div><div class="ttdef"><b>Definition:</b> <a href="analysis_8h_source.html#l00060">analysis.h:60</a></div></div>
<div class="ttc" id="classPopmap_html_a84116d0a16650cde1b7d4bca949b81c6"><div class="ttname"><a href="classPopmap.html#a84116d0a16650cde1b7d4bca949b81c6">Popmap::get_count</a></div><div class="ttdeci">uint get_count(const std::string &amp;group) const</div><div class="ttdoc">Get individual count for a group. </div><div class="ttdef"><b>Definition:</b> <a href="popmap_8cpp_source.html#l00117">popmap.cpp:117</a></div></div>
<div class="ttc" id="utils_8h_html_ab33b713fe0754a5f7729a22cedc0fa9b"><div class="ttname"><a href="utils_8h.html#ab33b713fe0754a5f7729a22cedc0fa9b">open_output</a></div><div class="ttdeci">std::ofstream open_output(const std::string &amp;output_file_path)</div><div class="ttdoc">Open an output file and check that the file is open properly. </div><div class="ttdef"><b>Definition:</b> <a href="utils_8h_source.html#l00175">utils.h:175</a></div></div>
<div class="ttc" id="structParameters_html_a5da0bb1f08576f6646881a1e4f8b7c25"><div class="ttname"><a href="structParameters.html#a5da0bb1f08576f6646881a1e4f8b7c25">Parameters::output_fasta</a></div><div class="ttdeci">bool output_fasta</div><div class="ttdoc">If true, markers are outputted in FASTA format. </div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00046">parameters.h:46</a></div></div>
<div class="ttc" id="utils_8h_html_ac5169aeb75bd397c83c20b965cfdbfc6"><div class="ttname"><a href="utils_8h.html#ac5169aeb75bd397c83c20b965cfdbfc6">print_list</a></div><div class="ttdeci">std::string print_list(const T &amp;list, const std::string &amp;sep=&quot;, &quot;)</div><div class="ttdoc">Print a container as a &quot;sep&quot;-separated string. </div><div class="ttdef"><b>Definition:</b> <a href="utils_8h_source.html#l00281">utils.h:281</a></div></div>
<div class="ttc" id="structParameters_html_a3ce2dc3d06c4b8f4398fb119931ce88a"><div class="ttname"><a href="structParameters.html#a3ce2dc3d06c4b8f4398fb119931ce88a">Parameters::group1</a></div><div class="ttdeci">std::string group1</div><div class="ttdoc">Name of the first group for analysis comparing two groups. </div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00049">parameters.h:49</a></div></div>
<div class="ttc" id="classAnalysis_html_a8abd4de209925cb46571d4db97977d32"><div class="ttname"><a href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">Analysis::parameters</a></div><div class="ttdeci">Parameters parameters</div><div class="ttdoc">Store RADSex parameters. </div><div class="ttdef"><b>Definition:</b> <a href="analysis_8h_source.html#l00054">analysis.h:54</a></div></div>
<div class="ttc" id="classMarker_html_a6c79b442c33bf8de73d2f2c081347e2a"><div class="ttname"><a href="classMarker.html#a6c79b442c33bf8de73d2f2c081347e2a">Marker::group_counts</a></div><div class="ttdeci">std::unordered_map&lt; std::string, uint &gt; group_counts</div><div class="ttdoc">Map storing group counts for the marker {group -&gt; number of individuals in which the marker is presen...</div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00044">marker.h:44</a></div></div>
<div class="ttc" id="classMarker_html_ae4685d12aeaed673dc151a561af85db6"><div class="ttname"><a href="classMarker.html#ae4685d12aeaed673dc151a561af85db6">Marker::p</a></div><div class="ttdeci">float p</div><div class="ttdoc">P-value of association with group. </div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00046">marker.h:46</a></div></div>
<div class="ttc" id="classSignif_html_ac06a653925053d81985a36dcf6e96ad2"><div class="ttname"><a href="classSignif.html#ac06a653925053d81985a36dcf6e96ad2">Signif::process_marker</a></div><div class="ttdeci">void process_marker(Marker &amp;marker)</div><div class="ttdoc">Process a single marker. </div><div class="ttdef"><b>Definition:</b> <a href="signif_8cpp_source.html#l00027">signif.cpp:27</a></div></div>
<div class="ttc" id="structParameters_html_ab362fca31d273c139ca30abdf9d2966e"><div class="ttname"><a href="structParameters.html#ab362fca31d273c139ca30abdf9d2966e">Parameters::min_depth</a></div><div class="ttdeci">uint min_depth</div><div class="ttdoc">Minimum depth to consider a marker present in an individual. </div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00054">parameters.h:54</a></div></div>
<div class="ttc" id="stats_8cpp_html_a748519ef79463c2bc861ef5f2f950cd0"><div class="ttname"><a href="stats_8cpp.html#a748519ef79463c2bc861ef5f2f950cd0">get_p_association</a></div><div class="ttdeci">double get_p_association(uint n_group1, uint n_group2, uint total_group1, uint total_group2)</div><div class="ttdoc">Compute the p-value of association with group with a Chi-squared test. </div><div class="ttdef"><b>Definition:</b> <a href="stats_8cpp_source.html#l00065">stats.cpp:65</a></div></div>
<div class="ttc" id="structParameters_html_a9cb286258590de65042051e194654fdc"><div class="ttname"><a href="structParameters.html#a9cb286258590de65042051e194654fdc">Parameters::output_file_path</a></div><div class="ttdeci">std::string output_file_path</div><div class="ttdoc">Path to the output file for any analysis. </div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00042">parameters.h:42</a></div></div>
<div class="ttc" id="structParameters_html_a7a0aec37ff8b323f8924da94d0bc0d4d"><div class="ttname"><a href="structParameters.html#a7a0aec37ff8b323f8924da94d0bc0d4d">Parameters::signif_threshold</a></div><div class="ttdeci">float signif_threshold</div><div class="ttdoc">P-value threshold to consider a marker significantly associated with group. </div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00055">parameters.h:55</a></div></div>
<div class="ttc" id="classHeader_html_a3e5bb0f13d849e5635a0731f13ae58fd"><div class="ttname"><a href="classHeader.html#a3e5bb0f13d849e5635a0731f13ae58fd">Header::header</a></div><div class="ttdeci">std::vector&lt; std::string &gt; header</div><div class="ttdoc">Vector storing all the fields in the markers table&amp;#39;s header. </div><div class="ttdef"><b>Definition:</b> <a href="markers__table_8h_source.html#l00049">markers_table.h:49</a></div></div>
<div class="ttc" id="classMarkersTable_html_a355de34437483f69d063ebae100a8089"><div class="ttname"><a href="classMarkersTable.html#a355de34437483f69d063ebae100a8089">MarkersTable::header</a></div><div class="ttdeci">Header header</div><div class="ttdoc">Header instance storing information about the markers table. </div><div class="ttdef"><b>Definition:</b> <a href="markers__table_8h_source.html#l00088">markers_table.h:88</a></div></div>
<a href="signif_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span>&#160;<span class="comment">/*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span>&#160;<span class="comment">* Copyright (C) 2020 Romain Feron</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span>&#160;<span class="comment">* This file is part of RADSex.</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span>&#160;<span class="comment"></span> </div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span>&#160;<span class="comment">* RADSex is free software: you can redistribute it and/or modify</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span>&#160;<span class="comment">* it under the terms of the GNU General Public License as published by</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span>&#160;<span class="comment">* the Free Software Foundation, either version 3 of the License, or</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span>&#160;<span class="comment">* (at your option) any later version.</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span>&#160;<span class="comment"></span> </div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span>&#160;<span class="comment">* RADSex is distributed in the hope that it will be useful,</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span>&#160;<span class="comment">* but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span>&#160;<span class="comment">* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span>&#160;<span class="comment">* GNU General Public License for more details.</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span>&#160;<span class="comment"></span> </div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span>&#160;<span class="comment">* You should have received a copy of the GNU General Public License</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>&#160;<span class="comment">* along with RADSex. If not, see &lt;https://www.gnu.org/licenses/&gt;.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span>&#160;<span class="comment">*/</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>&#160; </div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="signif_8h.html">signif.h</a>&quot;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span>&#160; </div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span>&#160; </div>
<div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="classSignif.html#ac06a653925053d81985a36dcf6e96ad2"> 27</a></span>&#160;<span class="keywordtype">void</span> <a class="code" href="classSignif.html#ac06a653925053d81985a36dcf6e96ad2">Signif::process_marker</a>(<a class="code" href="classMarker.html">Marker</a>&amp; marker) {</div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span>&#160; </div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span>&#160; <span class="keywordflow">if</span> (marker.<a class="code" href="classMarker.html#a3dbbb17e3bd5a194b879d983714b04b2">n_individuals</a> &gt; 0) {</div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span>&#160; </div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span>&#160; ++this-&gt;<a class="code" href="classSignif.html#a2a256d1c80dc918b0c4f9453b0552d0f">results</a>.<a class="code" href="structSignifResults.html#aef081481be06826327d186e3a287e627">n_markers</a>; <span class="comment">// Increment total number of markers for Bonferroni correction</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span>&#160; </div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span>&#160; marker.<a class="code" href="classMarker.html#ae4685d12aeaed673dc151a561af85db6">p</a> = <a class="code" href="stats_8cpp.html#a748519ef79463c2bc861ef5f2f950cd0">get_p_association</a>(marker.<a class="code" href="classMarker.html#a6c79b442c33bf8de73d2f2c081347e2a">group_counts</a>[<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a3ce2dc3d06c4b8f4398fb119931ce88a">group1</a>], marker.<a class="code" href="classMarker.html#a6c79b442c33bf8de73d2f2c081347e2a">group_counts</a>[<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#aebb77195a9b4edb3f37df32bec3d9eba">group2</a>], this-&gt;popmap.get_count(this-&gt;parameters.group1), this-&gt;popmap.get_count(this-&gt;parameters.group2));</div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>&#160; </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>&#160; <span class="comment">// First pass: filter markers with non-corrected p &lt; 0.05</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span>&#160; <span class="keywordflow">if</span> (<span class="keyword">static_cast&lt;</span><span class="keywordtype">float</span><span class="keyword">&gt;</span>(marker.<a class="code" href="classMarker.html#ae4685d12aeaed673dc151a561af85db6">p</a>) &lt; this-&gt;parameters.signif_threshold) this-&gt;<a class="code" href="classSignif.html#a2a256d1c80dc918b0c4f9453b0552d0f">results</a>.<a class="code" href="structSignifResults.html#a5f27129d21aac037b5926eef1f3c18be">candidate_markers</a>.push_back(marker);</div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>&#160; </div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span>&#160; }</div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span>&#160; </div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>&#160;}</div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>&#160; </div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>&#160; </div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>&#160; </div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>&#160; </div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>&#160; </div>
<div class="line"><a name="l00046"></a><span class="lineno"><a class="line" href="classSignif.html#ac64b0e21aed03d3ef10ff1a0f1cea654"> 46</a></span>&#160;<span class="keywordtype">void</span> <a class="code" href="classSignif.html#ac64b0e21aed03d3ef10ff1a0f1cea654">Signif::generate_output</a>() {</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>&#160; </div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>&#160; std::ofstream output_file = <a class="code" href="utils_8h.html#ab33b713fe0754a5f7729a22cedc0fa9b">open_output</a>(this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a9cb286258590de65042051e194654fdc">output_file_path</a>);</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>&#160; </div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>&#160; <span class="keywordflow">if</span> (not this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a5da0bb1f08576f6646881a1e4f8b7c25">output_fasta</a>) output_file &lt;&lt; <a class="code" href="utils_8h.html#ac5169aeb75bd397c83c20b965cfdbfc6">print_list</a>(this-&gt;<a class="code" href="classAnalysis.html#a3b9bc8b0dcc0ecea11d3a12969397ba7">markers_table</a>.<a class="code" href="classMarkersTable.html#a355de34437483f69d063ebae100a8089">header</a>.<a class="code" href="classHeader.html#a3e5bb0f13d849e5635a0731f13ae58fd">header</a>, <span class="stringliteral">&quot;\t&quot;</span>) &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>&#160; </div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>&#160; <span class="keywordflow">if</span> (not this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a44b25c08718abd5476d0ee3eb2a1cec9">disable_correction</a>) this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a7a0aec37ff8b323f8924da94d0bc0d4d">signif_threshold</a> /= this-&gt;<a class="code" href="classSignif.html#a2a256d1c80dc918b0c4f9453b0552d0f">results</a>.<a class="code" href="structSignifResults.html#aef081481be06826327d186e3a287e627">n_markers</a>; <span class="comment">// Bonferroni correction: divide threshold by number of tests</span></div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>&#160; </div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>&#160; <span class="comment">// Second pass: filter markers with threshold corrected p &lt; 0.05</span></div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>&#160; <span class="keywordflow">for</span> (<span class="keyword">auto</span> marker: this-&gt;<a class="code" href="classSignif.html#a2a256d1c80dc918b0c4f9453b0552d0f">results</a>.<a class="code" href="structSignifResults.html#a5f27129d21aac037b5926eef1f3c18be">candidate_markers</a>) {</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>&#160; </div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>&#160; <span class="keywordflow">if</span> (<span class="keyword">static_cast&lt;</span><span class="keywordtype">float</span><span class="keyword">&gt;</span>(marker.p) &lt; this-&gt;parameters.signif_threshold) {</div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>&#160; </div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>&#160; this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#a5da0bb1f08576f6646881a1e4f8b7c25">output_fasta</a> ? marker.output_as_fasta(output_file, this-&gt;<a class="code" href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">parameters</a>.<a class="code" href="structParameters.html#ab362fca31d273c139ca30abdf9d2966e">min_depth</a>) : marker.output_as_table(output_file);</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>&#160; </div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>&#160; }</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>&#160; </div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>&#160; }</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>&#160; </div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>&#160; output_file.close();</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>&#160; </div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>&#160;}</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>&#160; </div>
</div><!-- fragment --></div><!-- contents -->
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<div class="ttc" id="astructSignifResults_html_a5f27129d21aac037b5926eef1f3c18be"><div class="ttname"><a href="structSignifResults.html#a5f27129d21aac037b5926eef1f3c18be">SignifResults::candidate_markers</a></div><div class="ttdeci">std::vector&lt; Marker &gt; candidate_markers</div><div class="ttdoc">Vector of markers significantly associated with groups before Bonferroni correction.</div><div class="ttdef"><b>Definition:</b> <a href="signif_8h_source.html#l00045">signif.h:45</a></div></div>
<div class="ttc" id="astructParameters_html_a9cb286258590de65042051e194654fdc"><div class="ttname"><a href="structParameters.html#a9cb286258590de65042051e194654fdc">Parameters::output_file_path</a></div><div class="ttdeci">std::string output_file_path</div><div class="ttdoc">Path to the output file for any analysis.</div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00042">parameters.h:42</a></div></div>
<div class="ttc" id="aclassSignif_html_a2a256d1c80dc918b0c4f9453b0552d0f"><div class="ttname"><a href="classSignif.html#a2a256d1c80dc918b0c4f9453b0552d0f">Signif::results</a></div><div class="ttdeci">SignifResults results</div><div class="ttdoc">SignifResults instance to store markers significantly associated with groups before Bonferroni correc...</div><div class="ttdef"><b>Definition:</b> <a href="signif_8h_source.html#l00108">signif.h:108</a></div></div>
<div class="ttc" id="autils_8h_html_ac5169aeb75bd397c83c20b965cfdbfc6"><div class="ttname"><a href="utils_8h.html#ac5169aeb75bd397c83c20b965cfdbfc6">print_list</a></div><div class="ttdeci">std::string print_list(const T &amp;list, const std::string &amp;sep=&quot;, &quot;)</div><div class="ttdoc">Print a container as a &quot;sep&quot;-separated string.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8h_source.html#l00281">utils.h:281</a></div></div>
<div class="ttc" id="asignif_8h_html"><div class="ttname"><a href="signif_8h.html">signif.h</a></div><div class="ttdoc">Defines the Signif class implementing the &quot;signif&quot; analysis.</div></div>
<div class="ttc" id="aclassAnalysis_html_a8abd4de209925cb46571d4db97977d32"><div class="ttname"><a href="classAnalysis.html#a8abd4de209925cb46571d4db97977d32">Analysis::parameters</a></div><div class="ttdeci">Parameters parameters</div><div class="ttdoc">Store RADSex parameters.</div><div class="ttdef"><b>Definition:</b> <a href="analysis_8h_source.html#l00054">analysis.h:54</a></div></div>
<div class="ttc" id="aclassMarker_html_a3dbbb17e3bd5a194b879d983714b04b2"><div class="ttname"><a href="classMarker.html#a3dbbb17e3bd5a194b879d983714b04b2">Marker::n_individuals</a></div><div class="ttdeci">uint n_individuals</div><div class="ttdoc">Total number of individuals in which the marker is present.</div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00045">marker.h:45</a></div></div>
<div class="ttc" id="aclassSignif_html_ac64b0e21aed03d3ef10ff1a0f1cea654"><div class="ttname"><a href="classSignif.html#ac64b0e21aed03d3ef10ff1a0f1cea654">Signif::generate_output</a></div><div class="ttdeci">void generate_output()</div><div class="ttdoc">Generate the output file.</div><div class="ttdef"><b>Definition:</b> <a href="signif_8cpp_source.html#l00046">signif.cpp:46</a></div></div>
<div class="ttc" id="autils_8h_html_ab33b713fe0754a5f7729a22cedc0fa9b"><div class="ttname"><a href="utils_8h.html#ab33b713fe0754a5f7729a22cedc0fa9b">open_output</a></div><div class="ttdeci">std::ofstream open_output(const std::string &amp;output_file_path)</div><div class="ttdoc">Open an output file and check that the file is open properly.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8h_source.html#l00175">utils.h:175</a></div></div>
<div class="ttc" id="astructParameters_html_aebb77195a9b4edb3f37df32bec3d9eba"><div class="ttname"><a href="structParameters.html#aebb77195a9b4edb3f37df32bec3d9eba">Parameters::group2</a></div><div class="ttdeci">std::string group2</div><div class="ttdoc">Name of the secondfirst group for analysis comparing two groups.</div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00050">parameters.h:50</a></div></div>
<div class="ttc" id="astructParameters_html_a44b25c08718abd5476d0ee3eb2a1cec9"><div class="ttname"><a href="structParameters.html#a44b25c08718abd5476d0ee3eb2a1cec9">Parameters::disable_correction</a></div><div class="ttdeci">bool disable_correction</div><div class="ttdoc">If true, Bonferroni correction will NOT be applied when estimating significance of association with g...</div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00056">parameters.h:56</a></div></div>
<div class="ttc" id="aclassMarker_html_ae4685d12aeaed673dc151a561af85db6"><div class="ttname"><a href="classMarker.html#ae4685d12aeaed673dc151a561af85db6">Marker::p</a></div><div class="ttdeci">float p</div><div class="ttdoc">P-value of association with group.</div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00046">marker.h:46</a></div></div>
<div class="ttc" id="astructSignifResults_html_aef081481be06826327d186e3a287e627"><div class="ttname"><a href="structSignifResults.html#aef081481be06826327d186e3a287e627">SignifResults::n_markers</a></div><div class="ttdeci">uint64_t n_markers</div><div class="ttdoc">Number of markers present in at least one individual with depth higher than min_depth (for Bonferroni...</div><div class="ttdef"><b>Definition:</b> <a href="signif_8h_source.html#l00046">signif.h:46</a></div></div>
<div class="ttc" id="aclassMarker_html_a6c79b442c33bf8de73d2f2c081347e2a"><div class="ttname"><a href="classMarker.html#a6c79b442c33bf8de73d2f2c081347e2a">Marker::group_counts</a></div><div class="ttdeci">std::unordered_map&lt; std::string, uint &gt; group_counts</div><div class="ttdoc">Map storing group counts for the marker {group -&gt; number of individuals in which the marker is presen...</div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00044">marker.h:44</a></div></div>
<div class="ttc" id="astructParameters_html_a3ce2dc3d06c4b8f4398fb119931ce88a"><div class="ttname"><a href="structParameters.html#a3ce2dc3d06c4b8f4398fb119931ce88a">Parameters::group1</a></div><div class="ttdeci">std::string group1</div><div class="ttdoc">Name of the first group for analysis comparing two groups.</div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00049">parameters.h:49</a></div></div>
<div class="ttc" id="aclassSignif_html_ac06a653925053d81985a36dcf6e96ad2"><div class="ttname"><a href="classSignif.html#ac06a653925053d81985a36dcf6e96ad2">Signif::process_marker</a></div><div class="ttdeci">void process_marker(Marker &amp;marker)</div><div class="ttdoc">Process a single marker.</div><div class="ttdef"><b>Definition:</b> <a href="signif_8cpp_source.html#l00027">signif.cpp:27</a></div></div>
<div class="ttc" id="astructParameters_html_a5da0bb1f08576f6646881a1e4f8b7c25"><div class="ttname"><a href="structParameters.html#a5da0bb1f08576f6646881a1e4f8b7c25">Parameters::output_fasta</a></div><div class="ttdeci">bool output_fasta</div><div class="ttdoc">If true, markers are outputted in FASTA format.</div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00046">parameters.h:46</a></div></div>
<div class="ttc" id="astats_8cpp_html_a748519ef79463c2bc861ef5f2f950cd0"><div class="ttname"><a href="stats_8cpp.html#a748519ef79463c2bc861ef5f2f950cd0">get_p_association</a></div><div class="ttdeci">double get_p_association(uint n_group1, uint n_group2, uint total_group1, uint total_group2)</div><div class="ttdoc">Compute the p-value of association with group with a Chi-squared test.</div><div class="ttdef"><b>Definition:</b> <a href="stats_8cpp_source.html#l00065">stats.cpp:65</a></div></div>
<div class="ttc" id="aclassHeader_html_a3e5bb0f13d849e5635a0731f13ae58fd"><div class="ttname"><a href="classHeader.html#a3e5bb0f13d849e5635a0731f13ae58fd">Header::header</a></div><div class="ttdeci">std::vector&lt; std::string &gt; header</div><div class="ttdoc">Vector storing all the fields in the markers table's header.</div><div class="ttdef"><b>Definition:</b> <a href="markers__table_8h_source.html#l00049">markers_table.h:49</a></div></div>
<div class="ttc" id="aclassAnalysis_html_a3b9bc8b0dcc0ecea11d3a12969397ba7"><div class="ttname"><a href="classAnalysis.html#a3b9bc8b0dcc0ecea11d3a12969397ba7">Analysis::markers_table</a></div><div class="ttdeci">MarkersTable markers_table</div><div class="ttdoc">Markers table instance implementing the markers table parser and markers queue.</div><div class="ttdef"><b>Definition:</b> <a href="analysis_8h_source.html#l00060">analysis.h:60</a></div></div>
<div class="ttc" id="aclassMarkersTable_html_a355de34437483f69d063ebae100a8089"><div class="ttname"><a href="classMarkersTable.html#a355de34437483f69d063ebae100a8089">MarkersTable::header</a></div><div class="ttdeci">Header header</div><div class="ttdoc">Header instance storing information about the markers table.</div><div class="ttdef"><b>Definition:</b> <a href="markers__table_8h_source.html#l00088">markers_table.h:88</a></div></div>
<div class="ttc" id="astructParameters_html_ab362fca31d273c139ca30abdf9d2966e"><div class="ttname"><a href="structParameters.html#ab362fca31d273c139ca30abdf9d2966e">Parameters::min_depth</a></div><div class="ttdeci">uint min_depth</div><div class="ttdoc">Minimum depth to consider a marker present in an individual.</div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00054">parameters.h:54</a></div></div>
<div class="ttc" id="aclassMarker_html"><div class="ttname"><a href="classMarker.html">Marker</a></div><div class="ttdoc">Marker class.</div><div class="ttdef"><b>Definition:</b> <a href="marker_8h_source.html#l00037">marker.h:37</a></div></div>
<div class="ttc" id="astructParameters_html_a7a0aec37ff8b323f8924da94d0bc0d4d"><div class="ttname"><a href="structParameters.html#a7a0aec37ff8b323f8924da94d0bc0d4d">Parameters::signif_threshold</a></div><div class="ttdeci">float signif_threshold</div><div class="ttdoc">P-value threshold to consider a marker significantly associated with group.</div><div class="ttdef"><b>Definition:</b> <a href="parameters_8h_source.html#l00055">parameters.h:55</a></div></div>
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<p>Defines the <a class="el" href="classSignif.html" title="Implements the &quot;signif&quot; analysis. ">Signif</a> class implementing the "signif" analysis.
<p>Defines the <a class="el" href="classSignif.html" title="Implements the &quot;signif&quot; analysis.">Signif</a> class implementing the "signif" analysis.
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<div class="textblock"><code>#include &lt;fstream&gt;</code><br />
<code>#include &lt;string&gt;</code><br />
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classSignif.html">Signif</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Implements the "signif" analysis. <a href="classSignif.html#details">More...</a><br /></td></tr>
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<a href="signif_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span>&#160;<span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span>&#160;<span class="comment">* Copyright (C) 2020 Romain Feron</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span>&#160;<span class="comment">* This file is part of RADSex.</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span>&#160;<span class="comment">* RADSex is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span>&#160;<span class="comment">* it under the terms of the GNU General Public License as published by</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span>&#160;<span class="comment">* the Free Software Foundation, either version 3 of the License, or</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span>&#160;<span class="comment">* (at your option) any later version.</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span>&#160;<span class="comment">* RADSex is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span>&#160;<span class="comment">* but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span>&#160;<span class="comment">* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span>&#160;<span class="comment">* GNU General Public License for more details.</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span>&#160;<span class="comment">* You should have received a copy of the GNU General Public License</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span>&#160;<span class="comment">* along with RADSex. If not, see &lt;https://www.gnu.org/licenses/&gt;.</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span>&#160;<span class="comment">*/</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span>&#160;</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>&#160;<span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>&#160;<span class="preprocessor">#include &lt;fstream&gt;</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>&#160;<span class="preprocessor">#include &lt;string&gt;</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>&#160;<span cla