<divclass="ttc"id="aclassCustomFormatter_html_a8976f459918d11b5696efdb76dc2cff2"><divclass="ttname"><ahref="classCustomFormatter.html#a8976f459918d11b5696efdb76dc2cff2">CustomFormatter::border_width</a></div><divclass="ttdeci">uint border_width</div><divclass="ttdoc">Define number of spaces between two columns.</div><divclass="ttdef"><b>Definition:</b> arg_parser.h:75</div></div>
<divclass="ttc"id="aclassCustomFormatter_html_a2545ecf41317fd8bc529daae51edad24"><divclass="ttname"><ahref="classCustomFormatter.html#a2545ecf41317fd8bc529daae51edad24">CustomFormatter::set_column_widths</a></div><divclass="ttdeci">void set_column_widths(CLI::App &parser)</div><divclass="ttdoc">Set column widths in help message for a CLI::App.</div><divclass="ttdef"><b>Definition:</b> arg_parser.h:147</div></div>
<divclass="ttc"id="aclassCustomFormatter_html_a7c1d208d52c932ca0cb40b35b0b1c673"><divclass="ttname"><ahref="classCustomFormatter.html#a7c1d208d52c932ca0cb40b35b0b1c673">CustomFormatter::make_option</a></div><divclass="ttdeci">virtual std::string make_option(const CLI::Option *opt, bool is_positional) const</div><divclass="ttdoc">Format help message for an option.</div><divclass="ttdef"><b>Definition:</b> arg_parser.h:89</div></div>
<divclass="ttc"id="aclassCustomFormatter_html_a2578999ac91d0136d0349ebdeb3c6435"><divclass="ttname"><ahref="classCustomFormatter.html#a2578999ac91d0136d0349ebdeb3c6435">CustomFormatter::set_column_widths</a></div><divclass="ttdeci">void set_column_widths(const CLI::App &parser)</div><divclass="ttdoc">Set column widths in help message for a CLI::App.</div><divclass="ttdef"><b>Definition:</b> arg_parser.h:147</div></div>
<divclass="ttc"id="aclassCustomFormatter_html_abbcaea7bc716a16ed5fe23ed8caf5c9b"><divclass="ttname"><ahref="classCustomFormatter.html#abbcaea7bc716a16ed5fe23ed8caf5c9b">CustomFormatter::column_widths</a></div><divclass="ttdeci">uint column_widths[3]</div><divclass="ttdoc">Maximum width of each column, in order: flags, type, description.</div><divclass="ttdef"><b>Definition:</b> arg_parser.h:74</div></div>
<divclass="ttc"id="aclassCustomFormatter_html_a2cd26a35befd81c507255cc61f2ea0c6"><divclass="ttname"><ahref="classCustomFormatter.html#a2cd26a35befd81c507255cc61f2ea0c6">CustomFormatter::make_option</a></div><divclass="ttdeci">virtual std::string make_option(const CLI::Option *opt, const bool is_positional) const</div><divclass="ttdoc">Format help message for an option.</div><divclass="ttdef"><b>Definition:</b> arg_parser.h:89</div></div>
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<trclass="memdesc:a7c1d208d52c932ca0cb40b35b0b1c673"><tdclass="mdescLeft"> </td><tdclass="mdescRight">Format help message for an option. <ahref="classCustomFormatter.html#a7c1d208d52c932ca0cb40b35b0b1c673">More...</a><br/></td></tr>
<trclass="memdesc:a2cd26a35befd81c507255cc61f2ea0c6"><tdclass="mdescLeft"> </td><tdclass="mdescRight">Format help message for an option. <ahref="classCustomFormatter.html#a2cd26a35befd81c507255cc61f2ea0c6">More...</a><br/></td></tr>
<trclass="memdesc:a2545ecf41317fd8bc529daae51edad24"><tdclass="mdescLeft"> </td><tdclass="mdescRight">Set column widths in help message for a CLI::App. <ahref="classCustomFormatter.html#a2545ecf41317fd8bc529daae51edad24">More...</a><br/></td></tr>
<trclass="memdesc:a2578999ac91d0136d0349ebdeb3c6435"><tdclass="mdescLeft"> </td><tdclass="mdescRight">Set column widths in help message for a CLI::App. <ahref="classCustomFormatter.html#a2578999ac91d0136d0349ebdeb3c6435">More...</a><br/></td></tr>
<trclass="memdesc:ab2291110e5c4c1c90506c1cd6902e00e"><tdclass="mdescLeft"> </td><tdclass="mdescRight">Main function called by the depth command. <ahref="depth_8h.html#ab2291110e5c4c1c90506c1cd6902e00e">More...</a><br/></td></tr>
<trclass="memdesc:a050775c9b8c0513cf3ced6ac4350cdb4"><tdclass="mdescLeft"> </td><tdclass="mdescRight">Process markers from a <aclass="el"href="structMarkersQueue.html">MarkersQueue</a>. <ahref="depth_8h.html#a050775c9b8c0513cf3ced6ac4350cdb4">More...</a><br/></td></tr>
<p>Main function called by the depth command. </p>
<p>Compute the minimum, maximum, median, and average marker depth for each individual. <br/>
This function creates a parsing thread which reads a markers table file and stores markers into a queue, and a processing thread which reads batches of markers from the queue and compute metrics. <br/>
After all markers are processed, the function generates an tabulated output file with columns: <br/>
<tr><tdclass="paramname">parameters</td><td><aclass="el"href="structParameters.html">Parameters</a> object storing the value of all RADSex parameters </td></tr>
<p>Process markers from a <aclass="el"href="structMarkersQueue.html">MarkersQueue</a>. </p>
<p>Read batches of markers from a markers queue, store individual marker depths and update individual marker counts in results. Only retain markers present in >75% of individuals to compute depth metrics.</p>
<tr><tdclass="paramname">parsing_ended</td><td>A flag indicating that the parsing ended, updated by the <aclass="el"href="table__parser_8h.html#acae38db5e782a3fd35d349c195888fda"title="Read markers from a markers depth table and store them in a queue.">table_parser()</a> function </td></tr>
<divclass="line"><aname="l00035"></a><spanclass="lineno"> 35</span> <spanclass="comment">// Calculate the number of reads retained in each individual</span></div>
<divclass="ttc"id="astructDepthResults_html_a371ba5f5c8b3673f0574441163178461"><divclass="ttname"><ahref="structDepthResults.html#a371ba5f5c8b3673f0574441163178461">DepthResults::individual_markers_count</a></div><divclass="ttdeci">std::vector< uint32_t > individual_markers_count</div><divclass="ttdoc">Vector of size individuals storing the number of markers retained in each individual.</div><divclass="ttdef"><b>Definition:</b> depth.h:44</div></div>
<divclass="ttc"id="astructDepthResults_html_a5cc6408a27ba2fcd31ce3961a15b60a0"><divclass="ttname"><ahref="structDepthResults.html#a5cc6408a27ba2fcd31ce3961a15b60a0">DepthResults::depths</a></div><divclass="ttdeci">std::vector< std::vector< uint16_t >> depths</div><divclass="ttdoc">Vector of size n_individuals storing the depth of each marker in each individual.</div><divclass="ttdef"><b>Definition:</b> depth.h:43</div></div>
<divclass="ttc"id="adepth_8h_html_ab2291110e5c4c1c90506c1cd6902e00e"><divclass="ttname"><ahref="depth_8h.html#ab2291110e5c4c1c90506c1cd6902e00e">depth</a></div><divclass="ttdeci">void depth(const Parameters &parameters)</div><divclass="ttdoc">Main function called by the depth command.</div></div>
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<trclass="memdesc:a531e432e384f0579eb6eaa9f12bbf08f"><tdclass="mdescLeft"> </td><tdclass="mdescRight">Main function called by the distrib command. <ahref="distrib_8h.html#a531e432e384f0579eb6eaa9f12bbf08f">More...</a><br/></td></tr>
<trclass="memdesc:a79b07da8680d163c920bc13827c8a836"><tdclass="mdescLeft"> </td><tdclass="mdescRight">Process markers from a <aclass="el"href="structMarkersQueue.html">MarkersQueue</a>. <ahref="distrib_8h.html#a79b07da8680d163c920bc13827c8a836">More...</a><br/></td></tr>
<p>Main function called by the distrib command. </p>
<p>Compute the distribution of markers between two groups. <br/>
This function creates a parsing thread which reads a markers table file and stores markers into a queue, and a processing thread which reads batches of markers from the queue and compute metrics. <br/>
After all markers are processed, the function generates an tabulated output file with columns: <br/>
Group1 | Group2 | Markers | P | Signif Bias</p>
<dlclass="params"><dt>Parameters</dt><dd>
<tableclass="params">
<tr><tdclass="paramname">parameters</td><td><aclass="el"href="structParameters.html">Parameters</a> object storing the value of all RADSex parameters </td></tr>
