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<a href="xsample03_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> <span class="comment">/*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">Copyright(c) 2018 Anatoliy Kuznetsov(anatoliy_kuznetsov at yahoo.com)</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"></span> </div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">Licensed under the Apache License, Version 2.0 (the "License");</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">you may not use this file except in compliance with the License.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">You may obtain a copy of the License at</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"></span> </div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> http://www.apache.org/licenses/LICENSE-2.0</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">Unless required by applicable law or agreed to in writing, software</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">distributed under the License is distributed on an "AS IS" BASIS,</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">See the License for the specific language governing permissions and</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">limitations under the License.</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"></span> </div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">For more information please visit: http://bitmagic.io</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">*/</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment"></span> </div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">/** \example xsample03.cpp</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment"> Seach for human mutation (SNP) in within chr1.</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment"> Benchmark comaprison of different methods</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment"> </span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment"> \sa bm::sparse_vector</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment"> \sa bm::rsc_sparse_vector</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment"> \sa bm::sparse_vector_scanner</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">*/</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment"></span> </div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">/*! \file xsample03.cpp</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment"> \brief Example: SNP search in human genome</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment"> </span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment"> Brief description of used method:</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment"> 1. Parse SNP chromosome report and extract information about SNP number and</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment"> location in the chromosome</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="comment"> 2. Use this information to build bit-transposed sparse_vector<></span></div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="comment"> where vector position matches chromosome position and SNP ids (aka rsid)</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="comment"> is kept as a bit-transposed matrix</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="comment"> 3. Build rank-select compressed sparse vector, dropping all NULL columns</span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="comment"> (this data format is pretty sparse, since number of SNPs is significantly</span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="comment"> less than number of chromosome bases (1:5 or less)</span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="comment"> Use memory report to understand memory footprint for each form of storage</span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="comment"> 4. Run benchmarks searching for 500 randomly selected SNPs using</span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="comment"> - bm::sparse_vector<></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="comment"> - bm::rsc_sparse_vector<></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="comment"> - std::vector<pair<unsigned, unsigned> ></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="comment"> </span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="comment"> This example should be useful for construction of compressed columnar</span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="comment"> tables with parallel search capabilities.</span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="comment"> </span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="comment">*/</span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#include <iostream></span></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="preprocessor">#include <sstream></span></div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#include <chrono></span></div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="preprocessor">#include <regex></span></div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="preprocessor">#include <time.h></span></div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="preprocessor">#include <stdio.h></span></div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  </div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  </div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="preprocessor">#include <chrono></span></div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> <span class="preprocessor">#include <map></span></div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> <span class="preprocessor">#include <utility></span></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> <span class="preprocessor">#include "<a class="code" href="bm_8h.html">bm.h</a>"</span></div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="preprocessor">#include "<a class="code" href="bmalgo_8h.html">bmalgo.h</a>"</span></div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="preprocessor">#include "<a class="code" href="bmserial_8h.html">bmserial.h</a>"</span></div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="preprocessor">#include "<a class="code" href="bmrandom_8h.html">bmrandom.h</a>"</span></div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> <span class="preprocessor">#include "<a class="code" href="bmsparsevec_8h.html">bmsparsevec.h</a>"</span></div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="preprocessor">#include "<a class="code" href="bmsparsevec__compr_8h.html">bmsparsevec_compr.h</a>"</span></div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> <span class="preprocessor">#include "<a class="code" href="bmsparsevec__algo_8h.html">bmsparsevec_algo.h</a>"</span></div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="preprocessor">#include "<a class="code" href="bmsparsevec__serial_8h.html">bmsparsevec_serial.h</a>"</span></div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="preprocessor">#include "<a class="code" href="bmalgo__similarity_8h.html">bmalgo_similarity.h</a>"</span></div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span> <span class="preprocessor">#include "<a class="code" href="bmsparsevec__util_8h.html">bmsparsevec_util.h</a>"</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>  </div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <span class="preprocessor">#include "bmdbg.h"</span></div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> <span class="preprocessor">#include "<a class="code" href="bmtimer_8h.html">bmtimer.h</a>"</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> <span class="keyword">static</span></div>
<div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26"> 80</a></span> <span class="keywordtype">void</span> <a class="code" href="xsample03_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a>()</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>  std::cerr</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  << <span class="stringliteral">"BitMagic SNP Search Sample Utility (c) 2018"</span> << std::endl</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  << <span class="stringliteral">"-isnp file-name -- input set file (SNP FASTA) to parse"</span> << std::endl</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  << <span class="stringliteral">"-svout spase vector output -- sparse vector name to save"</span> << std::endl</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  << <span class="stringliteral">"-rscout rs-compressed spase vector output -- name to save"</span> << std::endl</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  << <span class="stringliteral">"-svin sparse vector input -- sparse vector file name to load "</span> << std::endl</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  << <span class="stringliteral">"-rscin rs-compressed sparse vector input -- file name to load "</span> << std::endl</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  << <span class="stringliteral">"-diag -- run diagnostics"</span> << std::endl</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  << <span class="stringliteral">"-timing -- collect timings"</span> << std::endl</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  ;</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> }</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  </div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  </div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  </div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> <span class="comment">// Arguments</span></div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> <span class="comment">//</span></div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#aaf0266ddaa79e04e2229808d9dabf477"> 99</a></span> std::string <a class="code" href="xsample03_8cpp.html#aaf0266ddaa79e04e2229808d9dabf477">sv_out_name</a>;</div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#ac614e9d91f99f72d08dd8aab8eb19efb"> 100</a></span> std::string <a class="code" href="xsample03_8cpp.html#ac614e9d91f99f72d08dd8aab8eb19efb">rsc_out_name</a>;</div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a501736bde7958b6e05f5fa0f5ca954c1"> 101</a></span> std::string <a class="code" href="xsample03_8cpp.html#a501736bde7958b6e05f5fa0f5ca954c1">sv_in_name</a>;</div>
<div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a519cb8a8927b640f3faa740d68ee0f60"> 102</a></span> std::string <a class="code" href="xsample03_8cpp.html#a519cb8a8927b640f3faa740d68ee0f60">rsc_in_name</a>;</div>
<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a829fcf419d2596071ac6382e7bab7cb3"> 103</a></span> std::string <a class="code" href="xsample03_8cpp.html#a829fcf419d2596071ac6382e7bab7cb3">isnp_name</a>;</div>
<div class="line"><a name="l00104"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#aa592d3fbead57ca8423ac5caaccada07"> 104</a></span> <span class="keywordtype">bool</span> <a class="code" href="xsample03_8cpp.html#aa592d3fbead57ca8423ac5caaccada07">is_diag</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#aece8e90d91aaea144d41103f7d2825ee"> 105</a></span> <span class="keywordtype">bool</span> <a class="code" href="xsample03_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a4dd1e4b402061691109d356faa4513b5"> 106</a></span> <span class="keywordtype">bool</span> <a class="code" href="xsample03_8cpp.html#a4dd1e4b402061691109d356faa4513b5">is_bench</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  </div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> <span class="keyword">static</span></div>
<div class="line"><a name="l00109"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a1c6cda197a32141227af69a440929ac6"> 109</a></span> <span class="keywordtype">int</span> <a class="code" href="xsample03_8cpp.html#a1c6cda197a32141227af69a440929ac6">parse_args</a>(<span class="keywordtype">int</span> argc, <span class="keywordtype">char</span> *argv[])</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> {</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 1; i < argc; ++i)</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>  std::string arg = argv[i];</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="keywordflow">if</span> ((arg == <span class="stringliteral">"-h"</span>) || (arg == <span class="stringliteral">"--help"</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>  <a class="code" href="xsample03_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a>();</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="keywordflow">return</span> 0;</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="keywordflow">if</span> (arg == <span class="stringliteral">"-svout"</span> || arg == <span class="stringliteral">"--svout"</span>)</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  {</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keywordflow">if</span> (i + 1 < argc)</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  {</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <a class="code" href="xsample03_8cpp.html#aaf0266ddaa79e04e2229808d9dabf477">sv_out_name</a> = argv[++i];</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  }</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  {</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  std::cerr << <span class="stringliteral">"Error: -svout requires file name"</span> << std::endl;</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  }</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  }</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-rscout"</span> || arg == <span class="stringliteral">"--rscout"</span>)</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  {</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keywordflow">if</span> (i + 1 < argc)</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  {</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <a class="code" href="xsample03_8cpp.html#ac614e9d91f99f72d08dd8aab8eb19efb">rsc_out_name</a> = argv[++i];</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  }</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  {</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  std::cerr << <span class="stringliteral">"Error: -rscout requires file name"</span> << std::endl;</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  }</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  }</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  </div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-svin"</span> || arg == <span class="stringliteral">"--svin"</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>  <span class="keywordflow">if</span> (i + 1 < argc)</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  {</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <a class="code" href="xsample03_8cpp.html#a501736bde7958b6e05f5fa0f5ca954c1">sv_in_name</a> = argv[++i];</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  }</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  {</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  std::cerr << <span class="stringliteral">"Error: -svin requires file name"</span> << std::endl;</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  }</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  }</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  </div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-rscin"</span> || arg == <span class="stringliteral">"--rscin"</span>)</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  {</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="keywordflow">if</span> (i + 1 < argc)</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  {</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <a class="code" href="xsample03_8cpp.html#a519cb8a8927b640f3faa740d68ee0f60">rsc_in_name</a> = argv[++i];</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  }</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  {</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  std::cerr << <span class="stringliteral">"Error: -rscin requires file name"</span> << std::endl;</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  }</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  }</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  </div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-isnp"</span> || arg == <span class="stringliteral">"--isnp"</span> || arg == <span class="stringliteral">"-snp"</span> || arg == <span class="stringliteral">"--snp"</span>)</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  {</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keywordflow">if</span> (i + 1 < argc)</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  {</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <a class="code" href="xsample03_8cpp.html#a829fcf419d2596071ac6382e7bab7cb3">isnp_name</a> = argv[++i];</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  }</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  {</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  std::cerr << <span class="stringliteral">"Error: -isnp requires file name"</span> << std::endl;</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  }</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  }</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  </div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-diag"</span> || arg == <span class="stringliteral">"--diag"</span> || arg == <span class="stringliteral">"-d"</span> || arg == <span class="stringliteral">"--d"</span>)</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  <a class="code" href="xsample03_8cpp.html#aa592d3fbead57ca8423ac5caaccada07">is_diag</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-timing"</span> || arg == <span class="stringliteral">"--timing"</span> || arg == <span class="stringliteral">"-t"</span> || arg == <span class="stringliteral">"--t"</span>)</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <a class="code" href="xsample03_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  <span class="keywordflow">if</span> (arg == <span class="stringliteral">"-bench"</span> || arg == <span class="stringliteral">"--bench"</span> || arg == <span class="stringliteral">"-b"</span> || arg == <span class="stringliteral">"--b"</span>)</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <a class="code" href="xsample03_8cpp.html#a4dd1e4b402061691109d356faa4513b5">is_bench</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  </div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  } <span class="comment">// for i</span></div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <span class="keywordflow">return</span> 0;</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span> }</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">// Global types</span></div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span> <span class="comment">//</span></div>
<div class="line"><a name="l00203"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a71d75c77694afe022fe5ed0f0b98ec66"> 203</a></span> <span class="keyword">typedef</span> <a class="code" href="classbm_1_1sparse__vector.html">bm::sparse_vector<unsigned, bm::bvector<></a> > <a class="code" href="xsample03_8cpp.html#a71d75c77694afe022fe5ed0f0b98ec66">sparse_vector_u32</a>;</div>
<div class="line"><a name="l00204"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#aa737b7acabde8bce0f655d3f1f72cdaf"> 204</a></span> <span class="keyword">typedef</span> <a class="code" href="classbm_1_1rsc__sparse__vector.html">bm::rsc_sparse_vector<unsigned, sparse_vector_u32 ></a> <a class="code" href="xsample03_8cpp.html#aa737b7acabde8bce0f655d3f1f72cdaf">rsc_sparse_vector_u32</a>;</div>
<div class="line"><a name="l00205"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a2c69294a76e8f5f3766c5580bf194597"> 205</a></span> <span class="keyword">typedef</span> std::vector<std::pair<unsigned, unsigned> > <a class="code" href="xsample03_8cpp.html#a2c69294a76e8f5f3766c5580bf194597">vector_pairs</a>;</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  </div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span> <span class="comment">// ----------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  </div>
<div class="line"><a name="l00209"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc"> 209</a></span> <a class="code" href="classbm_1_1chrono__taker.html#add1676592117ed0eaa2fa6279a71b46a">bm::chrono_taker::duration_map_type</a> <a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>;</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  </div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span> <span class="comment">// SNP report format parser (extraction and transformation)</span></div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> <span class="comment">// Parser extracts SNP id (rsid) and positio on genome to build</span></div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span> <span class="comment">// sparse vector where index (position in vector) metches position on the</span></div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span> <span class="comment">// chromosome 1.</span></div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> <span class="comment">//</span></div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span> <span class="keyword">static</span></div>
<div class="line"><a name="l00217"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#ad94101be38fa6f784dc9539eb6e0fe85"> 217</a></span> <span class="keywordtype">int</span> <a class="code" href="xsample03_8cpp.html#ad94101be38fa6f784dc9539eb6e0fe85">load_snp_report</a>(<span class="keyword">const</span> std::string& fname, <a class="code" href="classbm_1_1sparse__vector.html">sparse_vector_u32</a>& sv)</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> {</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"1. parse input SNP chr report"</span>, 1, &<a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  </div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  std::ifstream fin(fname.c_str(), std::ios::in);</div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <span class="keywordflow">if</span> (!fin.good())</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  <span class="keywordflow">return</span> -1;</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  </div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  <span class="keywordtype">unsigned</span> rs_id, rs_pos;</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  <span class="keywordtype">size_t</span> idx;</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  </div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  std::string line;</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  std::string delim = <span class="stringliteral">" \t"</span>;</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  </div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  std::regex reg(<span class="stringliteral">"\\s+"</span>);</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  std::sregex_token_iterator it_end;</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  </div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> bv_rs; </div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  bv_rs.<a class="code" href="classbm_1_1bvector.html#aaceb8d31d9da05f977de5c6a6cd62e24">init</a>();</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  </div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  <span class="keywordtype">unsigned</span> rs_cnt = 0;</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; std::getline(fin, line); ++i)</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  {</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="keywordflow">if</span> (line.empty() ||</div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  !isdigit(line.front())</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  )</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  </div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <span class="comment">// regex based tokenizer</span></div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  std::sregex_token_iterator it(line.begin(), line.end(), reg, -1);</div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  std::vector<std::string> line_vec(it, it_end);</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="keywordflow">if</span> (line_vec.empty())</div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="keywordflow">continue</span>; </div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  </div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  <span class="comment">// parse columns of interest</span></div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  {</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  rs_id = unsigned(std::stoul(line_vec.at(0), &idx));</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  </div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="keywordflow">if</span> (bv_rs.<a class="code" href="classbm_1_1bvector.html#a16d902c3df4aa6aa88d8e137af4a4b9b">test</a>(rs_id))</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  {</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  }</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  rs_pos = unsigned(std::stoul(line_vec.at(11), &idx));</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  </div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  bv_rs.<a class="code" href="classbm_1_1bvector.html#aff4c0900eed72eaccff6f5804e33ce97">set_bit_no_check</a>(rs_id);</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  sv.<a class="code" href="classbm_1_1sparse__vector.html#a56101ce9a559b30f8e14153133063ca7">set</a>(rs_pos, rs_id);</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  </div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  ++rs_cnt;</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  }</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="keywordflow">catch</span> (std::exception& <span class="comment">/*ex*/</span>)</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  {</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <span class="keywordflow">continue</span>; <span class="comment">// detailed disgnostics commented out</span></div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="comment">// error detected, because some columns are sometimes missing</span></div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <span class="comment">// just ignore it</span></div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="comment">/*</span></div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span> <span class="comment"> std::cerr << ex.what() << "; ";</span></div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span> <span class="comment"> std::cerr << "rs=" << line_vec.at(0) << " pos=" << line_vec.at(11) << std::endl;</span></div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span> <span class="comment"> continue;</span></div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  }</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  <span class="keywordflow">if</span> (rs_cnt % (4 * 1024) == 0)</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  std::cout << <span class="stringliteral">"\r"</span> << rs_cnt << <span class="stringliteral">" / "</span> << i; <span class="comment">// PROGRESS report</span></div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  } <span class="comment">// for i</span></div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  </div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  std::cout << std::endl;</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  std::cout << <span class="stringliteral">"SNP count="</span> << rs_cnt << std::endl;</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <span class="keywordflow">return</span> 0;</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span> }</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  </div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span> <span class="comment">// Generate random subset of random values from a sparse vector</span></div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span> <span class="comment">//</span></div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span> <span class="keyword">static</span></div>
<div class="line"><a name="l00291"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#aacb20d26faea4c3ca196ac6b888636c8"> 291</a></span> <span class="keywordtype">void</span> <a class="code" href="xsample03_8cpp.html#aacb20d26faea4c3ca196ac6b888636c8">generate_random_subset</a>(<span class="keyword">const</span> <a class="code" href="classbm_1_1sparse__vector.html">sparse_vector_u32</a>& sv, std::vector<unsigned>& vect, <span class="keywordtype">unsigned</span> count)</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span> {</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  <span class="keyword">const</span> <a class="code" href="classbm_1_1bvector.html">sparse_vector_u32::bvector_type</a>* bv_null = sv.<a class="code" href="classbm_1_1base__sparse__vector.html#aacbde903b5a180ec493d34dd209fe542">get_null_bvector</a>();</div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  </div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <a class="code" href="classbm_1_1random__subset.html">bm::random_subset<bm::bvector<></a> > rand_sampler;</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> bv_sample;</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  rand_sampler.<a class="code" href="classbm_1_1random__subset.html#abdf1e716e124ff4d7ad8ccef1646c99e">sample</a>(bv_sample, *bv_null, count);</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  </div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  <a class="code" href="classbm_1_1bvector_1_1enumerator.html">bm::bvector<>::enumerator</a> en = bv_sample.<a class="code" href="classbm_1_1bvector.html#a86b939f3aed555dc073e8c26e9efea71">first</a>();</div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  <span class="keywordflow">for</span> (; en.<a class="code" href="classbm_1_1bvector_1_1iterator__base.html#a3f6af7f5b46c0219b28916187d302c43">valid</a>(); ++en)</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  {</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  <span class="keywordtype">unsigned</span> idx = *en;</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  <span class="keywordtype">unsigned</span> v = sv[idx];</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  vect.<a class="code" href="classbm_1_1sparse__vector.html#a2f8aadebd1cfecd8e70fc771dbbd748d">push_back</a>(v);</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  }</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span> }</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  </div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span> <span class="comment">// build std::vector of pairs (position to rs)</span></div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span> <span class="comment">//</span></div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span> <span class="keyword">static</span></div>
<div class="line"><a name="l00311"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a55e67f6ac4991215f8c33fba1fadf317"> 311</a></span> <span class="keywordtype">void</span> <a class="code" href="xsample03_8cpp.html#a55e67f6ac4991215f8c33fba1fadf317">build_vector_pairs</a>(<span class="keyword">const</span> <a class="code" href="classbm_1_1sparse__vector.html">sparse_vector_u32</a>& sv, <a class="code" href="xsample03_8cpp.html#a2c69294a76e8f5f3766c5580bf194597">vector_pairs</a>& vp)</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span> {</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <a class="code" href="classbm_1_1sparse__vector.html#a73134a0c2f6d595d3cf165236622f5da">sparse_vector_u32::const_iterator</a> it = sv.<a class="code" href="classbm_1_1sparse__vector.html#ae60eed242dd6ca5ac13a046f3f75b2f7">begin</a>();</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  <a class="code" href="classbm_1_1sparse__vector.html#a73134a0c2f6d595d3cf165236622f5da">sparse_vector_u32::const_iterator</a> it_end = sv.<a class="code" href="classbm_1_1sparse__vector.html#a60bdc29e0f6731410372e3518ab0940b">end</a>();</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  </div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  <span class="keywordflow">for</span> (; it != it_end; ++it)</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  {</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <span class="keywordflow">if</span> (!it.is_null())</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  {</div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  std::pair<unsigned, unsigned> pos2rs = std::make_pair(it.pos(), it.value());</div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  vp.push_back(pos2rs);</div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  }</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  }</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span> }</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  </div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span> <span class="comment">// O(N) -- O(N/2) linear search in vector of pairs (position - rsid)</span></div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span> <span class="comment">//</span></div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span> <span class="keyword">static</span></div>
<div class="line"><a name="l00329"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a73d3c18ad1011694ad2b47075a7a2722"> 329</a></span> <span class="keywordtype">bool</span> <a class="code" href="xsample03_8cpp.html#a73d3c18ad1011694ad2b47075a7a2722">search_vector_pairs</a>(<span class="keyword">const</span> <a class="code" href="xsample03_8cpp.html#a2c69294a76e8f5f3766c5580bf194597">vector_pairs</a>& vp, <span class="keywordtype">unsigned</span> rs_id, <span class="keywordtype">unsigned</span>& pos)</div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span> {</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; i < vp.size(); ++i)</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  {</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  <span class="keywordflow">if</span> (vp[i].second == rs_id)</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  {</div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  pos = vp[i].first;</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  }</div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  }</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span> }</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  </div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span> <span class="comment">// SNP search benchmark</span></div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span> <span class="comment">// Search for SNPs using different data structures (Bitmagic and STL)</span></div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span> <span class="comment">//</span></div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span> <span class="comment">// An extra step is verification, to make sure all methods are consistent</span></div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span> <span class="comment">//</span></div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span> <span class="keyword">static</span></div>
<div class="line"><a name="l00348"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#adb75765b8dcd96f522e158c738abab77"> 348</a></span> <span class="keywordtype">void</span> <a class="code" href="xsample03_8cpp.html#adb75765b8dcd96f522e158c738abab77">run_benchmark</a>(<span class="keyword">const</span> <a class="code" href="classbm_1_1sparse__vector.html">sparse_vector_u32</a>& sv, <span class="keyword">const</span> <a class="code" href="classbm_1_1rsc__sparse__vector.html">rsc_sparse_vector_u32</a>& csv)</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span> {</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> rs_sample_count = 2000;</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  </div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  std::vector<unsigned> rs_vect;</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  <a class="code" href="xsample03_8cpp.html#aacb20d26faea4c3ca196ac6b888636c8">generate_random_subset</a>(sv, rs_vect, rs_sample_count);</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  <span class="keywordflow">if</span> (rs_vect.empty())</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  {</div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  std::cerr << <span class="stringliteral">"Benchmark subset empty!"</span> << std::endl;</div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  }</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  </div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  <span class="comment">// build traditional sparse vector</span></div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  <a class="code" href="xsample03_8cpp.html#a2c69294a76e8f5f3766c5580bf194597">vector_pairs</a> vp;</div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  <a class="code" href="xsample03_8cpp.html#a55e67f6ac4991215f8c33fba1fadf317">build_vector_pairs</a>(sv, vp);</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  </div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  <span class="comment">// search result bit-vectors</span></div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> bv_found1;</div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> bv_found2;</div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> bv_found3;</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  </div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  bv_found1.<a class="code" href="classbm_1_1bvector.html#aaceb8d31d9da05f977de5c6a6cd62e24">init</a>(); bv_found2.<a class="code" href="classbm_1_1bvector.html#aaceb8d31d9da05f977de5c6a6cd62e24">init</a>(); bv_found3.<a class="code" href="classbm_1_1bvector.html#aaceb8d31d9da05f977de5c6a6cd62e24">init</a>();<span class="comment">// pre-initialize vectors</span></div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  </div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  <span class="keywordflow">if</span> (!sv.<a class="code" href="classbm_1_1sparse__vector.html#a8a2eb22c48d618a18f73fc87a7053060">empty</a>())</div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  {</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"09. rs search (sv)"</span>, <span class="keywordtype">unsigned</span>(rs_vect.size()), &<a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  </div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  <span class="comment">// scanner class</span></div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  <span class="comment">// it's important to keep scanner class outside the loop to avoid</span></div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <span class="comment">// unnecessary re-allocs and construction costs</span></div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  </div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  <a class="code" href="classbm_1_1sparse__vector__scanner.html">bm::sparse_vector_scanner<sparse_vector_u32></a> scanner;</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  </div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; i < rs_vect.size(); ++i)</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  {</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  <span class="keywordtype">unsigned</span> rs_id = rs_vect[i];</div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  <span class="keywordtype">unsigned</span> rs_pos;</div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  <span class="keywordtype">bool</span> found = scanner.<a class="code" href="classbm_1_1sparse__vector__scanner.html#aa2439360def2f3fe3c788872c0e70997">find_eq</a>(sv, rs_id, rs_pos);</div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  </div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  <span class="keywordflow">if</span> (found)</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  {</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  bv_found1.<a class="code" href="classbm_1_1bvector.html#aff4c0900eed72eaccff6f5804e33ce97">set_bit_no_check</a>(rs_pos);</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  }</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  {</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  std::cout << <span class="stringliteral">"Error: rs_id = "</span> << rs_id << <span class="stringliteral">" not found!"</span> << std::endl;</div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  }</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  } <span class="comment">// for</span></div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  }</div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  </div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  <span class="keywordflow">if</span> (!csv.<a class="code" href="classbm_1_1rsc__sparse__vector.html#a69824966c9fd4d13592da1955e6aba28">empty</a>())</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  {</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"10. rs search (rsc_sv)"</span>, <span class="keywordtype">unsigned</span>(rs_vect.size()), &<a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  </div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  <a class="code" href="classbm_1_1sparse__vector__scanner.html">bm::sparse_vector_scanner<rsc_sparse_vector_u32></a> scanner; <span class="comment">// scanner class</span></div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  </div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; i < rs_vect.size(); ++i)</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  {</div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  <span class="keywordtype">unsigned</span> rs_id = rs_vect[i];</div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  <span class="keywordtype">unsigned</span> rs_pos;</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  <span class="keywordtype">bool</span> found = scanner.<a class="code" href="classbm_1_1sparse__vector__scanner.html#aa2439360def2f3fe3c788872c0e70997">find_eq</a>(csv, rs_id, rs_pos);</div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  </div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  <span class="keywordflow">if</span> (found)</div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  {</div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  bv_found2.<a class="code" href="classbm_1_1bvector.html#aff4c0900eed72eaccff6f5804e33ce97">set_bit_no_check</a>(rs_pos);</div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  }</div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  {</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  std::cout << <span class="stringliteral">"rs_id = "</span> << rs_id << <span class="stringliteral">" not found!"</span> << std::endl;</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  }</div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  } <span class="comment">// for</span></div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  }</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  </div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  <span class="keywordflow">if</span> (vp.size())</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  {</div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"11. rs search (std::vector<>)"</span>, <span class="keywordtype">unsigned</span>(rs_vect.size()), &<a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  </div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; i < rs_vect.size(); ++i)</div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  {</div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  <span class="keywordtype">unsigned</span> rs_id = rs_vect[i];</div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  <span class="keywordtype">unsigned</span> rs_pos;</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  <span class="keywordtype">bool</span> found = <a class="code" href="xsample03_8cpp.html#a73d3c18ad1011694ad2b47075a7a2722">search_vector_pairs</a>(vp, rs_id, rs_pos);</div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  </div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  <span class="keywordflow">if</span> (found)</div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  {</div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  bv_found3.<a class="code" href="classbm_1_1bvector.html#aff4c0900eed72eaccff6f5804e33ce97">set_bit_no_check</a>(rs_pos);</div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  }</div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  {</div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  std::cout << <span class="stringliteral">"rs_id = "</span> << rs_id << <span class="stringliteral">" not found!"</span> << std::endl;</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  }</div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  } <span class="comment">// for</span></div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  }</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  </div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  <span class="comment">// compare results from various methods (check integrity)</span></div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  <span class="keywordtype">int</span> res = bv_found1.<a class="code" href="classbm_1_1bvector.html#acfb4e0f923e55057db5ed518853fbecf">compare</a>(bv_found2);</div>
<div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  <span class="keywordflow">if</span> (res != 0)</div>
<div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  {</div>
<div class="line"><a name="l00448"></a><span class="lineno"> 448</span>  std::cerr << <span class="stringliteral">"Error: search discrepancy (sparse search) detected!"</span> << std::endl;</div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  }</div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  res = bv_found1.<a class="code" href="classbm_1_1bvector.html#acfb4e0f923e55057db5ed518853fbecf">compare</a>(bv_found3);</div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  <span class="keywordflow">if</span> (res != 0)</div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  {</div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  std::cerr << <span class="stringliteral">"Error: search discrepancy (std::vector<>) detected!"</span> << std::endl;</div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  }</div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  </div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span> }</div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  </div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  </div>
<div class="line"><a name="l00459"></a><span class="lineno"><a class="line" href="xsample03_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97"> 459</a></span> <span class="keywordtype">int</span> <a class="code" href="xsample03_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97">main</a>(<span class="keywordtype">int</span> argc, <span class="keywordtype">char</span> *argv[])</div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span> {</div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  <span class="keywordflow">if</span> (argc < 3)</div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  {</div>
<div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  <a class="code" href="xsample03_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a>();</div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  }</div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  </div>
<div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  <a class="code" href="classbm_1_1sparse__vector.html">sparse_vector_u32</a> sv(<a class="code" href="group__bvector.html#ggab0835910831729c806840cd5c8f40b2ba095db184b37a1341cbbbf813a70aed79">bm::use_null</a>);</div>
<div class="line"><a name="l00468"></a><span class="lineno"> 468</span>  <a class="code" href="classbm_1_1rsc__sparse__vector.html">rsc_sparse_vector_u32</a> csv;</div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span>  </div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span>  {</div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  <span class="keyword">auto</span> ret = <a class="code" href="xsample03_8cpp.html#a1c6cda197a32141227af69a440929ac6">parse_args</a>(argc, argv);</div>
<div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  <span class="keywordflow">if</span> (ret != 0)</div>
<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  <span class="keywordflow">return</span> ret;</div>
<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  </div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  <span class="keywordflow">if</span> (!<a class="code" href="xsample03_8cpp.html#a829fcf419d2596071ac6382e7bab7cb3">isnp_name</a>.empty())</div>
<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  {</div>
<div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  <span class="keyword">auto</span> res = <a class="code" href="xsample03_8cpp.html#ad94101be38fa6f784dc9539eb6e0fe85">load_snp_report</a>(<a class="code" href="xsample03_8cpp.html#a829fcf419d2596071ac6382e7bab7cb3">isnp_name</a>, sv);</div>
<div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  <span class="keywordflow">if</span> (res != 0)</div>
<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  {</div>
<div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  <span class="keywordflow">return</span> res;</div>
<div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  }</div>
<div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  }</div>
<div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  <span class="keywordflow">if</span> (!<a class="code" href="xsample03_8cpp.html#a501736bde7958b6e05f5fa0f5ca954c1">sv_in_name</a>.empty())</div>
<div class="line"><a name="l00485"></a><span class="lineno"> 485</span>  {</div>
<div class="line"><a name="l00486"></a><span class="lineno"> 486</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"02. Load sparse vector"</span>, 1, &<a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00487"></a><span class="lineno"> 487</span>  file_load_svector(sv, <a class="code" href="xsample03_8cpp.html#a501736bde7958b6e05f5fa0f5ca954c1">sv_in_name</a>);</div>
<div class="line"><a name="l00488"></a><span class="lineno"> 488</span>  }</div>
<div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  </div>
<div class="line"><a name="l00490"></a><span class="lineno"> 490</span>  <span class="comment">// load rs-compressed sparse vector</span></div>
<div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  <span class="keywordflow">if</span> (!<a class="code" href="xsample03_8cpp.html#a519cb8a8927b640f3faa740d68ee0f60">rsc_in_name</a>.empty())</div>
<div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  {</div>
<div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"03. Load rsc sparse vector"</span>, 1, &<a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00494"></a><span class="lineno"> 494</span>  file_load_svector(csv, <a class="code" href="xsample03_8cpp.html#a519cb8a8927b640f3faa740d68ee0f60">rsc_in_name</a>);</div>
<div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  }</div>
<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  </div>
<div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  <span class="comment">// if rs-compressed vector is not available - build it on the fly</span></div>
<div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  <span class="keywordflow">if</span> (csv.<a class="code" href="classbm_1_1rsc__sparse__vector.html#a69824966c9fd4d13592da1955e6aba28">empty</a>() && !sv.<a class="code" href="classbm_1_1sparse__vector.html#a8a2eb22c48d618a18f73fc87a7053060">empty</a>())</div>
<div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  {</div>
<div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  <a class="code" href="classbm_1_1sparse__vector.html">sparse_vector_u32</a> sv2(<a class="code" href="group__bvector.html#ggab0835910831729c806840cd5c8f40b2ba095db184b37a1341cbbbf813a70aed79">bm::use_null</a>);</div>
<div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  {</div>
<div class="line"><a name="l00502"></a><span class="lineno"> 502</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"04. rs compress sparse vector"</span>, 1, &<a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  csv.<a class="code" href="classbm_1_1rsc__sparse__vector.html#a179790d1026899539804351a8039653b">load_from</a>(sv);</div>
<div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  }</div>
<div class="line"><a name="l00505"></a><span class="lineno"> 505</span>  {</div>
<div class="line"><a name="l00506"></a><span class="lineno"> 506</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"05. rs de-compress sparse vector"</span>, 1, &<a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00507"></a><span class="lineno"> 507</span>  csv.<a class="code" href="classbm_1_1rsc__sparse__vector.html#a3af47b18d3bb08c849788ac7efa48766">load_to</a>(sv2);</div>
<div class="line"><a name="l00508"></a><span class="lineno"> 508</span>  }</div>
<div class="line"><a name="l00509"></a><span class="lineno"> 509</span>  </div>
<div class="line"><a name="l00510"></a><span class="lineno"> 510</span>  <span class="keywordflow">if</span> (!sv.<a class="code" href="classbm_1_1sparse__vector.html#a27be5c080f0bc67f8e886b7feb57e28e">equal</a>(sv2)) <span class="comment">// diagnostics check (just in case)</span></div>
<div class="line"><a name="l00511"></a><span class="lineno"> 511</span>  {</div>
<div class="line"><a name="l00512"></a><span class="lineno"> 512</span>  std::cerr << <span class="stringliteral">"Error: rs-compressed vector check failed!"</span> << std::endl;</div>
<div class="line"><a name="l00513"></a><span class="lineno"> 513</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00514"></a><span class="lineno"> 514</span>  }</div>
<div class="line"><a name="l00515"></a><span class="lineno"> 515</span>  }</div>
<div class="line"><a name="l00516"></a><span class="lineno"> 516</span>  </div>
<div class="line"><a name="l00517"></a><span class="lineno"> 517</span>  <span class="comment">// save SV vector</span></div>
<div class="line"><a name="l00518"></a><span class="lineno"> 518</span>  <span class="keywordflow">if</span> (!<a class="code" href="xsample03_8cpp.html#aaf0266ddaa79e04e2229808d9dabf477">sv_out_name</a>.empty() && !sv.<a class="code" href="classbm_1_1sparse__vector.html#a8a2eb22c48d618a18f73fc87a7053060">empty</a>())</div>
<div class="line"><a name="l00519"></a><span class="lineno"> 519</span>  {</div>
<div class="line"><a name="l00520"></a><span class="lineno"> 520</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"07. Save sparse vector"</span>, 1, &<a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  sv.<a class="code" href="classbm_1_1sparse__vector.html#af9f218aa3af25cdfc9088cc0affdaa8f">optimize</a>();</div>
<div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  file_save_svector(sv, <a class="code" href="xsample03_8cpp.html#aaf0266ddaa79e04e2229808d9dabf477">sv_out_name</a>);</div>
<div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  }</div>
<div class="line"><a name="l00524"></a><span class="lineno"> 524</span>  </div>
<div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  <span class="comment">// save RS sparse vector</span></div>
<div class="line"><a name="l00526"></a><span class="lineno"> 526</span>  <span class="keywordflow">if</span> (!<a class="code" href="xsample03_8cpp.html#ac614e9d91f99f72d08dd8aab8eb19efb">rsc_out_name</a>.empty() && !csv.<a class="code" href="classbm_1_1rsc__sparse__vector.html#a69824966c9fd4d13592da1955e6aba28">empty</a>())</div>
<div class="line"><a name="l00527"></a><span class="lineno"> 527</span>  {</div>
<div class="line"><a name="l00528"></a><span class="lineno"> 528</span>  <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"08. Save RS sparse vector"</span>, 1, &<a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  csv.<a class="code" href="classbm_1_1rsc__sparse__vector.html#a4550829bbd4b9506d9cc3112751d71a5">optimize</a>();</div>
<div class="line"><a name="l00530"></a><span class="lineno"> 530</span>  file_save_svector(csv, <a class="code" href="xsample03_8cpp.html#ac614e9d91f99f72d08dd8aab8eb19efb">rsc_out_name</a>);</div>
<div class="line"><a name="l00531"></a><span class="lineno"> 531</span>  }</div>
<div class="line"><a name="l00532"></a><span class="lineno"> 532</span>  </div>
<div class="line"><a name="l00533"></a><span class="lineno"> 533</span>  <span class="keywordflow">if</span> (<a class="code" href="xsample03_8cpp.html#aa592d3fbead57ca8423ac5caaccada07">is_diag</a>) <span class="comment">// print memory diagnostics</span></div>
<div class="line"><a name="l00534"></a><span class="lineno"> 534</span>  {</div>
<div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  <span class="keywordflow">if</span> (!sv.<a class="code" href="classbm_1_1sparse__vector.html#a8a2eb22c48d618a18f73fc87a7053060">empty</a>())</div>
<div class="line"><a name="l00536"></a><span class="lineno"> 536</span>  {</div>
<div class="line"><a name="l00537"></a><span class="lineno"> 537</span>  std::cout << std::endl</div>
<div class="line"><a name="l00538"></a><span class="lineno"> 538</span>  << <span class="stringliteral">"sparse vector statistics:"</span></div>
<div class="line"><a name="l00539"></a><span class="lineno"> 539</span>  << std::endl;</div>
<div class="line"><a name="l00540"></a><span class="lineno"> 540</span>  bm::print_svector_stat(sv, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00541"></a><span class="lineno"> 541</span>  }</div>
<div class="line"><a name="l00542"></a><span class="lineno"> 542</span>  <span class="keywordflow">if</span> (!csv.<a class="code" href="classbm_1_1rsc__sparse__vector.html#a69824966c9fd4d13592da1955e6aba28">empty</a>())</div>
<div class="line"><a name="l00543"></a><span class="lineno"> 543</span>  {</div>
<div class="line"><a name="l00544"></a><span class="lineno"> 544</span>  std::cout << std::endl</div>
<div class="line"><a name="l00545"></a><span class="lineno"> 545</span>  << <span class="stringliteral">"RS compressed sparse vector statistics:"</span></div>
<div class="line"><a name="l00546"></a><span class="lineno"> 546</span>  << std::endl;</div>
<div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  bm::print_svector_stat(csv, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00548"></a><span class="lineno"> 548</span>  }</div>
<div class="line"><a name="l00549"></a><span class="lineno"> 549</span>  }</div>
<div class="line"><a name="l00550"></a><span class="lineno"> 550</span>  </div>
<div class="line"><a name="l00551"></a><span class="lineno"> 551</span>  <span class="keywordflow">if</span> (<a class="code" href="xsample03_8cpp.html#a4dd1e4b402061691109d356faa4513b5">is_bench</a>) <span class="comment">// run set of benchmarks</span></div>
<div class="line"><a name="l00552"></a><span class="lineno"> 552</span>  {</div>
<div class="line"><a name="l00553"></a><span class="lineno"> 553</span>  <a class="code" href="xsample03_8cpp.html#adb75765b8dcd96f522e158c738abab77">run_benchmark</a>(sv, csv);</div>
<div class="line"><a name="l00554"></a><span class="lineno"> 554</span>  }</div>
<div class="line"><a name="l00555"></a><span class="lineno"> 555</span>  </div>
<div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  <span class="keywordflow">if</span> (<a class="code" href="xsample03_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a>) <span class="comment">// print all collected timings</span></div>
<div class="line"><a name="l00557"></a><span class="lineno"> 557</span>  {</div>
<div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  std::cout << std::endl << <span class="stringliteral">"Performance:"</span> << std::endl;</div>
<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  <a class="code" href="classbm_1_1chrono__taker.html#a30b45453d952d14afe56c29087970899">bm::chrono_taker::print_duration_map</a>(<a class="code" href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>, <a class="code" href="classbm_1_1chrono__taker.html#a9a41e5f2fe48ba472fd77a1dbd86457dad530ca7863ce7e60f4fa221e1dfa64a2">bm::chrono_taker::ct_ops_per_sec</a>);</div>
<div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  }</div>
<div class="line"><a name="l00561"></a><span class="lineno"> 561</span>  }</div>
<div class="line"><a name="l00562"></a><span class="lineno"> 562</span>  <span class="keywordflow">catch</span> (std::exception& ex)</div>
<div class="line"><a name="l00563"></a><span class="lineno"> 563</span>  {</div>
<div class="line"><a name="l00564"></a><span class="lineno"> 564</span>  std::cerr << <span class="stringliteral">"Error:"</span> << ex.what() << std::endl;</div>
<div class="line"><a name="l00565"></a><span class="lineno"> 565</span>  <span class="keywordflow">return</span> 1;</div>
<div class="line"><a name="l00566"></a><span class="lineno"> 566</span>  }</div>
<div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  </div>
<div class="line"><a name="l00568"></a><span class="lineno"> 568</span>  <span class="keywordflow">return</span> 0;</div>
<div class="line"><a name="l00569"></a><span class="lineno"> 569</span> }</div>
<div class="line"><a name="l00570"></a><span class="lineno"> 570</span>  </div>
</div><!-- fragment --></div><!-- contents -->
<div class="ttc" id="axsample03_8cpp_html_a55e67f6ac4991215f8c33fba1fadf317"><div class="ttname"><a href="xsample03_8cpp.html#a55e67f6ac4991215f8c33fba1fadf317">build_vector_pairs</a></div><div class="ttdeci">static void build_vector_pairs(const sparse_vector_u32 &sv, vector_pairs &vp)</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00311">xsample03.cpp:311</a></div></div>
<div class="ttc" id="aclassbm_1_1rsc__sparse__vector_html_a69824966c9fd4d13592da1955e6aba28"><div class="ttname"><a href="classbm_1_1rsc__sparse__vector.html#a69824966c9fd4d13592da1955e6aba28">bm::rsc_sparse_vector::empty</a></div><div class="ttdeci">bool empty() const</div><div class="ttdoc">return true if vector is empty</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__compr_8h_source.html#l00361">bmsparsevec_compr.h:361</a></div></div>
<div class="ttc" id="abmsparsevec__algo_8h_html"><div class="ttname"><a href="bmsparsevec__algo_8h.html">bmsparsevec_algo.h</a></div><div class="ttdoc">Algorithms for bm::sparse_vector.</div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_af9f218aa3af25cdfc9088cc0affdaa8f"><div class="ttname"><a href="classbm_1_1sparse__vector.html#af9f218aa3af25cdfc9088cc0affdaa8f">bm::sparse_vector::optimize</a></div><div class="ttdeci">void optimize(bm::word_t *temp_block=0, typename bvector_type::optmode opt_mode=bvector_type::opt_compress, typename sparse_vector< Val, BV >::statistics *stat=0)</div><div class="ttdoc">run memory optimization for all vector plains</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l01728">bmsparsevec.h:1728</a></div></div>
<div class="ttc" id="abmrandom_8h_html"><div class="ttname"><a href="bmrandom_8h.html">bmrandom.h</a></div><div class="ttdoc">Generation of random subset.</div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a73134a0c2f6d595d3cf165236622f5da"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a73134a0c2f6d595d3cf165236622f5da">bm::sparse_vector::const_iterator</a></div><div class="ttdeci">friend const_iterator</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00348">bmsparsevec.h:348</a></div></div>
<div class="ttc" id="aclassbm_1_1rsc__sparse__vector_html_a3af47b18d3bb08c849788ac7efa48766"><div class="ttname"><a href="classbm_1_1rsc__sparse__vector.html#a3af47b18d3bb08c849788ac7efa48766">bm::rsc_sparse_vector::load_to</a></div><div class="ttdeci">void load_to(sparse_vector_type &sv) const</div><div class="ttdoc">Exort compressed vector to a sparse vector (with NULLs)</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__compr_8h_source.html#l00930">bmsparsevec_compr.h:930</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_a2c69294a76e8f5f3766c5580bf194597"><div class="ttname"><a href="xsample03_8cpp.html#a2c69294a76e8f5f3766c5580bf194597">vector_pairs</a></div><div class="ttdeci">std::vector< std::pair< unsigned, unsigned > > vector_pairs</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00205">xsample03.cpp:205</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html"><div class="ttname"><a href="classbm_1_1sparse__vector.html">bm::sparse_vector</a></div><div class="ttdoc">sparse vector with runtime compression using bit transposition method</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00081">bmsparsevec.h:81</a></div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html"><div class="ttname"><a href="classbm_1_1chrono__taker.html">bm::chrono_taker</a></div><div class="ttdoc">Utility class to collect performance measurements and statistics.</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00039">bmtimer.h:39</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_a519cb8a8927b640f3faa740d68ee0f60"><div class="ttname"><a href="xsample03_8cpp.html#a519cb8a8927b640f3faa740d68ee0f60">rsc_in_name</a></div><div class="ttdeci">std::string rsc_in_name</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00102">xsample03.cpp:102</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_aaf0266ddaa79e04e2229808d9dabf477"><div class="ttname"><a href="xsample03_8cpp.html#aaf0266ddaa79e04e2229808d9dabf477">sv_out_name</a></div><div class="ttdeci">std::string sv_out_name</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00099">xsample03.cpp:99</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html_aff4c0900eed72eaccff6f5804e33ce97"><div class="ttname"><a href="classbm_1_1bvector.html#aff4c0900eed72eaccff6f5804e33ce97">bm::bvector::set_bit_no_check</a></div><div class="ttdeci">void set_bit_no_check(size_type n)</div><div class="ttdoc">Set bit without checking preconditions (size, etc)</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l03468">bm.h:3468</a></div></div>
<div class="ttc" id="abmsparsevec_8h_html"><div class="ttname"><a href="bmsparsevec_8h.html">bmsparsevec.h</a></div><div class="ttdoc">Sparse constainer sparse_vector<> for integer types using bit-transposition transform.</div></div>
<div class="ttc" id="aclassbm_1_1bvector_1_1enumerator_html"><div class="ttname"><a href="classbm_1_1bvector_1_1enumerator.html">bm::bvector::enumerator</a></div><div class="ttdoc">Constant iterator designed to enumerate "ON" bits.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l00599">bm.h:599</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector__scanner_html"><div class="ttname"><a href="classbm_1_1sparse__vector__scanner.html">bm::sparse_vector_scanner</a></div><div class="ttdoc">algorithms for sparse_vector scan/search</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__algo_8h_source.html#l00481">bmsparsevec_algo.h:481</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html_acfb4e0f923e55057db5ed518853fbecf"><div class="ttname"><a href="classbm_1_1bvector.html#acfb4e0f923e55057db5ed518853fbecf">bm::bvector::compare</a></div><div class="ttdeci">int compare(const bvector< Alloc > &bvect) const BMNOEXCEPT</div><div class="ttdoc">Lexicographical comparison with a bitvector.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l03159">bm.h:3159</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_aece8e90d91aaea144d41103f7d2825ee"><div class="ttname"><a href="xsample03_8cpp.html#aece8e90d91aaea144d41103f7d2825ee">is_timing</a></div><div class="ttdeci">bool is_timing</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00105">xsample03.cpp:105</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_ad94101be38fa6f784dc9539eb6e0fe85"><div class="ttname"><a href="xsample03_8cpp.html#ad94101be38fa6f784dc9539eb6e0fe85">load_snp_report</a></div><div class="ttdeci">static int load_snp_report(const std::string &fname, sparse_vector_u32 &sv)</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00217">xsample03.cpp:217</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_aa592d3fbead57ca8423ac5caaccada07"><div class="ttname"><a href="xsample03_8cpp.html#aa592d3fbead57ca8423ac5caaccada07">is_diag</a></div><div class="ttdeci">bool is_diag</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00104">xsample03.cpp:104</a></div></div>
<div class="ttc" id="abmsparsevec__serial_8h_html"><div class="ttname"><a href="bmsparsevec__serial_8h.html">bmsparsevec_serial.h</a></div><div class="ttdoc">Serialization for sparse_vector<></div></div>
<div class="ttc" id="abmalgo_8h_html"><div class="ttname"><a href="bmalgo_8h.html">bmalgo.h</a></div><div class="ttdoc">Algorithms for bvector<> (main include)</div></div>
<div class="ttc" id="axsample03_8cpp_html_a829fcf419d2596071ac6382e7bab7cb3"><div class="ttname"><a href="xsample03_8cpp.html#a829fcf419d2596071ac6382e7bab7cb3">isnp_name</a></div><div class="ttdeci">std::string isnp_name</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00103">xsample03.cpp:103</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a27be5c080f0bc67f8e886b7feb57e28e"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a27be5c080f0bc67f8e886b7feb57e28e">bm::sparse_vector::equal</a></div><div class="ttdeci">bool equal(const sparse_vector< Val, BV > &sv, bm::null_support null_able=bm::use_null) const BMNOEXCEPT</div><div class="ttdoc">check if another sparse vector has the same content and size</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l01890">bmsparsevec.h:1890</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_ac614e9d91f99f72d08dd8aab8eb19efb"><div class="ttname"><a href="xsample03_8cpp.html#ac614e9d91f99f72d08dd8aab8eb19efb">rsc_out_name</a></div><div class="ttdeci">std::string rsc_out_name</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00100">xsample03.cpp:100</a></div></div>
<div class="ttc" id="abmsparsevec__compr_8h_html"><div class="ttname"><a href="bmsparsevec__compr_8h.html">bmsparsevec_compr.h</a></div><div class="ttdoc">Compressed sparse container rsc_sparse_vector<> for integer types.</div></div>
<div class="ttc" id="aclassbm_1_1bvector_html"><div class="ttname"><a href="classbm_1_1bvector.html">bm::bvector<></a></div></div>
<div class="ttc" id="axsample03_8cpp_html_a81962ff36a3740bd2a6a458b74e57e26"><div class="ttname"><a href="xsample03_8cpp.html#a81962ff36a3740bd2a6a458b74e57e26">show_help</a></div><div class="ttdeci">static void show_help()</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00080">xsample03.cpp:80</a></div></div>
<div class="ttc" id="agroup__bvector_html_ggab0835910831729c806840cd5c8f40b2ba095db184b37a1341cbbbf813a70aed79"><div class="ttname"><a href="group__bvector.html#ggab0835910831729c806840cd5c8f40b2ba095db184b37a1341cbbbf813a70aed79">bm::use_null</a></div><div class="ttdeci">@ use_null</div><div class="ttdoc">support "non-assigned" or "NULL" logic</div><div class="ttdef"><b>Definition:</b> <a href="bmconst_8h_source.html#l00215">bmconst.h:215</a></div></div>
<div class="ttc" id="aclassbm_1_1random__subset_html_abdf1e716e124ff4d7ad8ccef1646c99e"><div class="ttname"><a href="classbm_1_1random__subset.html#abdf1e716e124ff4d7ad8ccef1646c99e">bm::random_subset::sample</a></div><div class="ttdeci">void sample(BV &bv_out, const BV &bv_in, size_type sample_count)</div><div class="ttdoc">Get random subset of input vector.</div><div class="ttdef"><b>Definition:</b> <a href="bmrandom_8h_source.html#l00140">bmrandom.h:140</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a60bdc29e0f6731410372e3518ab0940b"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a60bdc29e0f6731410372e3518ab0940b">bm::sparse_vector::end</a></div><div class="ttdeci">const_iterator end() const BMNOEXCEPT</div><div class="ttdoc">Provide const iterator access to the end</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00493">bmsparsevec.h:493</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_1_1iterator__base_html_a3f6af7f5b46c0219b28916187d302c43"><div class="ttname"><a href="classbm_1_1bvector_1_1iterator__base.html#a3f6af7f5b46c0219b28916187d302c43">bm::bvector::iterator_base::valid</a></div><div class="ttdeci">bool valid() const BMNOEXCEPT</div><div class="ttdoc">Checks if iterator is still valid. Analog of != 0 comparison for pointers.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l00280">bm.h:280</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_a6cb51d150528a5d2d87acb3e88f450bc"><div class="ttname"><a href="xsample03_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a></div><div class="ttdeci">bm::chrono_taker::duration_map_type timing_map</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00209">xsample03.cpp:209</a></div></div>
<div class="ttc" id="abmsparsevec__util_8h_html"><div class="ttname"><a href="bmsparsevec__util_8h.html">bmsparsevec_util.h</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_a501736bde7958b6e05f5fa0f5ca954c1"><div class="ttname"><a href="xsample03_8cpp.html#a501736bde7958b6e05f5fa0f5ca954c1">sv_in_name</a></div><div class="ttdeci">std::string sv_in_name</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00101">xsample03.cpp:101</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html_aaceb8d31d9da05f977de5c6a6cd62e24"><div class="ttname"><a href="classbm_1_1bvector.html#aaceb8d31d9da05f977de5c6a6cd62e24">bm::bvector::init</a></div><div class="ttdeci">void init()</div><div class="ttdoc">Explicit post-construction initialization.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l02123">bm.h:2123</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_a1c6cda197a32141227af69a440929ac6"><div class="ttname"><a href="xsample03_8cpp.html#a1c6cda197a32141227af69a440929ac6">parse_args</a></div><div class="ttdeci">static int parse_args(int argc, char *argv[])</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00109">xsample03.cpp:109</a></div></div>
<div class="ttc" id="abmtimer_8h_html"><div class="ttname"><a href="bmtimer_8h.html">bmtimer.h</a></div><div class="ttdoc">Timing utilities for benchmarking (internal)</div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_ae60eed242dd6ca5ac13a046f3f75b2f7"><div class="ttname"><a href="classbm_1_1sparse__vector.html#ae60eed242dd6ca5ac13a046f3f75b2f7">bm::sparse_vector::begin</a></div><div class="ttdeci">const_iterator begin() const BMNOEXCEPT</div><div class="ttdoc">Provide const iterator access to container content</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l01900">bmsparsevec.h:1900</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_a4dd1e4b402061691109d356faa4513b5"><div class="ttname"><a href="xsample03_8cpp.html#a4dd1e4b402061691109d356faa4513b5">is_bench</a></div><div class="ttdeci">bool is_bench</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00106">xsample03.cpp:106</a></div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html_a9a41e5f2fe48ba472fd77a1dbd86457dad530ca7863ce7e60f4fa221e1dfa64a2"><div class="ttname"><a href="classbm_1_1chrono__taker.html#a9a41e5f2fe48ba472fd77a1dbd86457dad530ca7863ce7e60f4fa221e1dfa64a2">bm::chrono_taker::ct_ops_per_sec</a></div><div class="ttdeci">@ ct_ops_per_sec</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00059">bmtimer.h:59</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_a73d3c18ad1011694ad2b47075a7a2722"><div class="ttname"><a href="xsample03_8cpp.html#a73d3c18ad1011694ad2b47075a7a2722">search_vector_pairs</a></div><div class="ttdeci">static bool search_vector_pairs(const vector_pairs &vp, unsigned rs_id, unsigned &pos)</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00329">xsample03.cpp:329</a></div></div>
<div class="ttc" id="aclassbm_1_1random__subset_html"><div class="ttname"><a href="classbm_1_1random__subset.html">bm::random_subset</a></div><div class="ttdef"><b>Definition:</b> <a href="bmrandom_8h_source.html#l00056">bmrandom.h:56</a></div></div>
<div class="ttc" id="aclassbm_1_1rsc__sparse__vector_html_a179790d1026899539804351a8039653b"><div class="ttname"><a href="classbm_1_1rsc__sparse__vector.html#a179790d1026899539804351a8039653b">bm::rsc_sparse_vector::load_from</a></div><div class="ttdeci">void load_from(const sparse_vector_type &sv_src)</div><div class="ttdoc">Load compressed vector from a sparse vector (with NULLs)</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__compr_8h_source.html#l00889">bmsparsevec_compr.h:889</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_a71d75c77694afe022fe5ed0f0b98ec66"><div class="ttname"><a href="xsample03_8cpp.html#a71d75c77694afe022fe5ed0f0b98ec66">sparse_vector_u32</a></div><div class="ttdeci">bm::sparse_vector< unsigned, bm::bvector<> > sparse_vector_u32</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00203">xsample03.cpp:203</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a2f8aadebd1cfecd8e70fc771dbbd748d"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a2f8aadebd1cfecd8e70fc771dbbd748d">bm::sparse_vector::push_back</a></div><div class="ttdeci">void push_back(value_type v)</div><div class="ttdoc">push value back into vector</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l01498">bmsparsevec.h:1498</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_aa737b7acabde8bce0f655d3f1f72cdaf"><div class="ttname"><a href="xsample03_8cpp.html#aa737b7acabde8bce0f655d3f1f72cdaf">rsc_sparse_vector_u32</a></div><div class="ttdeci">bm::rsc_sparse_vector< unsigned, sparse_vector_u32 > rsc_sparse_vector_u32</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00204">xsample03.cpp:204</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html_a16d902c3df4aa6aa88d8e137af4a4b9b"><div class="ttname"><a href="classbm_1_1bvector.html#a16d902c3df4aa6aa88d8e137af4a4b9b">bm::bvector::test</a></div><div class="ttdeci">bool test(size_type n) const BMNOEXCEPT</div><div class="ttdoc">returns true if bit n is set and false is bit n is 0.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l01440">bm.h:1440</a></div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html_add1676592117ed0eaa2fa6279a71b46a"><div class="ttname"><a href="classbm_1_1chrono__taker.html#add1676592117ed0eaa2fa6279a71b46a">bm::chrono_taker::duration_map_type</a></div><div class="ttdeci">std::map< std::string, statistics > duration_map_type</div><div class="ttdoc">test name to duration map</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00065">bmtimer.h:65</a></div></div>
<div class="ttc" id="aclassbm_1_1rsc__sparse__vector_html"><div class="ttname"><a href="classbm_1_1rsc__sparse__vector.html">bm::rsc_sparse_vector</a></div><div class="ttdoc">Rank-Select compressed sparse vector.</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__compr_8h_source.html#l00058">bmsparsevec_compr.h:58</a></div></div>
<div class="ttc" id="abmserial_8h_html"><div class="ttname"><a href="bmserial_8h.html">bmserial.h</a></div><div class="ttdoc">Serialization / compression of bvector<>. Set theoretical operations on compressed BLOBs.</div></div>
<div class="ttc" id="aclassbm_1_1rsc__sparse__vector_html_a4550829bbd4b9506d9cc3112751d71a5"><div class="ttname"><a href="classbm_1_1rsc__sparse__vector.html#a4550829bbd4b9506d9cc3112751d71a5">bm::rsc_sparse_vector::optimize</a></div><div class="ttdeci">void optimize(bm::word_t *temp_block=0, typename bvector_type::optmode opt_mode=bvector_type::opt_compress, statistics *stat=0)</div><div class="ttdoc">run memory optimization for all vector plains</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__compr_8h_source.html#l01081">bmsparsevec_compr.h:1081</a></div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html_a30b45453d952d14afe56c29087970899"><div class="ttname"><a href="classbm_1_1chrono__taker.html#a30b45453d952d14afe56c29087970899">bm::chrono_taker::print_duration_map</a></div><div class="ttdeci">static void print_duration_map(const duration_map_type &dmap, format fmt=ct_time)</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00127">bmtimer.h:127</a></div></div>
<div class="ttc" id="abmalgo__similarity_8h_html"><div class="ttname"><a href="bmalgo__similarity_8h.html">bmalgo_similarity.h</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a8a2eb22c48d618a18f73fc87a7053060"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a8a2eb22c48d618a18f73fc87a7053060">bm::sparse_vector::empty</a></div><div class="ttdeci">bool empty() const BMNOEXCEPT</div><div class="ttdoc">return true if vector is empty</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00649">bmsparsevec.h:649</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html_a86b939f3aed555dc073e8c26e9efea71"><div class="ttname"><a href="classbm_1_1bvector.html#a86b939f3aed555dc073e8c26e9efea71">bm::bvector::first</a></div><div class="ttdeci">enumerator first() const</div><div class="ttdoc">Returns enumerator pointing on the first non-zero bit.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l01770">bm.h:1770</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_a0ddf1224851353fc92bfbff6f499fa97"><div class="ttname"><a href="xsample03_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97">main</a></div><div class="ttdeci">int main(int argc, char *argv[])</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00459">xsample03.cpp:459</a></div></div>
<div class="ttc" id="abm_8h_html"><div class="ttname"><a href="bm_8h.html">bm.h</a></div><div class="ttdoc">Compressed bit-vector bvector<> container, set algebraic methods, traversal iterators.</div></div>
<div class="ttc" id="axsample03_8cpp_html_aacb20d26faea4c3ca196ac6b888636c8"><div class="ttname"><a href="xsample03_8cpp.html#aacb20d26faea4c3ca196ac6b888636c8">generate_random_subset</a></div><div class="ttdeci">static void generate_random_subset(const sparse_vector_u32 &sv, std::vector< unsigned > &vect, unsigned count)</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00291">xsample03.cpp:291</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a56101ce9a559b30f8e14153133063ca7"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a56101ce9a559b30f8e14153133063ca7">bm::sparse_vector::set</a></div><div class="ttdeci">void set(size_type idx, value_type v)</div><div class="ttdoc">set specified element with bounds checking and automatic resize</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l01469">bmsparsevec.h:1469</a></div></div>
<div class="ttc" id="axsample03_8cpp_html_adb75765b8dcd96f522e158c738abab77"><div class="ttname"><a href="xsample03_8cpp.html#adb75765b8dcd96f522e158c738abab77">run_benchmark</a></div><div class="ttdeci">static void run_benchmark(const sparse_vector_u32 &sv, const rsc_sparse_vector_u32 &csv)</div><div class="ttdef"><b>Definition:</b> <a href="xsample03_8cpp_source.html#l00348">xsample03.cpp:348</a></div></div>
<div class="ttc" id="aclassbm_1_1base__sparse__vector_html_aacbde903b5a180ec493d34dd209fe542"><div class="ttname"><a href="classbm_1_1base__sparse__vector.html#aacbde903b5a180ec493d34dd209fe542">bm::base_sparse_vector::get_null_bvector</a></div><div class="ttdeci">const bvector_type * get_null_bvector() const BMNOEXCEPT</div><div class="ttdoc">Get bit-vector of assigned values or NULL (if not constructed that way)</div><div class="ttdef"><b>Definition:</b> <a href="bmbmatrix_8h_source.html#l00329">bmbmatrix.h:329</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector__scanner_html_aa2439360def2f3fe3c788872c0e70997"><div class="ttname"><a href="classbm_1_1sparse__vector__scanner.html#aa2439360def2f3fe3c788872c0e70997">bm::sparse_vector_scanner::find_eq</a></div><div class="ttdeci">void find_eq(const SV &sv, typename SV::value_type value, typename SV::bvector_type &bv_out)</div><div class="ttdoc">find all sparse vector elements EQ to search value</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__algo_8h_source.html#l02033">bmsparsevec_algo.h:2033</a></div></div>
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