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<div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="preprocessor">#pragma once</span></div>
<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span> </div>
<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="preprocessor">#include <array></span></div>
<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span><span class="preprocessor">#include <cstdint></span></div>
<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span><span class="preprocessor">#include <cstring></span></div>
<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="preprocessor">#include <deque></span></div>
<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span><span class="preprocessor">#include <memory></span></div>
<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span><span class="preprocessor">#include <string></span></div>
<div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span><span class="preprocessor">#include <string_view></span></div>
<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span><span class="preprocessor">#include <vector></span></div>
<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span> </div>
<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span><span class="preprocessor">#include <btllib/hashing_internals.hpp></span></div>
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include <btllib/status.hpp></span></div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> </div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="keyword">namespace </span>btllib::hashing_internals {</div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> </div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="keyword">using </span>SpacedSeed = std::vector<unsigned>;</div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="keyword">using </span>SpacedSeedBlocks = std::vector<std::array<unsigned, 2>>;</div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span><span class="keyword">using </span>SpacedSeedMonomers = std::vector<unsigned>;</div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> </div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span>get_blocks(<span class="keyword">const</span> std::vector<std::string>& seed_strings,</div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> std::vector<SpacedSeedBlocks>& blocks,</div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> std::vector<SpacedSeedMonomers>& monomers)</div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span>{</div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& seed_string : seed_strings) {</div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> <span class="keyword">const</span> <span class="keywordtype">char</span> pad = seed_string[seed_string.length() - 1] == <span class="charliteral">'1'</span> ? <span class="charliteral">'0'</span> : <span class="charliteral">'1'</span>;</div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> <span class="keyword">const</span> std::string padded_string = seed_string + pad;</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> SpacedSeedBlocks care_blocks, ignore_blocks;</div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> std::vector<unsigned> care_monos, ignore_monos;</div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span> <span class="keywordtype">unsigned</span> i_start = 0;</div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> <span class="keywordtype">bool</span> is_care_block = padded_string[0] == <span class="charliteral">'1'</span>;</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> pos = 0; pos < padded_string.length(); pos++) {</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> <span class="keywordflow">if</span> (is_care_block && padded_string[pos] == <span class="charliteral">'0'</span>) {</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> <span class="keywordflow">if</span> (pos - i_start == 1) {</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> care_monos.push_back(i_start);</div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> <span class="keyword">const</span> std::array<unsigned, 2> block{ { i_start, pos } };</div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> care_blocks.push_back(block);</div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> }</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> i_start = pos;</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> is_care_block = <span class="keyword">false</span>;</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (!is_care_block && padded_string[pos] == <span class="charliteral">'1'</span>) {</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> <span class="keywordflow">if</span> (pos - i_start == 1) {</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> ignore_monos.push_back(i_start);</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keyword">const</span> std::array<unsigned, 2> block{ { i_start, pos } };</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> ignore_blocks.push_back(block);</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> }</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> i_start = pos;</div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> is_care_block = <span class="keyword">true</span>;</div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> }</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> }</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> num_cares = care_blocks.size() * 2 + care_monos.size();</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> num_ignores =</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> ignore_blocks.size() * 2 + ignore_monos.size() + 2;</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> <span class="keywordflow">if</span> (num_ignores < num_cares) {</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> string_end = seed_string.length();</div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> <span class="keyword">const</span> std::array<unsigned, 2> block{ { 0, string_end } };</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> ignore_blocks.push_back(block);</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> blocks.push_back(ignore_blocks);</div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> monomers.push_back(ignore_monos);</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> blocks.push_back(care_blocks);</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> monomers.push_back(care_monos);</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> }</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> }</div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span>}</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span>parsed_seeds_to_blocks(<span class="keyword">const</span> std::vector<std::vector<unsigned>>& seeds,</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> std::vector<SpacedSeedBlocks>& blocks,</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> std::vector<SpacedSeedMonomers>& monomers)</div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span>{</div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> std::vector<std::string> seed_strings;</div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& seed : seeds) {</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> std::string seed_string(k, <span class="charliteral">'1'</span>);</div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& i : seed) {</div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> seed_string[i] = <span class="charliteral">'0'</span>;</div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> }</div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> seed_strings.push_back(seed_string);</div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> }</div>
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> get_blocks(seed_strings, blocks, monomers);</div>
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span>}</div>
<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span>check_seeds(<span class="keyword">const</span> std::vector<std::string>& seeds, <span class="keywordtype">unsigned</span> k)</div>
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span>{</div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& seed : seeds) {</div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> <a class="code hl_function" href="namespacebtllib.html#a540bce0213b7718e519ddc4466361bf7">btllib::check_error</a>(seed.length() != k,</div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> <span class="stringliteral">"SeedNtHash: Spaced seed string length ("</span> +</div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> std::to_string(seed.length()) + <span class="stringliteral">") not equal to k="</span> +</div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> std::to_string(k) + <span class="stringliteral">" in "</span> + seed);</div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> <span class="keyword">const</span> std::string reversed(seed.rbegin(), seed.rend());</div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> <a class="code hl_function" href="namespacebtllib.html#a60a36f4583a7eb03001f8bdb7b395507">btllib::check_warning</a>(</div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> seed != reversed,</div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> <span class="stringliteral">"SeedNtHash: Seed "</span> + seed +</div>
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> <span class="stringliteral">" is not symmetric, reverse-complement hashing will be inconsistent"</span>);</div>
<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> }</div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span>}</div>
<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> </div>
<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span><span class="keyword">inline</span> <span class="keywordtype">bool</span></div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span>ntmsm64(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> uint64_t* fh_val,</div>
<div class="line"><a id="l00137" name="l00137"></a><span class="lineno"> 137</span> uint64_t* rh_val,</div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> <span class="keywordtype">unsigned</span>& loc_n,</div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> uint64_t* h_val)</div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span>{</div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span> <span class="keywordtype">unsigned</span> i_base;</div>
<div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> uint64_t fh_seed, rh_seed;</div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i_seed = 0; i_seed < m; i_seed++) {</div>
<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</span> fh_seed = 0;</div>
<div class="line"><a id="l00145" name="l00145"></a><span class="lineno"> 145</span> rh_seed = 0;</div>
<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"> 146</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& block : seeds_blocks[i_seed]) {</div>
<div class="line"><a id="l00147" name="l00147"></a><span class="lineno"> 147</span> uint8_t fh_loc, rh_loc, d;</div>
<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</span> uint64_t x;</div>
<div class="line"><a id="l00149" name="l00149"></a><span class="lineno"> 149</span> <span class="keywordtype">unsigned</span> i = block[0];</div>
<div class="line"><a id="l00150" name="l00150"></a><span class="lineno"> 150</span> <span class="keywordtype">unsigned</span> j = block[1];</div>
<div class="line"><a id="l00151" name="l00151"></a><span class="lineno"> 151</span> <span class="keywordflow">switch</span> (j - i) {</div>
<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"> 152</span> <span class="keywordflow">case</span> 2: {</div>
<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</span> fh_loc = (CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i]] << 2) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00154" name="l00154"></a><span class="lineno"> 154</span> (CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 1]]); <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"> 155</span> rh_loc =</div>
<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span> (RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 1]] << 2) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> (RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i]]); <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> x = DIMER_TAB[fh_loc]; <span class="comment">// cppcheck-suppress arrayIndexOutOfBounds</span></div>
<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> d = k - i - 2; <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> fh_seed ^= d > 0 ? srol(x, d) : x;</div>
<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> x = DIMER_TAB[rh_loc]; <span class="comment">// cppcheck-suppress arrayIndexOutOfBounds</span></div>
<div class="line"><a id="l00162" name="l00162"></a><span class="lineno"> 162</span> d = i;</div>
<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"> 163</span> rh_seed ^= d > 0 ? srol(x, d) : x;</div>
<div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span> } <span class="keywordflow">break</span>;</div>
<div class="line"><a id="l00165" name="l00165"></a><span class="lineno"> 165</span> <span class="keywordflow">case</span> 3: {</div>
<div class="line"><a id="l00166" name="l00166"></a><span class="lineno"> 166</span> fh_loc =</div>
<div class="line"><a id="l00167" name="l00167"></a><span class="lineno"> 167</span> (CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i]] << 4) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00168" name="l00168"></a><span class="lineno"> 168</span> (CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 1]] << 2) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span> (CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 2]]); <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> rh_loc =</div>
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span> (RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 2]] << 4) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> (RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 1]] << 2) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span> (RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i]]);</div>
<div class="line"><a id="l00174" name="l00174"></a><span class="lineno"> 174</span> x = TRIMER_TAB[fh_loc]; <span class="comment">// cppcheck-suppress arrayIndexOutOfBounds</span></div>
<div class="line"><a id="l00175" name="l00175"></a><span class="lineno"> 175</span> d = k - i - 3; <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00176" name="l00176"></a><span class="lineno"> 176</span> fh_seed ^= d > 0 ? srol(x, d) : x;</div>
<div class="line"><a id="l00177" name="l00177"></a><span class="lineno"> 177</span> x = TRIMER_TAB[rh_loc]; <span class="comment">// cppcheck-suppress arrayIndexOutOfBounds</span></div>
<div class="line"><a id="l00178" name="l00178"></a><span class="lineno"> 178</span> d = i;</div>
<div class="line"><a id="l00179" name="l00179"></a><span class="lineno"> 179</span> rh_seed ^= d > 0 ? srol(x, d) : x;</div>
<div class="line"><a id="l00180" name="l00180"></a><span class="lineno"> 180</span> } <span class="keywordflow">break</span>;</div>
<div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</span> <span class="keywordflow">case</span> 4: {</div>
<div class="line"><a id="l00182" name="l00182"></a><span class="lineno"> 182</span> fh_loc =</div>
<div class="line"><a id="l00183" name="l00183"></a><span class="lineno"> 183</span> (CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i]] << 6) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00184" name="l00184"></a><span class="lineno"> 184</span> (CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 1]] << 4) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00185" name="l00185"></a><span class="lineno"> 185</span> (CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 2]] << 2) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"> 186</span> (CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 3]]); <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"> 187</span> rh_loc =</div>
<div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span> (RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 3]] << 6) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00189" name="l00189"></a><span class="lineno"> 189</span> (RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 2]] << 4) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00190" name="l00190"></a><span class="lineno"> 190</span> (RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i + 1]] << 2) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span> (RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i]]);</div>
<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</span> x = TETRAMER_TAB[fh_loc]; <span class="comment">// cppcheck-suppress arrayIndexOutOfBounds</span></div>
<div class="line"><a id="l00193" name="l00193"></a><span class="lineno"> 193</span> d = k - i - 4; <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> fh_seed ^= d > 0 ? srol(x, d) : x;</div>
<div class="line"><a id="l00195" name="l00195"></a><span class="lineno"> 195</span> x = TETRAMER_TAB[rh_loc]; <span class="comment">// cppcheck-suppress arrayIndexOutOfBounds</span></div>
<div class="line"><a id="l00196" name="l00196"></a><span class="lineno"> 196</span> d = i;</div>
<div class="line"><a id="l00197" name="l00197"></a><span class="lineno"> 197</span> rh_seed ^= d > 0 ? srol(x, d) : x;</div>
<div class="line"><a id="l00198" name="l00198"></a><span class="lineno"> 198</span> } <span class="keywordflow">break</span>;</div>
<div class="line"><a id="l00199" name="l00199"></a><span class="lineno"> 199</span> <span class="keywordflow">default</span>: {</div>
<div class="line"><a id="l00200" name="l00200"></a><span class="lineno"> 200</span> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> pos = block[0]; pos < block[1]; pos++) {</div>
<div class="line"><a id="l00201" name="l00201"></a><span class="lineno"> 201</span> <span class="keywordflow">if</span> (kmer_seq[pos] == SEED_N) {</div>
<div class="line"><a id="l00202" name="l00202"></a><span class="lineno"> 202</span> loc_n = pos;</div>
<div class="line"><a id="l00203" name="l00203"></a><span class="lineno"> 203</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00204" name="l00204"></a><span class="lineno"> 204</span> }</div>
<div class="line"><a id="l00205" name="l00205"></a><span class="lineno"> 205</span> fh_seed ^= srol_table((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[pos], k - 1 - pos);</div>
<div class="line"><a id="l00206" name="l00206"></a><span class="lineno"> 206</span> rh_seed ^= srol_table((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[pos] & CP_OFF, pos);</div>
<div class="line"><a id="l00207" name="l00207"></a><span class="lineno"> 207</span> }</div>
<div class="line"><a id="l00208" name="l00208"></a><span class="lineno"> 208</span> }</div>
<div class="line"><a id="l00209" name="l00209"></a><span class="lineno"> 209</span> }</div>
<div class="line"><a id="l00210" name="l00210"></a><span class="lineno"> 210</span> }</div>
<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"> 211</span> fh_nomonos[i_seed] = fh_seed;</div>
<div class="line"><a id="l00212" name="l00212"></a><span class="lineno"> 212</span> rh_nomonos[i_seed] = rh_seed;</div>
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& pos : seeds_monomers[i_seed]) {</div>
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> fh_seed ^= srol_table((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[pos], k - 1 - pos);</div>
<div class="line"><a id="l00215" name="l00215"></a><span class="lineno"> 215</span> rh_seed ^= srol_table((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[pos] & CP_OFF, pos);</div>
<div class="line"><a id="l00216" name="l00216"></a><span class="lineno"> 216</span> }</div>
<div class="line"><a id="l00217" name="l00217"></a><span class="lineno"> 217</span> fh_val[i_seed] = fh_seed;</div>
<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> rh_val[i_seed] = rh_seed;</div>
<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"> 219</span> i_base = i_seed * m2;</div>
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span> h_val[i_base] = canonical(fh_seed, rh_seed);</div>
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i_hash = 1; i_hash < m2; i_hash++) {</div>
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> h_val[i_base + i_hash] = h_val[i_base] * (i_hash ^ k * MULTISEED);</div>
<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"> 223</span> h_val[i_base + i_hash] ^= h_val[i_base + i_hash] >> MULTISHIFT;</div>
<div class="line"><a id="l00224" name="l00224"></a><span class="lineno"> 224</span> }</div>
<div class="line"><a id="l00225" name="l00225"></a><span class="lineno"> 225</span> }</div>
<div class="line"><a id="l00226" name="l00226"></a><span class="lineno"> 226</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00227" name="l00227"></a><span class="lineno"> 227</span>}</div>
<div class="line"><a id="l00228" name="l00228"></a><span class="lineno"> 228</span> </div>
<div class="line"><a id="l00229" name="l00229"></a><span class="lineno"> 229</span><span class="preprocessor">#define NTMSM64(ROL_HANDLING, IN_HANDLING, OUT_HANDLING, ROR_HANDLING) \</span></div>
<div class="line"><a id="l00230" name="l00230"></a><span class="lineno"> 230</span><span class="preprocessor"> unsigned char char_out, char_in; \</span></div>
<div class="line"><a id="l00231" name="l00231"></a><span class="lineno"> 231</span><span class="preprocessor"> uint64_t fh_seed, rh_seed; \</span></div>
<div class="line"><a id="l00232" name="l00232"></a><span class="lineno"> 232</span><span class="preprocessor"> unsigned i_out, i_in, i_base; \</span></div>
<div class="line"><a id="l00233" name="l00233"></a><span class="lineno"> 233</span><span class="preprocessor"> for (unsigned i_seed = 0; i_seed < m; i_seed++) { \</span></div>
<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span><span class="preprocessor"> ROL_HANDLING </span><span class="comment">/* NOLINT(bugprone-macro-parentheses) */</span><span class="preprocessor"> \</span></div>
<div class="line"><a id="l00235" name="l00235"></a><span class="lineno"> 235</span><span class="preprocessor"> for (const auto& block : seeds_blocks[i_seed]) \</span></div>
<div class="line"><a id="l00236" name="l00236"></a><span class="lineno"> 236</span><span class="preprocessor"> { \</span></div>
<div class="line"><a id="l00237" name="l00237"></a><span class="lineno"> 237</span><span class="preprocessor"> IN_HANDLING \</span></div>
<div class="line"><a id="l00238" name="l00238"></a><span class="lineno"> 238</span><span class="preprocessor"> OUT_HANDLING \</span></div>
<div class="line"><a id="l00239" name="l00239"></a><span class="lineno"> 239</span><span class="preprocessor"> fh_seed ^= srol_table(char_out, k - i_out); \</span></div>
<div class="line"><a id="l00240" name="l00240"></a><span class="lineno"> 240</span><span class="preprocessor"> fh_seed ^= srol_table(char_in, k - i_in); \</span></div>
<div class="line"><a id="l00241" name="l00241"></a><span class="lineno"> 241</span><span class="preprocessor"> rh_seed ^= srol_table(char_out & CP_OFF, i_out); \</span></div>
<div class="line"><a id="l00242" name="l00242"></a><span class="lineno"> 242</span><span class="preprocessor"> rh_seed ^= srol_table(char_in & CP_OFF, i_in); \</span></div>
<div class="line"><a id="l00243" name="l00243"></a><span class="lineno"> 243</span><span class="preprocessor"> } \</span></div>
<div class="line"><a id="l00244" name="l00244"></a><span class="lineno"> 244</span><span class="preprocessor"> ROR_HANDLING </span><span class="comment">/* NOLINT(bugprone-macro-parentheses) */</span><span class="preprocessor"> \</span></div>
<div class="line"><a id="l00245" name="l00245"></a><span class="lineno"> 245</span><span class="preprocessor"> fh_nomonos[i_seed] = fh_seed; \</span></div>
<div class="line"><a id="l00246" name="l00246"></a><span class="lineno"> 246</span><span class="preprocessor"> rh_nomonos[i_seed] = rh_seed; \</span></div>
<div class="line"><a id="l00247" name="l00247"></a><span class="lineno"> 247</span><span class="preprocessor"> for (const auto& pos : seeds_monomers[i_seed]) { \</span></div>
<div class="line"><a id="l00248" name="l00248"></a><span class="lineno"> 248</span><span class="preprocessor"> fh_seed ^= srol_table((unsigned char)kmer_seq[pos + 1], k - 1 - pos); \</span></div>
<div class="line"><a id="l00249" name="l00249"></a><span class="lineno"> 249</span><span class="preprocessor"> rh_seed ^= srol_table((unsigned char)kmer_seq[pos + 1] & CP_OFF, pos); \</span></div>
<div class="line"><a id="l00250" name="l00250"></a><span class="lineno"> 250</span><span class="preprocessor"> } \</span></div>
<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"> 251</span><span class="preprocessor"> fh_val[i_seed] = fh_seed; \</span></div>
<div class="line"><a id="l00252" name="l00252"></a><span class="lineno"> 252</span><span class="preprocessor"> rh_val[i_seed] = rh_seed; \</span></div>
<div class="line"><a id="l00253" name="l00253"></a><span class="lineno"> 253</span><span class="preprocessor"> i_base = i_seed * m2; \</span></div>
<div class="line"><a id="l00254" name="l00254"></a><span class="lineno"> 254</span><span class="preprocessor"> h_val[i_base] = canonical(fh_seed, rh_seed); \</span></div>
<div class="line"><a id="l00255" name="l00255"></a><span class="lineno"> 255</span><span class="preprocessor"> for (unsigned i_hash = 1; i_hash < m2; i_hash++) { \</span></div>
<div class="line"><a id="l00256" name="l00256"></a><span class="lineno"> 256</span><span class="preprocessor"> h_val[i_base + i_hash] = h_val[i_base] * (i_hash ^ k * MULTISEED); \</span></div>
<div class="line"><a id="l00257" name="l00257"></a><span class="lineno"> 257</span><span class="preprocessor"> h_val[i_base + i_hash] ^= h_val[i_base + i_hash] >> MULTISHIFT; \</span></div>
<div class="line"><a id="l00258" name="l00258"></a><span class="lineno"> 258</span><span class="preprocessor"> } \</span></div>
<div class="line"><a id="l00259" name="l00259"></a><span class="lineno"> 259</span><span class="preprocessor"> }</span></div>
<div class="line"><a id="l00260" name="l00260"></a><span class="lineno"> 260</span> </div>
<div class="line"><a id="l00282" name="l00282"></a><span class="lineno"> 282</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00283" name="l00283"></a><span class="lineno"> 283</span>ntmsm64(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00284" name="l00284"></a><span class="lineno"> 284</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l00285" name="l00285"></a><span class="lineno"> 285</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l00286" name="l00286"></a><span class="lineno"> 286</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00287" name="l00287"></a><span class="lineno"> 287</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00288" name="l00288"></a><span class="lineno"> 288</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l00289" name="l00289"></a><span class="lineno"> 289</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l00290" name="l00290"></a><span class="lineno"> 290</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l00291" name="l00291"></a><span class="lineno"> 291</span> uint64_t* fh_val,</div>
<div class="line"><a id="l00292" name="l00292"></a><span class="lineno"> 292</span> uint64_t* rh_val,</div>
<div class="line"><a id="l00293" name="l00293"></a><span class="lineno"> 293</span> uint64_t* h_val)</div>
<div class="line"><a id="l00294" name="l00294"></a><span class="lineno"> 294</span>{</div>
<div class="line"><a id="l00295" name="l00295"></a><span class="lineno"> 295</span> NTMSM64(fh_seed = srol(fh_nomonos[i_seed]); rh_seed = rh_nomonos[i_seed];</div>
<div class="line"><a id="l00296" name="l00296"></a><span class="lineno"> 296</span> , i_in = block[1];</div>
<div class="line"><a id="l00297" name="l00297"></a><span class="lineno"> 297</span> char_in = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_in];</div>
<div class="line"><a id="l00298" name="l00298"></a><span class="lineno"> 298</span> , i_out = block[0];</div>
<div class="line"><a id="l00299" name="l00299"></a><span class="lineno"> 299</span> char_out = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_out];</div>
<div class="line"><a id="l00300" name="l00300"></a><span class="lineno"> 300</span> , rh_seed = sror(rh_seed);)</div>
<div class="line"><a id="l00301" name="l00301"></a><span class="lineno"> 301</span>}</div>
<div class="line"><a id="l00302" name="l00302"></a><span class="lineno"> 302</span> </div>
<div class="line"><a id="l00303" name="l00303"></a><span class="lineno"> 303</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00304" name="l00304"></a><span class="lineno"> 304</span>ntmsm64(<span class="keyword">const</span> std::deque<char>& kmer_seq,</div>
<div class="line"><a id="l00305" name="l00305"></a><span class="lineno"> 305</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l00306" name="l00306"></a><span class="lineno"> 306</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l00307" name="l00307"></a><span class="lineno"> 307</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00308" name="l00308"></a><span class="lineno"> 308</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00309" name="l00309"></a><span class="lineno"> 309</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l00310" name="l00310"></a><span class="lineno"> 310</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l00311" name="l00311"></a><span class="lineno"> 311</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l00312" name="l00312"></a><span class="lineno"> 312</span> uint64_t* fh_val,</div>
<div class="line"><a id="l00313" name="l00313"></a><span class="lineno"> 313</span> uint64_t* rh_val,</div>
<div class="line"><a id="l00314" name="l00314"></a><span class="lineno"> 314</span> uint64_t* h_val)</div>
<div class="line"><a id="l00315" name="l00315"></a><span class="lineno"> 315</span>{</div>
<div class="line"><a id="l00316" name="l00316"></a><span class="lineno"> 316</span> NTMSM64(fh_seed = srol(fh_nomonos[i_seed]); rh_seed = rh_nomonos[i_seed];</div>
<div class="line"><a id="l00317" name="l00317"></a><span class="lineno"> 317</span> , i_in = block[1];</div>
<div class="line"><a id="l00318" name="l00318"></a><span class="lineno"> 318</span> char_in = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_in];</div>
<div class="line"><a id="l00319" name="l00319"></a><span class="lineno"> 319</span> , i_out = block[0];</div>
<div class="line"><a id="l00320" name="l00320"></a><span class="lineno"> 320</span> char_out = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_out];</div>
<div class="line"><a id="l00321" name="l00321"></a><span class="lineno"> 321</span> , rh_seed = sror(rh_seed);)</div>
<div class="line"><a id="l00322" name="l00322"></a><span class="lineno"> 322</span>}</div>
<div class="line"><a id="l00323" name="l00323"></a><span class="lineno"> 323</span> </div>
<div class="line"><a id="l00345" name="l00345"></a><span class="lineno"> 345</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00346" name="l00346"></a><span class="lineno"> 346</span>ntmsm64l(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00347" name="l00347"></a><span class="lineno"> 347</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l00348" name="l00348"></a><span class="lineno"> 348</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l00349" name="l00349"></a><span class="lineno"> 349</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00350" name="l00350"></a><span class="lineno"> 350</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00351" name="l00351"></a><span class="lineno"> 351</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l00352" name="l00352"></a><span class="lineno"> 352</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l00353" name="l00353"></a><span class="lineno"> 353</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l00354" name="l00354"></a><span class="lineno"> 354</span> uint64_t* fh_val,</div>
<div class="line"><a id="l00355" name="l00355"></a><span class="lineno"> 355</span> uint64_t* rh_val,</div>
<div class="line"><a id="l00356" name="l00356"></a><span class="lineno"> 356</span> uint64_t* h_val)</div>
<div class="line"><a id="l00357" name="l00357"></a><span class="lineno"> 357</span>{</div>
<div class="line"><a id="l00358" name="l00358"></a><span class="lineno"> 358</span> NTMSM64(fh_seed = fh_nomonos[i_seed]; rh_seed = srol(rh_nomonos[i_seed]);</div>
<div class="line"><a id="l00359" name="l00359"></a><span class="lineno"> 359</span> , i_in = block[0];</div>
<div class="line"><a id="l00360" name="l00360"></a><span class="lineno"> 360</span> char_in = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_in];</div>
<div class="line"><a id="l00361" name="l00361"></a><span class="lineno"> 361</span> , i_out = block[1];</div>
<div class="line"><a id="l00362" name="l00362"></a><span class="lineno"> 362</span> char_out = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_out];</div>
<div class="line"><a id="l00363" name="l00363"></a><span class="lineno"> 363</span> , fh_seed = sror(fh_seed);)</div>
<div class="line"><a id="l00364" name="l00364"></a><span class="lineno"> 364</span>}</div>
<div class="line"><a id="l00365" name="l00365"></a><span class="lineno"> 365</span> </div>
<div class="line"><a id="l00366" name="l00366"></a><span class="lineno"> 366</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00367" name="l00367"></a><span class="lineno"> 367</span>ntmsm64l(<span class="keyword">const</span> std::deque<char>& kmer_seq,</div>
<div class="line"><a id="l00368" name="l00368"></a><span class="lineno"> 368</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l00369" name="l00369"></a><span class="lineno"> 369</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l00370" name="l00370"></a><span class="lineno"> 370</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00371" name="l00371"></a><span class="lineno"> 371</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00372" name="l00372"></a><span class="lineno"> 372</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l00373" name="l00373"></a><span class="lineno"> 373</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l00374" name="l00374"></a><span class="lineno"> 374</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l00375" name="l00375"></a><span class="lineno"> 375</span> uint64_t* fh_val,</div>
<div class="line"><a id="l00376" name="l00376"></a><span class="lineno"> 376</span> uint64_t* rh_val,</div>
<div class="line"><a id="l00377" name="l00377"></a><span class="lineno"> 377</span> uint64_t* h_val)</div>
<div class="line"><a id="l00378" name="l00378"></a><span class="lineno"> 378</span>{</div>
<div class="line"><a id="l00379" name="l00379"></a><span class="lineno"> 379</span> NTMSM64(fh_seed = fh_nomonos[i_seed]; rh_seed = srol(rh_nomonos[i_seed]);</div>
<div class="line"><a id="l00380" name="l00380"></a><span class="lineno"> 380</span> , i_in = block[0];</div>
<div class="line"><a id="l00381" name="l00381"></a><span class="lineno"> 381</span> char_in = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_in];</div>
<div class="line"><a id="l00382" name="l00382"></a><span class="lineno"> 382</span> , i_out = block[1];</div>
<div class="line"><a id="l00383" name="l00383"></a><span class="lineno"> 383</span> char_out = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_out];</div>
<div class="line"><a id="l00384" name="l00384"></a><span class="lineno"> 384</span> , fh_seed = sror(fh_seed);)</div>
<div class="line"><a id="l00385" name="l00385"></a><span class="lineno"> 385</span>}</div>
<div class="line"><a id="l00386" name="l00386"></a><span class="lineno"> 386</span> </div>
<div class="line"><a id="l00408" name="l00408"></a><span class="lineno"> 408</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00409" name="l00409"></a><span class="lineno"> 409</span>ntmsm64(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00410" name="l00410"></a><span class="lineno"> 410</span> <span class="keywordtype">char</span> in,</div>
<div class="line"><a id="l00411" name="l00411"></a><span class="lineno"> 411</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l00412" name="l00412"></a><span class="lineno"> 412</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l00413" name="l00413"></a><span class="lineno"> 413</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00414" name="l00414"></a><span class="lineno"> 414</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00415" name="l00415"></a><span class="lineno"> 415</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l00416" name="l00416"></a><span class="lineno"> 416</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l00417" name="l00417"></a><span class="lineno"> 417</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l00418" name="l00418"></a><span class="lineno"> 418</span> uint64_t* fh_val,</div>
<div class="line"><a id="l00419" name="l00419"></a><span class="lineno"> 419</span> uint64_t* rh_val,</div>
<div class="line"><a id="l00420" name="l00420"></a><span class="lineno"> 420</span> uint64_t* h_val)</div>
<div class="line"><a id="l00421" name="l00421"></a><span class="lineno"> 421</span>{</div>
<div class="line"><a id="l00422" name="l00422"></a><span class="lineno"> 422</span> NTMSM64(</div>
<div class="line"><a id="l00423" name="l00423"></a><span class="lineno"> 423</span> fh_seed = srol(fh_nomonos[i_seed]); rh_seed = rh_nomonos[i_seed];</div>
<div class="line"><a id="l00424" name="l00424"></a><span class="lineno"> 424</span> , i_in = block[1];</div>
<div class="line"><a id="l00425" name="l00425"></a><span class="lineno"> 425</span> <span class="keywordflow">if</span> (i_in > k - 1) { char_in = in; } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00426" name="l00426"></a><span class="lineno"> 426</span> char_in = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_in];</div>
<div class="line"><a id="l00427" name="l00427"></a><span class="lineno"> 427</span> },</div>
<div class="line"><a id="l00428" name="l00428"></a><span class="lineno"> 428</span> i_out = block[0];</div>
<div class="line"><a id="l00429" name="l00429"></a><span class="lineno"> 429</span> char_out = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_out];</div>
<div class="line"><a id="l00430" name="l00430"></a><span class="lineno"> 430</span> , rh_seed = sror(rh_seed);)</div>
<div class="line"><a id="l00431" name="l00431"></a><span class="lineno"> 431</span>}</div>
<div class="line"><a id="l00432" name="l00432"></a><span class="lineno"> 432</span> </div>
<div class="line"><a id="l00454" name="l00454"></a><span class="lineno"> 454</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00455" name="l00455"></a><span class="lineno"> 455</span>ntmsm64l(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00456" name="l00456"></a><span class="lineno"> 456</span> <span class="keywordtype">char</span> in,</div>
<div class="line"><a id="l00457" name="l00457"></a><span class="lineno"> 457</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l00458" name="l00458"></a><span class="lineno"> 458</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l00459" name="l00459"></a><span class="lineno"> 459</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00460" name="l00460"></a><span class="lineno"> 460</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00461" name="l00461"></a><span class="lineno"> 461</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l00462" name="l00462"></a><span class="lineno"> 462</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l00463" name="l00463"></a><span class="lineno"> 463</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l00464" name="l00464"></a><span class="lineno"> 464</span> uint64_t* fh_val,</div>
<div class="line"><a id="l00465" name="l00465"></a><span class="lineno"> 465</span> uint64_t* rh_val,</div>
<div class="line"><a id="l00466" name="l00466"></a><span class="lineno"> 466</span> uint64_t* h_val)</div>
<div class="line"><a id="l00467" name="l00467"></a><span class="lineno"> 467</span>{</div>
<div class="line"><a id="l00468" name="l00468"></a><span class="lineno"> 468</span> NTMSM64(</div>
<div class="line"><a id="l00469" name="l00469"></a><span class="lineno"> 469</span> fh_seed = fh_nomonos[i_seed]; rh_seed = srol(rh_nomonos[i_seed]);</div>
<div class="line"><a id="l00470" name="l00470"></a><span class="lineno"> 470</span> , i_in = block[0];</div>
<div class="line"><a id="l00471" name="l00471"></a><span class="lineno"> 471</span> <span class="keywordflow">if</span> (i_in > k - 1) { char_in = in; } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00472" name="l00472"></a><span class="lineno"> 472</span> char_in = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_in];</div>
<div class="line"><a id="l00473" name="l00473"></a><span class="lineno"> 473</span> },</div>
<div class="line"><a id="l00474" name="l00474"></a><span class="lineno"> 474</span> i_out = block[1];</div>
<div class="line"><a id="l00475" name="l00475"></a><span class="lineno"> 475</span> char_out = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_out];</div>
<div class="line"><a id="l00476" name="l00476"></a><span class="lineno"> 476</span> , fh_seed = sror(fh_seed);)</div>
<div class="line"><a id="l00477" name="l00477"></a><span class="lineno"> 477</span>}</div>
<div class="line"><a id="l00478" name="l00478"></a><span class="lineno"> 478</span> </div>
<div class="line"><a id="l00479" name="l00479"></a><span class="lineno"> 479</span>} <span class="comment">// namespace btllib::hashing_internals</span></div>
<div class="line"><a id="l00480" name="l00480"></a><span class="lineno"> 480</span> </div>
<div class="line"><a id="l00481" name="l00481"></a><span class="lineno"> 481</span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacebtllib.html">btllib</a> {</div>
<div class="line"><a id="l00482" name="l00482"></a><span class="lineno"> 482</span> </div>
<div class="line"><a id="l00483" name="l00483"></a><span class="lineno"> 483</span><span class="keyword">using </span>hashing_internals::check_seeds;</div>
<div class="line"><a id="l00484" name="l00484"></a><span class="lineno"> 484</span><span class="keyword">using </span>hashing_internals::get_blocks;</div>
<div class="line"><a id="l00485" name="l00485"></a><span class="lineno"> 485</span><span class="keyword">using </span>hashing_internals::ntmsm64;</div>
<div class="line"><a id="l00486" name="l00486"></a><span class="lineno"> 486</span><span class="keyword">using </span>hashing_internals::ntmsm64l;</div>
<div class="line"><a id="l00487" name="l00487"></a><span class="lineno"> 487</span><span class="keyword">using </span>hashing_internals::parsed_seeds_to_blocks;</div>
<div class="line"><a id="l00488" name="l00488"></a><span class="lineno"> 488</span><span class="keyword">using </span>hashing_internals::SEED_N;</div>
<div class="line"><a id="l00489" name="l00489"></a><span class="lineno"> 489</span><span class="keyword">using </span>hashing_internals::SEED_TAB;</div>
<div class="line"><a id="l00490" name="l00490"></a><span class="lineno"> 490</span> </div>
<div class="line"><a id="l00495" name="l00495"></a><span class="lineno"> 495</span><span class="keyword">inline</span> std::vector<std::vector<unsigned>></div>
<div class="foldopen" id="foldopen00496" data-start="{" data-end="}">
<div class="line"><a id="l00496" name="l00496"></a><span class="lineno"><a class="line" href="namespacebtllib.html#ac954d7c54d302d9f285beb797dbe84a5"> 496</a></span><a class="code hl_function" href="namespacebtllib.html#ac954d7c54d302d9f285beb797dbe84a5">parse_seeds</a>(<span class="keyword">const</span> std::vector<std::string>& seed_strings)</div>
<div class="line"><a id="l00497" name="l00497"></a><span class="lineno"> 497</span>{</div>
<div class="line"><a id="l00498" name="l00498"></a><span class="lineno"> 498</span> std::vector<std::vector<unsigned>> seed_set;</div>
<div class="line"><a id="l00499" name="l00499"></a><span class="lineno"> 499</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& seed_string : seed_strings) {</div>
<div class="line"><a id="l00500" name="l00500"></a><span class="lineno"> 500</span> std::vector<unsigned> seed;</div>
<div class="line"><a id="l00501" name="l00501"></a><span class="lineno"> 501</span> <span class="keywordtype">size_t</span> pos = 0;</div>
<div class="line"><a id="l00502" name="l00502"></a><span class="lineno"> 502</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& c : seed_string) {</div>
<div class="line"><a id="l00503" name="l00503"></a><span class="lineno"> 503</span> <span class="keywordflow">if</span> (c != <span class="charliteral">'1'</span>) {</div>
<div class="line"><a id="l00504" name="l00504"></a><span class="lineno"> 504</span> seed.push_back(pos);</div>
<div class="line"><a id="l00505" name="l00505"></a><span class="lineno"> 505</span> }</div>
<div class="line"><a id="l00506" name="l00506"></a><span class="lineno"> 506</span> ++pos;</div>
<div class="line"><a id="l00507" name="l00507"></a><span class="lineno"> 507</span> }</div>
<div class="line"><a id="l00508" name="l00508"></a><span class="lineno"> 508</span> seed_set.push_back(seed);</div>
<div class="line"><a id="l00509" name="l00509"></a><span class="lineno"> 509</span> }</div>
<div class="line"><a id="l00510" name="l00510"></a><span class="lineno"> 510</span> <span class="keywordflow">return</span> seed_set;</div>
<div class="line"><a id="l00511" name="l00511"></a><span class="lineno"> 511</span>}</div>
</div>
<div class="line"><a id="l00512" name="l00512"></a><span class="lineno"> 512</span> </div>
<div class="foldopen" id="foldopen00516" data-start="{" data-end="};">
<div class="line"><a id="l00516" name="l00516"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html"> 516</a></span><span class="keyword">class </span><a class="code hl_class" href="classbtllib_1_1SeedNtHash.html">SeedNtHash</a></div>
<div class="line"><a id="l00517" name="l00517"></a><span class="lineno"> 517</span>{</div>
<div class="line"><a id="l00518" name="l00518"></a><span class="lineno"> 518</span> </div>
<div class="line"><a id="l00519" name="l00519"></a><span class="lineno"> 519</span><span class="keyword">public</span>:</div>
<div class="foldopen" id="foldopen00530" data-start="{" data-end="}">
<div class="line"><a id="l00530" name="l00530"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#adc6e950dac4dbdd41190f1e1159c27a8"> 530</a></span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#adc6e950dac4dbdd41190f1e1159c27a8">SeedNtHash</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* seq,</div>
<div class="line"><a id="l00531" name="l00531"></a><span class="lineno"> 531</span> <span class="keywordtype">size_t</span> seq_len,</div>
<div class="line"><a id="l00532" name="l00532"></a><span class="lineno"> 532</span> <span class="keyword">const</span> std::vector<std::string>& seeds,</div>
<div class="line"><a id="l00533" name="l00533"></a><span class="lineno"> 533</span> hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed,</div>
<div class="line"><a id="l00534" name="l00534"></a><span class="lineno"> 534</span> hashing_internals::K_TYPE k,</div>
<div class="line"><a id="l00535" name="l00535"></a><span class="lineno"> 535</span> <span class="keywordtype">size_t</span> pos = 0)</div>
<div class="line"><a id="l00536" name="l00536"></a><span class="lineno"> 536</span> : seq(seq)</div>
<div class="line"><a id="l00537" name="l00537"></a><span class="lineno"> 537</span> , seq_len(seq_len)</div>
<div class="line"><a id="l00538" name="l00538"></a><span class="lineno"> 538</span> , num_hashes_per_seed(num_hashes_per_seed)</div>
<div class="line"><a id="l00539" name="l00539"></a><span class="lineno"> 539</span> , k(k)</div>
<div class="line"><a id="l00540" name="l00540"></a><span class="lineno"> 540</span> , pos(pos)</div>
<div class="line"><a id="l00541" name="l00541"></a><span class="lineno"> 541</span> , initialized(false)</div>
<div class="line"><a id="l00542" name="l00542"></a><span class="lineno"> 542</span> , fwd_hash_nomonos(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00543" name="l00543"></a><span class="lineno"> 543</span> , rev_hash_nomonos(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00544" name="l00544"></a><span class="lineno"> 544</span> , fwd_hash(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00545" name="l00545"></a><span class="lineno"> 545</span> , rev_hash(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00546" name="l00546"></a><span class="lineno"> 546</span> , hash_arr(new uint64_t[num_hashes_per_seed * seeds.size()])</div>
<div class="line"><a id="l00547" name="l00547"></a><span class="lineno"> 547</span> {</div>
<div class="line"><a id="l00548" name="l00548"></a><span class="lineno"> 548</span> check_seeds(seeds, k);</div>
<div class="line"><a id="l00549" name="l00549"></a><span class="lineno"> 549</span> <a class="code hl_function" href="namespacebtllib.html#a540bce0213b7718e519ddc4466361bf7">check_error</a>(seeds[0].size() != k,</div>
<div class="line"><a id="l00550" name="l00550"></a><span class="lineno"> 550</span> <span class="stringliteral">"SeedNtHash: k should be equal to seed string lengths"</span>);</div>
<div class="line"><a id="l00551" name="l00551"></a><span class="lineno"> 551</span> get_blocks(seeds, blocks, monomers);</div>
<div class="line"><a id="l00552" name="l00552"></a><span class="lineno"> 552</span> }</div>
</div>
<div class="line"><a id="l00553" name="l00553"></a><span class="lineno"> 553</span> </div>
<div class="foldopen" id="foldopen00563" data-start="{" data-end="}">
<div class="line"><a id="l00563" name="l00563"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#a650de4cf7e6ed95ee9dead6e23171d44"> 563</a></span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a650de4cf7e6ed95ee9dead6e23171d44">SeedNtHash</a>(<span class="keyword">const</span> std::string& seq,</div>
<div class="line"><a id="l00564" name="l00564"></a><span class="lineno"> 564</span> <span class="keyword">const</span> std::vector<std::string>& seeds,</div>
<div class="line"><a id="l00565" name="l00565"></a><span class="lineno"> 565</span> hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed,</div>
<div class="line"><a id="l00566" name="l00566"></a><span class="lineno"> 566</span> hashing_internals::K_TYPE k,</div>
<div class="line"><a id="l00567" name="l00567"></a><span class="lineno"> 567</span> <span class="keywordtype">size_t</span> pos = 0)</div>
<div class="line"><a id="l00568" name="l00568"></a><span class="lineno"> 568</span> : <a class="code hl_class" href="classbtllib_1_1SeedNtHash.html">SeedNtHash</a>(seq.data(), seq.size(), seeds, num_hashes_per_seed, k, pos)</div>
<div class="line"><a id="l00569" name="l00569"></a><span class="lineno"> 569</span> {</div>
<div class="line"><a id="l00570" name="l00570"></a><span class="lineno"> 570</span> }</div>
</div>
<div class="line"><a id="l00571" name="l00571"></a><span class="lineno"> 571</span> </div>
<div class="foldopen" id="foldopen00582" data-start="{" data-end="}">
<div class="line"><a id="l00582" name="l00582"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#a8148bacf86867fb48d4bb61a61e505cb"> 582</a></span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a8148bacf86867fb48d4bb61a61e505cb">SeedNtHash</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* seq,</div>
<div class="line"><a id="l00583" name="l00583"></a><span class="lineno"> 583</span> <span class="keywordtype">size_t</span> seq_len,</div>
<div class="line"><a id="l00584" name="l00584"></a><span class="lineno"> 584</span> <span class="keyword">const</span> std::vector<std::vector<unsigned>>& seeds,</div>
<div class="line"><a id="l00585" name="l00585"></a><span class="lineno"> 585</span> hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed,</div>
<div class="line"><a id="l00586" name="l00586"></a><span class="lineno"> 586</span> hashing_internals::K_TYPE k,</div>
<div class="line"><a id="l00587" name="l00587"></a><span class="lineno"> 587</span> <span class="keywordtype">size_t</span> pos = 0)</div>
<div class="line"><a id="l00588" name="l00588"></a><span class="lineno"> 588</span> : seq(seq)</div>
<div class="line"><a id="l00589" name="l00589"></a><span class="lineno"> 589</span> , seq_len(seq_len)</div>
<div class="line"><a id="l00590" name="l00590"></a><span class="lineno"> 590</span> , num_hashes_per_seed(num_hashes_per_seed)</div>
<div class="line"><a id="l00591" name="l00591"></a><span class="lineno"> 591</span> , k(k)</div>
<div class="line"><a id="l00592" name="l00592"></a><span class="lineno"> 592</span> , pos(pos)</div>
<div class="line"><a id="l00593" name="l00593"></a><span class="lineno"> 593</span> , initialized(false)</div>
<div class="line"><a id="l00594" name="l00594"></a><span class="lineno"> 594</span> , fwd_hash_nomonos(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00595" name="l00595"></a><span class="lineno"> 595</span> , rev_hash_nomonos(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00596" name="l00596"></a><span class="lineno"> 596</span> , fwd_hash(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00597" name="l00597"></a><span class="lineno"> 597</span> , rev_hash(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00598" name="l00598"></a><span class="lineno"> 598</span> , hash_arr(new uint64_t[num_hashes_per_seed * seeds.size()])</div>
<div class="line"><a id="l00599" name="l00599"></a><span class="lineno"> 599</span> {</div>
<div class="line"><a id="l00600" name="l00600"></a><span class="lineno"> 600</span> parsed_seeds_to_blocks(seeds, k, blocks, monomers);</div>
<div class="line"><a id="l00601" name="l00601"></a><span class="lineno"> 601</span> }</div>
</div>
<div class="line"><a id="l00602" name="l00602"></a><span class="lineno"> 602</span> </div>
<div class="foldopen" id="foldopen00612" data-start="{" data-end="}">
<div class="line"><a id="l00612" name="l00612"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#a876aa5a1a091d61b9155adaae7a0d889"> 612</a></span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a876aa5a1a091d61b9155adaae7a0d889">SeedNtHash</a>(<span class="keyword">const</span> std::string& seq,</div>
<div class="line"><a id="l00613" name="l00613"></a><span class="lineno"> 613</span> <span class="keyword">const</span> std::vector<std::vector<unsigned>>& seeds,</div>
<div class="line"><a id="l00614" name="l00614"></a><span class="lineno"> 614</span> hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed,</div>
<div class="line"><a id="l00615" name="l00615"></a><span class="lineno"> 615</span> hashing_internals::K_TYPE k,</div>
<div class="line"><a id="l00616" name="l00616"></a><span class="lineno"> 616</span> <span class="keywordtype">size_t</span> pos = 0)</div>
<div class="line"><a id="l00617" name="l00617"></a><span class="lineno"> 617</span> : <a class="code hl_class" href="classbtllib_1_1SeedNtHash.html">SeedNtHash</a>(seq.data(), seq.size(), seeds, num_hashes_per_seed, k, pos)</div>
<div class="line"><a id="l00618" name="l00618"></a><span class="lineno"> 618</span> {</div>
<div class="line"><a id="l00619" name="l00619"></a><span class="lineno"> 619</span> }</div>
</div>
<div class="line"><a id="l00620" name="l00620"></a><span class="lineno"> 620</span> </div>
<div class="line"><a id="l00621" name="l00621"></a><span class="lineno"> 621</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#adc6e950dac4dbdd41190f1e1159c27a8">SeedNtHash</a>(<span class="keyword">const</span> <a class="code hl_class" href="classbtllib_1_1SeedNtHash.html">SeedNtHash</a>& obj)</div>
<div class="line"><a id="l00622" name="l00622"></a><span class="lineno"> 622</span> : seq(obj.seq)</div>
<div class="line"><a id="l00623" name="l00623"></a><span class="lineno"> 623</span> , seq_len(obj.seq_len)</div>
<div class="line"><a id="l00624" name="l00624"></a><span class="lineno"> 624</span> , num_hashes_per_seed(obj.num_hashes_per_seed)</div>
<div class="line"><a id="l00625" name="l00625"></a><span class="lineno"> 625</span> , k(obj.k)</div>
<div class="line"><a id="l00626" name="l00626"></a><span class="lineno"> 626</span> , pos(obj.pos)</div>
<div class="line"><a id="l00627" name="l00627"></a><span class="lineno"> 627</span> , initialized(obj.initialized)</div>
<div class="line"><a id="l00628" name="l00628"></a><span class="lineno"> 628</span> , blocks(obj.blocks)</div>
<div class="line"><a id="l00629" name="l00629"></a><span class="lineno"> 629</span> , monomers(obj.monomers)</div>
<div class="line"><a id="l00630" name="l00630"></a><span class="lineno"> 630</span> , fwd_hash_nomonos(new uint64_t[obj.blocks.size()])</div>
<div class="line"><a id="l00631" name="l00631"></a><span class="lineno"> 631</span> , rev_hash_nomonos(new uint64_t[obj.blocks.size()])</div>
<div class="line"><a id="l00632" name="l00632"></a><span class="lineno"> 632</span> , fwd_hash(new uint64_t[obj.blocks.size()])</div>
<div class="line"><a id="l00633" name="l00633"></a><span class="lineno"> 633</span> , rev_hash(new uint64_t[obj.blocks.size()])</div>
<div class="line"><a id="l00634" name="l00634"></a><span class="lineno"> 634</span> , hash_arr(new uint64_t[obj.num_hashes_per_seed * obj.blocks.size()])</div>
<div class="line"><a id="l00635" name="l00635"></a><span class="lineno"> 635</span> {</div>
<div class="line"><a id="l00636" name="l00636"></a><span class="lineno"> 636</span> std::memcpy(fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l00637" name="l00637"></a><span class="lineno"> 637</span> obj.fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l00638" name="l00638"></a><span class="lineno"> 638</span> obj.blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00639" name="l00639"></a><span class="lineno"> 639</span> std::memcpy(rev_hash_nomonos.get(),</div>
<div class="line"><a id="l00640" name="l00640"></a><span class="lineno"> 640</span> obj.rev_hash_nomonos.get(),</div>
<div class="line"><a id="l00641" name="l00641"></a><span class="lineno"> 641</span> obj.blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00642" name="l00642"></a><span class="lineno"> 642</span> std::memcpy(</div>
<div class="line"><a id="l00643" name="l00643"></a><span class="lineno"> 643</span> fwd_hash.get(), obj.fwd_hash.get(), obj.blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00644" name="l00644"></a><span class="lineno"> 644</span> std::memcpy(</div>
<div class="line"><a id="l00645" name="l00645"></a><span class="lineno"> 645</span> rev_hash.get(), obj.rev_hash.get(), obj.blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00646" name="l00646"></a><span class="lineno"> 646</span> std::memcpy(hash_arr.get(),</div>
<div class="line"><a id="l00647" name="l00647"></a><span class="lineno"> 647</span> obj.hash_arr.get(),</div>
<div class="line"><a id="l00648" name="l00648"></a><span class="lineno"> 648</span> obj.num_hashes_per_seed * obj.blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00649" name="l00649"></a><span class="lineno"> 649</span> }</div>
<div class="line"><a id="l00650" name="l00650"></a><span class="lineno"> 650</span> </div>
<div class="line"><a id="l00651" name="l00651"></a><span class="lineno"> 651</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#adc6e950dac4dbdd41190f1e1159c27a8">SeedNtHash</a>(<a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#adc6e950dac4dbdd41190f1e1159c27a8">SeedNtHash</a>&&) = <span class="keywordflow">default</span>;</div>
<div class="line"><a id="l00652" name="l00652"></a><span class="lineno"> 652</span> </div>
<div class="foldopen" id="foldopen00658" data-start="{" data-end="}">
<div class="line"><a id="l00658" name="l00658"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#aa817b8acaf7c57d7be8ce47fcf5ac758"> 658</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#aa817b8acaf7c57d7be8ce47fcf5ac758">roll</a>()</div>
<div class="line"><a id="l00659" name="l00659"></a><span class="lineno"> 659</span> {</div>
<div class="line"><a id="l00660" name="l00660"></a><span class="lineno"> 660</span> <span class="keywordflow">if</span> (!initialized) {</div>
<div class="line"><a id="l00661" name="l00661"></a><span class="lineno"> 661</span> <span class="keywordflow">return</span> init();</div>
<div class="line"><a id="l00662" name="l00662"></a><span class="lineno"> 662</span> }</div>
<div class="line"><a id="l00663" name="l00663"></a><span class="lineno"> 663</span> <span class="keywordflow">if</span> (pos >= seq_len - k) {</div>
<div class="line"><a id="l00664" name="l00664"></a><span class="lineno"> 664</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00665" name="l00665"></a><span class="lineno"> 665</span> }</div>
<div class="line"><a id="l00666" name="l00666"></a><span class="lineno"> 666</span> <span class="keywordflow">if</span> (SEED_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)seq[pos + k]] == SEED_N) {</div>
<div class="line"><a id="l00667" name="l00667"></a><span class="lineno"> 667</span> pos += k;</div>
<div class="line"><a id="l00668" name="l00668"></a><span class="lineno"> 668</span> <span class="keywordflow">return</span> init();</div>
<div class="line"><a id="l00669" name="l00669"></a><span class="lineno"> 669</span> }</div>
<div class="line"><a id="l00670" name="l00670"></a><span class="lineno"> 670</span> ntmsm64(seq + pos,</div>
<div class="line"><a id="l00671" name="l00671"></a><span class="lineno"> 671</span> blocks,</div>
<div class="line"><a id="l00672" name="l00672"></a><span class="lineno"> 672</span> monomers,</div>
<div class="line"><a id="l00673" name="l00673"></a><span class="lineno"> 673</span> k,</div>
<div class="line"><a id="l00674" name="l00674"></a><span class="lineno"> 674</span> blocks.size(),</div>
<div class="line"><a id="l00675" name="l00675"></a><span class="lineno"> 675</span> num_hashes_per_seed,</div>
<div class="line"><a id="l00676" name="l00676"></a><span class="lineno"> 676</span> fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l00677" name="l00677"></a><span class="lineno"> 677</span> rev_hash_nomonos.get(),</div>
<div class="line"><a id="l00678" name="l00678"></a><span class="lineno"> 678</span> fwd_hash.get(),</div>
<div class="line"><a id="l00679" name="l00679"></a><span class="lineno"> 679</span> rev_hash.get(),</div>
<div class="line"><a id="l00680" name="l00680"></a><span class="lineno"> 680</span> hash_arr.get());</div>
<div class="line"><a id="l00681" name="l00681"></a><span class="lineno"> 681</span> ++pos;</div>
<div class="line"><a id="l00682" name="l00682"></a><span class="lineno"> 682</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00683" name="l00683"></a><span class="lineno"> 683</span> }</div>
</div>
<div class="line"><a id="l00684" name="l00684"></a><span class="lineno"> 684</span> </div>
<div class="foldopen" id="foldopen00689" data-start="{" data-end="}">
<div class="line"><a id="l00689" name="l00689"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#a293e694de84eafbb19bf7123749f9ba6"> 689</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a293e694de84eafbb19bf7123749f9ba6">roll_back</a>()</div>
<div class="line"><a id="l00690" name="l00690"></a><span class="lineno"> 690</span> {</div>
<div class="line"><a id="l00691" name="l00691"></a><span class="lineno"> 691</span> <span class="keywordflow">if</span> (!initialized) {</div>
<div class="line"><a id="l00692" name="l00692"></a><span class="lineno"> 692</span> <span class="keywordflow">return</span> init();</div>
<div class="line"><a id="l00693" name="l00693"></a><span class="lineno"> 693</span> }</div>
<div class="line"><a id="l00694" name="l00694"></a><span class="lineno"> 694</span> <span class="keywordflow">if</span> (pos == 0) {</div>
<div class="line"><a id="l00695" name="l00695"></a><span class="lineno"> 695</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00696" name="l00696"></a><span class="lineno"> 696</span> }</div>
<div class="line"><a id="l00697" name="l00697"></a><span class="lineno"> 697</span> <span class="keywordflow">if</span> (SEED_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)seq[pos - 1]] == SEED_N && pos >= k) {</div>
<div class="line"><a id="l00698" name="l00698"></a><span class="lineno"> 698</span> pos -= k;</div>
<div class="line"><a id="l00699" name="l00699"></a><span class="lineno"> 699</span> <span class="keywordflow">return</span> init();</div>
<div class="line"><a id="l00700" name="l00700"></a><span class="lineno"> 700</span> }</div>
<div class="line"><a id="l00701" name="l00701"></a><span class="lineno"> 701</span> <span class="keywordflow">if</span> (SEED_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)seq[pos - 1]] == SEED_N) {</div>
<div class="line"><a id="l00702" name="l00702"></a><span class="lineno"> 702</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00703" name="l00703"></a><span class="lineno"> 703</span> }</div>
<div class="line"><a id="l00704" name="l00704"></a><span class="lineno"> 704</span> ntmsm64l(seq + pos - 1,</div>
<div class="line"><a id="l00705" name="l00705"></a><span class="lineno"> 705</span> blocks,</div>
<div class="line"><a id="l00706" name="l00706"></a><span class="lineno"> 706</span> monomers,</div>
<div class="line"><a id="l00707" name="l00707"></a><span class="lineno"> 707</span> k,</div>
<div class="line"><a id="l00708" name="l00708"></a><span class="lineno"> 708</span> blocks.size(),</div>
<div class="line"><a id="l00709" name="l00709"></a><span class="lineno"> 709</span> num_hashes_per_seed,</div>
<div class="line"><a id="l00710" name="l00710"></a><span class="lineno"> 710</span> fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l00711" name="l00711"></a><span class="lineno"> 711</span> rev_hash_nomonos.get(),</div>
<div class="line"><a id="l00712" name="l00712"></a><span class="lineno"> 712</span> fwd_hash.get(),</div>
<div class="line"><a id="l00713" name="l00713"></a><span class="lineno"> 713</span> rev_hash.get(),</div>
<div class="line"><a id="l00714" name="l00714"></a><span class="lineno"> 714</span> hash_arr.get());</div>
<div class="line"><a id="l00715" name="l00715"></a><span class="lineno"> 715</span> --pos;</div>
<div class="line"><a id="l00716" name="l00716"></a><span class="lineno"> 716</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00717" name="l00717"></a><span class="lineno"> 717</span> }</div>
</div>
<div class="line"><a id="l00718" name="l00718"></a><span class="lineno"> 718</span> </div>
<div class="foldopen" id="foldopen00724" data-start="{" data-end="}">
<div class="line"><a id="l00724" name="l00724"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#a9bbe1be0a6af592bc65fb5779f454029"> 724</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a9bbe1be0a6af592bc65fb5779f454029">peek</a>()</div>
<div class="line"><a id="l00725" name="l00725"></a><span class="lineno"> 725</span> {</div>
<div class="line"><a id="l00726" name="l00726"></a><span class="lineno"> 726</span> <span class="keywordflow">if</span> (pos >= seq_len - k) {</div>
<div class="line"><a id="l00727" name="l00727"></a><span class="lineno"> 727</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00728" name="l00728"></a><span class="lineno"> 728</span> }</div>
<div class="line"><a id="l00729" name="l00729"></a><span class="lineno"> 729</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a9bbe1be0a6af592bc65fb5779f454029">peek</a>(seq[pos + k]);</div>
<div class="line"><a id="l00730" name="l00730"></a><span class="lineno"> 730</span> }</div>
</div>
<div class="line"><a id="l00731" name="l00731"></a><span class="lineno"> 731</span> </div>
<div class="foldopen" id="foldopen00736" data-start="{" data-end="}">
<div class="line"><a id="l00736" name="l00736"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#a2db58d333504f97eaa807dbb4aaafc9d"> 736</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a2db58d333504f97eaa807dbb4aaafc9d">peek_back</a>()</div>
<div class="line"><a id="l00737" name="l00737"></a><span class="lineno"> 737</span> {</div>
<div class="line"><a id="l00738" name="l00738"></a><span class="lineno"> 738</span> <span class="keywordflow">if</span> (pos == 0) {</div>
<div class="line"><a id="l00739" name="l00739"></a><span class="lineno"> 739</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00740" name="l00740"></a><span class="lineno"> 740</span> }</div>
<div class="line"><a id="l00741" name="l00741"></a><span class="lineno"> 741</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a2db58d333504f97eaa807dbb4aaafc9d">peek_back</a>(seq[pos - 1]);</div>
<div class="line"><a id="l00742" name="l00742"></a><span class="lineno"> 742</span> }</div>
</div>
<div class="line"><a id="l00743" name="l00743"></a><span class="lineno"> 743</span> </div>
<div class="foldopen" id="foldopen00748" data-start="{" data-end="}">
<div class="line"><a id="l00748" name="l00748"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#abc4bcd67a4cb9b886665c07813d5b9e3"> 748</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#abc4bcd67a4cb9b886665c07813d5b9e3">peek</a>(<span class="keywordtype">char</span> char_in)</div>
<div class="line"><a id="l00749" name="l00749"></a><span class="lineno"> 749</span> {</div>
<div class="line"><a id="l00750" name="l00750"></a><span class="lineno"> 750</span> <span class="keywordflow">if</span> (!initialized) {</div>
<div class="line"><a id="l00751" name="l00751"></a><span class="lineno"> 751</span> <span class="keywordflow">return</span> init();</div>
<div class="line"><a id="l00752" name="l00752"></a><span class="lineno"> 752</span> }</div>
<div class="line"><a id="l00753" name="l00753"></a><span class="lineno"> 753</span> <span class="keyword">const</span> std::unique_ptr<uint64_t[]> fwd_hash_nomonos_cpy(</div>
<div class="line"><a id="l00754" name="l00754"></a><span class="lineno"> 754</span> <span class="keyword">new</span> uint64_t[blocks.size()]);</div>
<div class="line"><a id="l00755" name="l00755"></a><span class="lineno"> 755</span> <span class="keyword">const</span> std::unique_ptr<uint64_t[]> rev_hash_nomonos_cpy(</div>
<div class="line"><a id="l00756" name="l00756"></a><span class="lineno"> 756</span> <span class="keyword">new</span> uint64_t[blocks.size()]);</div>
<div class="line"><a id="l00757" name="l00757"></a><span class="lineno"> 757</span> <span class="keyword">const</span> std::unique_ptr<uint64_t[]> fwd_hash_cpy(<span class="keyword">new</span> uint64_t[blocks.size()]);</div>
<div class="line"><a id="l00758" name="l00758"></a><span class="lineno"> 758</span> <span class="keyword">const</span> std::unique_ptr<uint64_t[]> rev_hash_cpy(<span class="keyword">new</span> uint64_t[blocks.size()]);</div>
<div class="line"><a id="l00759" name="l00759"></a><span class="lineno"> 759</span> std::memcpy(fwd_hash_nomonos_cpy.get(),</div>
<div class="line"><a id="l00760" name="l00760"></a><span class="lineno"> 760</span> fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l00761" name="l00761"></a><span class="lineno"> 761</span> blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00762" name="l00762"></a><span class="lineno"> 762</span> std::memcpy(rev_hash_nomonos_cpy.get(),</div>
<div class="line"><a id="l00763" name="l00763"></a><span class="lineno"> 763</span> rev_hash_nomonos.get(),</div>
<div class="line"><a id="l00764" name="l00764"></a><span class="lineno"> 764</span> blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00765" name="l00765"></a><span class="lineno"> 765</span> std::memcpy(</div>
<div class="line"><a id="l00766" name="l00766"></a><span class="lineno"> 766</span> fwd_hash_cpy.get(), fwd_hash.get(), blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00767" name="l00767"></a><span class="lineno"> 767</span> std::memcpy(</div>
<div class="line"><a id="l00768" name="l00768"></a><span class="lineno"> 768</span> rev_hash_cpy.get(), rev_hash.get(), blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00769" name="l00769"></a><span class="lineno"> 769</span> ntmsm64(seq + pos,</div>
<div class="line"><a id="l00770" name="l00770"></a><span class="lineno"> 770</span> char_in,</div>
<div class="line"><a id="l00771" name="l00771"></a><span class="lineno"> 771</span> blocks,</div>
<div class="line"><a id="l00772" name="l00772"></a><span class="lineno"> 772</span> monomers,</div>
<div class="line"><a id="l00773" name="l00773"></a><span class="lineno"> 773</span> k,</div>
<div class="line"><a id="l00774" name="l00774"></a><span class="lineno"> 774</span> blocks.size(),</div>
<div class="line"><a id="l00775" name="l00775"></a><span class="lineno"> 775</span> num_hashes_per_seed,</div>
<div class="line"><a id="l00776" name="l00776"></a><span class="lineno"> 776</span> fwd_hash_nomonos_cpy.get(),</div>
<div class="line"><a id="l00777" name="l00777"></a><span class="lineno"> 777</span> rev_hash_nomonos_cpy.get(),</div>
<div class="line"><a id="l00778" name="l00778"></a><span class="lineno"> 778</span> fwd_hash_cpy.get(),</div>
<div class="line"><a id="l00779" name="l00779"></a><span class="lineno"> 779</span> rev_hash_cpy.get(),</div>
<div class="line"><a id="l00780" name="l00780"></a><span class="lineno"> 780</span> hash_arr.get());</div>
<div class="line"><a id="l00781" name="l00781"></a><span class="lineno"> 781</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00782" name="l00782"></a><span class="lineno"> 782</span> }</div>
</div>
<div class="line"><a id="l00783" name="l00783"></a><span class="lineno"> 783</span> </div>
<div class="foldopen" id="foldopen00788" data-start="{" data-end="}">
<div class="line"><a id="l00788" name="l00788"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#a0e8786dd693fd7da8ab6ffdfb5d39e1a"> 788</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a0e8786dd693fd7da8ab6ffdfb5d39e1a">peek_back</a>(<span class="keywordtype">char</span> char_in)</div>
<div class="line"><a id="l00789" name="l00789"></a><span class="lineno"> 789</span> {</div>
<div class="line"><a id="l00790" name="l00790"></a><span class="lineno"> 790</span> <span class="keywordflow">if</span> (!initialized) {</div>
<div class="line"><a id="l00791" name="l00791"></a><span class="lineno"> 791</span> <span class="keywordflow">return</span> init();</div>
<div class="line"><a id="l00792" name="l00792"></a><span class="lineno"> 792</span> }</div>
<div class="line"><a id="l00793" name="l00793"></a><span class="lineno"> 793</span> <span class="keyword">const</span> std::unique_ptr<uint64_t[]> fwd_hash_nomonos_cpy(</div>
<div class="line"><a id="l00794" name="l00794"></a><span class="lineno"> 794</span> <span class="keyword">new</span> uint64_t[blocks.size()]);</div>
<div class="line"><a id="l00795" name="l00795"></a><span class="lineno"> 795</span> <span class="keyword">const</span> std::unique_ptr<uint64_t[]> rev_hash_nomonos_cpy(</div>
<div class="line"><a id="l00796" name="l00796"></a><span class="lineno"> 796</span> <span class="keyword">new</span> uint64_t[blocks.size()]);</div>
<div class="line"><a id="l00797" name="l00797"></a><span class="lineno"> 797</span> <span class="keyword">const</span> std::unique_ptr<uint64_t[]> fwd_hash_cpy(<span class="keyword">new</span> uint64_t[blocks.size()]);</div>
<div class="line"><a id="l00798" name="l00798"></a><span class="lineno"> 798</span> <span class="keyword">const</span> std::unique_ptr<uint64_t[]> rev_hash_cpy(<span class="keyword">new</span> uint64_t[blocks.size()]);</div>
<div class="line"><a id="l00799" name="l00799"></a><span class="lineno"> 799</span> std::memcpy(fwd_hash_nomonos_cpy.get(),</div>
<div class="line"><a id="l00800" name="l00800"></a><span class="lineno"> 800</span> fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l00801" name="l00801"></a><span class="lineno"> 801</span> blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00802" name="l00802"></a><span class="lineno"> 802</span> std::memcpy(rev_hash_nomonos_cpy.get(),</div>
<div class="line"><a id="l00803" name="l00803"></a><span class="lineno"> 803</span> rev_hash_nomonos.get(),</div>
<div class="line"><a id="l00804" name="l00804"></a><span class="lineno"> 804</span> blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00805" name="l00805"></a><span class="lineno"> 805</span> std::memcpy(</div>
<div class="line"><a id="l00806" name="l00806"></a><span class="lineno"> 806</span> fwd_hash_cpy.get(), fwd_hash.get(), blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00807" name="l00807"></a><span class="lineno"> 807</span> std::memcpy(</div>
<div class="line"><a id="l00808" name="l00808"></a><span class="lineno"> 808</span> rev_hash_cpy.get(), rev_hash.get(), blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00809" name="l00809"></a><span class="lineno"> 809</span> ntmsm64l(seq + pos - 1,</div>
<div class="line"><a id="l00810" name="l00810"></a><span class="lineno"> 810</span> char_in,</div>
<div class="line"><a id="l00811" name="l00811"></a><span class="lineno"> 811</span> blocks,</div>
<div class="line"><a id="l00812" name="l00812"></a><span class="lineno"> 812</span> monomers,</div>
<div class="line"><a id="l00813" name="l00813"></a><span class="lineno"> 813</span> k,</div>
<div class="line"><a id="l00814" name="l00814"></a><span class="lineno"> 814</span> blocks.size(),</div>
<div class="line"><a id="l00815" name="l00815"></a><span class="lineno"> 815</span> num_hashes_per_seed,</div>
<div class="line"><a id="l00816" name="l00816"></a><span class="lineno"> 816</span> fwd_hash_nomonos_cpy.get(),</div>
<div class="line"><a id="l00817" name="l00817"></a><span class="lineno"> 817</span> rev_hash_nomonos_cpy.get(),</div>
<div class="line"><a id="l00818" name="l00818"></a><span class="lineno"> 818</span> fwd_hash_cpy.get(),</div>
<div class="line"><a id="l00819" name="l00819"></a><span class="lineno"> 819</span> rev_hash_cpy.get(),</div>
<div class="line"><a id="l00820" name="l00820"></a><span class="lineno"> 820</span> hash_arr.get());</div>
<div class="line"><a id="l00821" name="l00821"></a><span class="lineno"> 821</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00822" name="l00822"></a><span class="lineno"> 822</span> }</div>
</div>
<div class="line"><a id="l00823" name="l00823"></a><span class="lineno"> 823</span> </div>
<div class="line"><a id="l00828" name="l00828"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#ae28265c1630d54925a22b94d01dec9db"> 828</a></span> <span class="keyword">const</span> uint64_t* <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#ae28265c1630d54925a22b94d01dec9db">hashes</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> hash_arr.get(); }</div>
<div class="line"><a id="l00829" name="l00829"></a><span class="lineno"> 829</span> </div>
<div class="line"><a id="l00835" name="l00835"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#a4931b3de033fadd4472bd934a44c5eaa"> 835</a></span> <span class="keywordtype">size_t</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a4931b3de033fadd4472bd934a44c5eaa">get_pos</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> pos; }</div>
<div class="line"><a id="l00836" name="l00836"></a><span class="lineno"> 836</span> </div>
<div class="line"><a id="l00841" name="l00841"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#aafce9763427d377cd416880d1450cf9f"> 841</a></span> <span class="keywordtype">unsigned</span> <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#aafce9763427d377cd416880d1450cf9f">get_hash_num</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> num_hashes_per_seed * blocks.size(); }</div>
<div class="line"><a id="l00842" name="l00842"></a><span class="lineno"> 842</span> </div>
<div class="foldopen" id="foldopen00847" data-start="{" data-end="}">
<div class="line"><a id="l00847" name="l00847"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#ae992f944f85fb16b4956e74c7ccbe9e4"> 847</a></span> hashing_internals::NUM_HASHES_TYPE <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#ae992f944f85fb16b4956e74c7ccbe9e4">get_hash_num_per_seed</a>()<span class="keyword"> const</span></div>
<div class="line"><a id="l00848" name="l00848"></a><span class="lineno"> 848</span><span class="keyword"> </span>{</div>
<div class="line"><a id="l00849" name="l00849"></a><span class="lineno"> 849</span> <span class="keywordflow">return</span> num_hashes_per_seed;</div>
<div class="line"><a id="l00850" name="l00850"></a><span class="lineno"> 850</span> }</div>
</div>
<div class="line"><a id="l00851" name="l00851"></a><span class="lineno"> 851</span> </div>
<div class="line"><a id="l00856" name="l00856"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#ae18f9d65b17ccaa9457167ead16d4d75"> 856</a></span> hashing_internals::K_TYPE <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#ae18f9d65b17ccaa9457167ead16d4d75">get_k</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> k; }</div>
<div class="line"><a id="l00857" name="l00857"></a><span class="lineno"> 857</span> </div>
<div class="line"><a id="l00862" name="l00862"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#a1eb3ee60193f3303309c794150192ec0"> 862</a></span> uint64_t* <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a1eb3ee60193f3303309c794150192ec0">get_forward_hash</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> fwd_hash.get(); }</div>
<div class="line"><a id="l00863" name="l00863"></a><span class="lineno"> 863</span> </div>
<div class="line"><a id="l00868" name="l00868"></a><span class="lineno"><a class="line" href="classbtllib_1_1SeedNtHash.html#a2aec9116c2544ac084fbafedd30ece41"> 868</a></span> uint64_t* <a class="code hl_function" href="classbtllib_1_1SeedNtHash.html#a2aec9116c2544ac084fbafedd30ece41">get_reverse_hash</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> rev_hash.get(); }</div>
<div class="line"><a id="l00869" name="l00869"></a><span class="lineno"> 869</span> </div>
<div class="line"><a id="l00870" name="l00870"></a><span class="lineno"> 870</span><span class="keyword">private</span>:</div>
<div class="line"><a id="l00871" name="l00871"></a><span class="lineno"> 871</span> <span class="keyword">const</span> <span class="keywordtype">char</span>* seq;</div>
<div class="line"><a id="l00872" name="l00872"></a><span class="lineno"> 872</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> seq_len;</div>
<div class="line"><a id="l00873" name="l00873"></a><span class="lineno"> 873</span> hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed;</div>
<div class="line"><a id="l00874" name="l00874"></a><span class="lineno"> 874</span> hashing_internals::K_TYPE k;</div>
<div class="line"><a id="l00875" name="l00875"></a><span class="lineno"> 875</span> <span class="keywordtype">size_t</span> pos;</div>
<div class="line"><a id="l00876" name="l00876"></a><span class="lineno"> 876</span> <span class="keywordtype">bool</span> initialized;</div>
<div class="line"><a id="l00877" name="l00877"></a><span class="lineno"> 877</span> std::vector<hashing_internals::SpacedSeedBlocks> blocks;</div>
<div class="line"><a id="l00878" name="l00878"></a><span class="lineno"> 878</span> std::vector<hashing_internals::SpacedSeedMonomers> monomers;</div>
<div class="line"><a id="l00879" name="l00879"></a><span class="lineno"> 879</span> std::unique_ptr<uint64_t[]> fwd_hash_nomonos;</div>
<div class="line"><a id="l00880" name="l00880"></a><span class="lineno"> 880</span> std::unique_ptr<uint64_t[]> rev_hash_nomonos;</div>
<div class="line"><a id="l00881" name="l00881"></a><span class="lineno"> 881</span> std::unique_ptr<uint64_t[]> fwd_hash;</div>
<div class="line"><a id="l00882" name="l00882"></a><span class="lineno"> 882</span> std::unique_ptr<uint64_t[]> rev_hash;</div>
<div class="line"><a id="l00883" name="l00883"></a><span class="lineno"> 883</span> std::unique_ptr<uint64_t[]> hash_arr;</div>
<div class="line"><a id="l00884" name="l00884"></a><span class="lineno"> 884</span> </div>
<div class="line"><a id="l00889" name="l00889"></a><span class="lineno"> 889</span> <span class="keywordtype">bool</span> init()</div>
<div class="line"><a id="l00890" name="l00890"></a><span class="lineno"> 890</span> {</div>
<div class="line"><a id="l00891" name="l00891"></a><span class="lineno"> 891</span> <span class="keywordtype">unsigned</span> pos_n = 0;</div>
<div class="line"><a id="l00892" name="l00892"></a><span class="lineno"> 892</span> <span class="keywordflow">while</span> (pos < seq_len - k + 1 && !ntmsm64(seq + pos,</div>
<div class="line"><a id="l00893" name="l00893"></a><span class="lineno"> 893</span> blocks,</div>
<div class="line"><a id="l00894" name="l00894"></a><span class="lineno"> 894</span> monomers,</div>
<div class="line"><a id="l00895" name="l00895"></a><span class="lineno"> 895</span> k,</div>
<div class="line"><a id="l00896" name="l00896"></a><span class="lineno"> 896</span> blocks.size(),</div>
<div class="line"><a id="l00897" name="l00897"></a><span class="lineno"> 897</span> num_hashes_per_seed,</div>
<div class="line"><a id="l00898" name="l00898"></a><span class="lineno"> 898</span> fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l00899" name="l00899"></a><span class="lineno"> 899</span> rev_hash_nomonos.get(),</div>
<div class="line"><a id="l00900" name="l00900"></a><span class="lineno"> 900</span> fwd_hash.get(),</div>
<div class="line"><a id="l00901" name="l00901"></a><span class="lineno"> 901</span> rev_hash.get(),</div>
<div class="line"><a id="l00902" name="l00902"></a><span class="lineno"> 902</span> pos_n,</div>
<div class="line"><a id="l00903" name="l00903"></a><span class="lineno"> 903</span> hash_arr.get())) {</div>
<div class="line"><a id="l00904" name="l00904"></a><span class="lineno"> 904</span> pos += pos_n + 1;</div>
<div class="line"><a id="l00905" name="l00905"></a><span class="lineno"> 905</span> }</div>
<div class="line"><a id="l00906" name="l00906"></a><span class="lineno"> 906</span> <span class="keywordflow">if</span> (pos > seq_len - k) {</div>
<div class="line"><a id="l00907" name="l00907"></a><span class="lineno"> 907</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00908" name="l00908"></a><span class="lineno"> 908</span> }</div>
<div class="line"><a id="l00909" name="l00909"></a><span class="lineno"> 909</span> initialized = <span class="keyword">true</span>;</div>
<div class="line"><a id="l00910" name="l00910"></a><span class="lineno"> 910</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00911" name="l00911"></a><span class="lineno"> 911</span> }</div>
<div class="line"><a id="l00912" name="l00912"></a><span class="lineno"> 912</span>};</div>
</div>
<div class="line"><a id="l00913" name="l00913"></a><span class="lineno"> 913</span> </div>
<div class="foldopen" id="foldopen00918" data-start="{" data-end="};">
<div class="line"><a id="l00918" name="l00918"></a><span class="lineno"><a class="line" href="classbtllib_1_1BlindSeedNtHash.html"> 918</a></span><span class="keyword">class </span><a class="code hl_class" href="classbtllib_1_1BlindSeedNtHash.html">BlindSeedNtHash</a></div>
<div class="line"><a id="l00919" name="l00919"></a><span class="lineno"> 919</span>{</div>
<div class="line"><a id="l00920" name="l00920"></a><span class="lineno"> 920</span> </div>
<div class="line"><a id="l00921" name="l00921"></a><span class="lineno"> 921</span><span class="keyword">public</span>:</div>
<div class="foldopen" id="foldopen00932" data-start="{" data-end="}">
<div class="line"><a id="l00932" name="l00932"></a><span class="lineno"><a class="line" href="classbtllib_1_1BlindSeedNtHash.html#a18ddf0bb63594daca7bce886579bf4a3"> 932</a></span> <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#a18ddf0bb63594daca7bce886579bf4a3">BlindSeedNtHash</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* seq,</div>
<div class="line"><a id="l00933" name="l00933"></a><span class="lineno"> 933</span> <span class="keyword">const</span> std::vector<std::string>& seeds,</div>
<div class="line"><a id="l00934" name="l00934"></a><span class="lineno"> 934</span> hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed,</div>
<div class="line"><a id="l00935" name="l00935"></a><span class="lineno"> 935</span> hashing_internals::K_TYPE k,</div>
<div class="line"><a id="l00936" name="l00936"></a><span class="lineno"> 936</span> <span class="keywordtype">long</span> pos = 0)</div>
<div class="line"><a id="l00937" name="l00937"></a><span class="lineno"> 937</span> : seq(seq + pos, seq + pos + k)</div>
<div class="line"><a id="l00938" name="l00938"></a><span class="lineno"> 938</span> , num_hashes_per_seed(num_hashes_per_seed)</div>
<div class="line"><a id="l00939" name="l00939"></a><span class="lineno"> 939</span> , k(k)</div>
<div class="line"><a id="l00940" name="l00940"></a><span class="lineno"> 940</span> , pos(pos)</div>
<div class="line"><a id="l00941" name="l00941"></a><span class="lineno"> 941</span> , fwd_hash_nomonos(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00942" name="l00942"></a><span class="lineno"> 942</span> , rev_hash_nomonos(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00943" name="l00943"></a><span class="lineno"> 943</span> , fwd_hash(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00944" name="l00944"></a><span class="lineno"> 944</span> , rev_hash(new uint64_t[seeds.size()])</div>
<div class="line"><a id="l00945" name="l00945"></a><span class="lineno"> 945</span> , hash_arr(new uint64_t[num_hashes_per_seed * seeds.size()])</div>
<div class="line"><a id="l00946" name="l00946"></a><span class="lineno"> 946</span> {</div>
<div class="line"><a id="l00947" name="l00947"></a><span class="lineno"> 947</span> check_seeds(seeds, k);</div>
<div class="line"><a id="l00948" name="l00948"></a><span class="lineno"> 948</span> get_blocks(seeds, blocks, monomers);</div>
<div class="line"><a id="l00949" name="l00949"></a><span class="lineno"> 949</span> <span class="keywordtype">unsigned</span> pos_n = 0;</div>
<div class="line"><a id="l00950" name="l00950"></a><span class="lineno"> 950</span> ntmsm64(seq + pos,</div>
<div class="line"><a id="l00951" name="l00951"></a><span class="lineno"> 951</span> blocks,</div>
<div class="line"><a id="l00952" name="l00952"></a><span class="lineno"> 952</span> monomers,</div>
<div class="line"><a id="l00953" name="l00953"></a><span class="lineno"> 953</span> k,</div>
<div class="line"><a id="l00954" name="l00954"></a><span class="lineno"> 954</span> blocks.size(),</div>
<div class="line"><a id="l00955" name="l00955"></a><span class="lineno"> 955</span> num_hashes_per_seed,</div>
<div class="line"><a id="l00956" name="l00956"></a><span class="lineno"> 956</span> fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l00957" name="l00957"></a><span class="lineno"> 957</span> rev_hash_nomonos.get(),</div>
<div class="line"><a id="l00958" name="l00958"></a><span class="lineno"> 958</span> fwd_hash.get(),</div>
<div class="line"><a id="l00959" name="l00959"></a><span class="lineno"> 959</span> rev_hash.get(),</div>
<div class="line"><a id="l00960" name="l00960"></a><span class="lineno"> 960</span> pos_n,</div>
<div class="line"><a id="l00961" name="l00961"></a><span class="lineno"> 961</span> hash_arr.get());</div>
<div class="line"><a id="l00962" name="l00962"></a><span class="lineno"> 962</span> }</div>
</div>
<div class="line"><a id="l00963" name="l00963"></a><span class="lineno"> 963</span> </div>
<div class="line"><a id="l00964" name="l00964"></a><span class="lineno"> 964</span> <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#a18ddf0bb63594daca7bce886579bf4a3">BlindSeedNtHash</a>(<span class="keyword">const</span> <a class="code hl_class" href="classbtllib_1_1BlindSeedNtHash.html">BlindSeedNtHash</a>& seed_nthash)</div>
<div class="line"><a id="l00965" name="l00965"></a><span class="lineno"> 965</span> : seq(seed_nthash.seq)</div>
<div class="line"><a id="l00966" name="l00966"></a><span class="lineno"> 966</span> , num_hashes_per_seed(seed_nthash.num_hashes_per_seed)</div>
<div class="line"><a id="l00967" name="l00967"></a><span class="lineno"> 967</span> , k(seed_nthash.k)</div>
<div class="line"><a id="l00968" name="l00968"></a><span class="lineno"> 968</span> , pos(seed_nthash.pos)</div>
<div class="line"><a id="l00969" name="l00969"></a><span class="lineno"> 969</span> , blocks(seed_nthash.blocks)</div>
<div class="line"><a id="l00970" name="l00970"></a><span class="lineno"> 970</span> , monomers(seed_nthash.monomers)</div>
<div class="line"><a id="l00971" name="l00971"></a><span class="lineno"> 971</span> , fwd_hash_nomonos(new uint64_t[seed_nthash.blocks.size()])</div>
<div class="line"><a id="l00972" name="l00972"></a><span class="lineno"> 972</span> , rev_hash_nomonos(new uint64_t[seed_nthash.blocks.size()])</div>
<div class="line"><a id="l00973" name="l00973"></a><span class="lineno"> 973</span> , fwd_hash(new uint64_t[seed_nthash.blocks.size()])</div>
<div class="line"><a id="l00974" name="l00974"></a><span class="lineno"> 974</span> , rev_hash(new uint64_t[seed_nthash.blocks.size()])</div>
<div class="line"><a id="l00975" name="l00975"></a><span class="lineno"> 975</span> , hash_arr(new uint64_t[num_hashes_per_seed * seed_nthash.blocks.size()])</div>
<div class="line"><a id="l00976" name="l00976"></a><span class="lineno"> 976</span> {</div>
<div class="line"><a id="l00977" name="l00977"></a><span class="lineno"> 977</span> std::memcpy(fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l00978" name="l00978"></a><span class="lineno"> 978</span> seed_nthash.fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l00979" name="l00979"></a><span class="lineno"> 979</span> seed_nthash.blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00980" name="l00980"></a><span class="lineno"> 980</span> std::memcpy(rev_hash_nomonos.get(),</div>
<div class="line"><a id="l00981" name="l00981"></a><span class="lineno"> 981</span> seed_nthash.rev_hash_nomonos.get(),</div>
<div class="line"><a id="l00982" name="l00982"></a><span class="lineno"> 982</span> seed_nthash.blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00983" name="l00983"></a><span class="lineno"> 983</span> std::memcpy(fwd_hash.get(),</div>
<div class="line"><a id="l00984" name="l00984"></a><span class="lineno"> 984</span> seed_nthash.fwd_hash.get(),</div>
<div class="line"><a id="l00985" name="l00985"></a><span class="lineno"> 985</span> seed_nthash.blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00986" name="l00986"></a><span class="lineno"> 986</span> std::memcpy(rev_hash.get(),</div>
<div class="line"><a id="l00987" name="l00987"></a><span class="lineno"> 987</span> seed_nthash.rev_hash.get(),</div>
<div class="line"><a id="l00988" name="l00988"></a><span class="lineno"> 988</span> seed_nthash.blocks.size() * <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00989" name="l00989"></a><span class="lineno"> 989</span> std::memcpy(hash_arr.get(),</div>
<div class="line"><a id="l00990" name="l00990"></a><span class="lineno"> 990</span> seed_nthash.hash_arr.get(),</div>
<div class="line"><a id="l00991" name="l00991"></a><span class="lineno"> 991</span> num_hashes_per_seed * seed_nthash.blocks.size() *</div>
<div class="line"><a id="l00992" name="l00992"></a><span class="lineno"> 992</span> <span class="keyword">sizeof</span>(uint64_t));</div>
<div class="line"><a id="l00993" name="l00993"></a><span class="lineno"> 993</span> }</div>
<div class="line"><a id="l00994" name="l00994"></a><span class="lineno"> 994</span> </div>
<div class="line"><a id="l00995" name="l00995"></a><span class="lineno"> 995</span> <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#a18ddf0bb63594daca7bce886579bf4a3">BlindSeedNtHash</a>(<a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#a18ddf0bb63594daca7bce886579bf4a3">BlindSeedNtHash</a>&&) = <span class="keywordflow">default</span>;</div>
<div class="line"><a id="l00996" name="l00996"></a><span class="lineno"> 996</span> </div>
<div class="foldopen" id="foldopen01002" data-start="{" data-end="}">
<div class="line"><a id="l01002" name="l01002"></a><span class="lineno"><a class="line" href="classbtllib_1_1BlindSeedNtHash.html#a210be6425f3188dc373bb3fb6634ed01"> 1002</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#a210be6425f3188dc373bb3fb6634ed01">roll</a>(<span class="keywordtype">char</span> char_in)</div>
<div class="line"><a id="l01003" name="l01003"></a><span class="lineno"> 1003</span> {</div>
<div class="line"><a id="l01004" name="l01004"></a><span class="lineno"> 1004</span> seq.push_back(char_in);</div>
<div class="line"><a id="l01005" name="l01005"></a><span class="lineno"> 1005</span> ntmsm64(seq,</div>
<div class="line"><a id="l01006" name="l01006"></a><span class="lineno"> 1006</span> blocks,</div>
<div class="line"><a id="l01007" name="l01007"></a><span class="lineno"> 1007</span> monomers,</div>
<div class="line"><a id="l01008" name="l01008"></a><span class="lineno"> 1008</span> k,</div>
<div class="line"><a id="l01009" name="l01009"></a><span class="lineno"> 1009</span> blocks.size(),</div>
<div class="line"><a id="l01010" name="l01010"></a><span class="lineno"> 1010</span> num_hashes_per_seed,</div>
<div class="line"><a id="l01011" name="l01011"></a><span class="lineno"> 1011</span> fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l01012" name="l01012"></a><span class="lineno"> 1012</span> rev_hash_nomonos.get(),</div>
<div class="line"><a id="l01013" name="l01013"></a><span class="lineno"> 1013</span> fwd_hash.get(),</div>
<div class="line"><a id="l01014" name="l01014"></a><span class="lineno"> 1014</span> rev_hash.get(),</div>
<div class="line"><a id="l01015" name="l01015"></a><span class="lineno"> 1015</span> hash_arr.get());</div>
<div class="line"><a id="l01016" name="l01016"></a><span class="lineno"> 1016</span> seq.pop_front();</div>
<div class="line"><a id="l01017" name="l01017"></a><span class="lineno"> 1017</span> ++pos;</div>
<div class="line"><a id="l01018" name="l01018"></a><span class="lineno"> 1018</span> }</div>
</div>
<div class="line"><a id="l01019" name="l01019"></a><span class="lineno"> 1019</span> </div>
<div class="foldopen" id="foldopen01023" data-start="{" data-end="}">
<div class="line"><a id="l01023" name="l01023"></a><span class="lineno"><a class="line" href="classbtllib_1_1BlindSeedNtHash.html#a18522427b5f52dcc4cec91cfc230ac5b"> 1023</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#a18522427b5f52dcc4cec91cfc230ac5b">roll_back</a>(<span class="keywordtype">char</span> char_in)</div>
<div class="line"><a id="l01024" name="l01024"></a><span class="lineno"> 1024</span> {</div>
<div class="line"><a id="l01025" name="l01025"></a><span class="lineno"> 1025</span> seq.push_front(char_in);</div>
<div class="line"><a id="l01026" name="l01026"></a><span class="lineno"> 1026</span> ntmsm64l(seq,</div>
<div class="line"><a id="l01027" name="l01027"></a><span class="lineno"> 1027</span> blocks,</div>
<div class="line"><a id="l01028" name="l01028"></a><span class="lineno"> 1028</span> monomers,</div>
<div class="line"><a id="l01029" name="l01029"></a><span class="lineno"> 1029</span> k,</div>
<div class="line"><a id="l01030" name="l01030"></a><span class="lineno"> 1030</span> blocks.size(),</div>
<div class="line"><a id="l01031" name="l01031"></a><span class="lineno"> 1031</span> num_hashes_per_seed,</div>
<div class="line"><a id="l01032" name="l01032"></a><span class="lineno"> 1032</span> fwd_hash_nomonos.get(),</div>
<div class="line"><a id="l01033" name="l01033"></a><span class="lineno"> 1033</span> rev_hash_nomonos.get(),</div>
<div class="line"><a id="l01034" name="l01034"></a><span class="lineno"> 1034</span> fwd_hash.get(),</div>
<div class="line"><a id="l01035" name="l01035"></a><span class="lineno"> 1035</span> rev_hash.get(),</div>
<div class="line"><a id="l01036" name="l01036"></a><span class="lineno"> 1036</span> hash_arr.get());</div>
<div class="line"><a id="l01037" name="l01037"></a><span class="lineno"> 1037</span> seq.pop_back();</div>
<div class="line"><a id="l01038" name="l01038"></a><span class="lineno"> 1038</span> --pos;</div>
<div class="line"><a id="l01039" name="l01039"></a><span class="lineno"> 1039</span> }</div>
</div>
<div class="line"><a id="l01040" name="l01040"></a><span class="lineno"> 1040</span> </div>
<div class="line"><a id="l01045" name="l01045"></a><span class="lineno"><a class="line" href="classbtllib_1_1BlindSeedNtHash.html#af253096d6159a23f5282672815f72ac7"> 1045</a></span> <span class="keyword">const</span> uint64_t* <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#af253096d6159a23f5282672815f72ac7">hashes</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> hash_arr.get(); }</div>
<div class="line"><a id="l01046" name="l01046"></a><span class="lineno"> 1046</span> </div>
<div class="line"><a id="l01052" name="l01052"></a><span class="lineno"><a class="line" href="classbtllib_1_1BlindSeedNtHash.html#a5cf5d88504d3f768bba2ab46ee01b6c7"> 1052</a></span> <span class="keywordtype">long</span> <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#a5cf5d88504d3f768bba2ab46ee01b6c7">get_pos</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> pos; }</div>
<div class="line"><a id="l01053" name="l01053"></a><span class="lineno"> 1053</span> </div>
<div class="line"><a id="l01058" name="l01058"></a><span class="lineno"><a class="line" href="classbtllib_1_1BlindSeedNtHash.html#ab6968cfbfa0dea74bbd0fec5457154ee"> 1058</a></span> <span class="keywordtype">unsigned</span> <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#ab6968cfbfa0dea74bbd0fec5457154ee">get_hash_num</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> num_hashes_per_seed * blocks.size(); }</div>
<div class="line"><a id="l01059" name="l01059"></a><span class="lineno"> 1059</span> </div>
<div class="foldopen" id="foldopen01064" data-start="{" data-end="}">
<div class="line"><a id="l01064" name="l01064"></a><span class="lineno"><a class="line" href="classbtllib_1_1BlindSeedNtHash.html#a958e1d781cba419320f451a85f094225"> 1064</a></span> hashing_internals::NUM_HASHES_TYPE <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#a958e1d781cba419320f451a85f094225">get_hash_num_per_seed</a>()<span class="keyword"> const</span></div>
<div class="line"><a id="l01065" name="l01065"></a><span class="lineno"> 1065</span><span class="keyword"> </span>{</div>
<div class="line"><a id="l01066" name="l01066"></a><span class="lineno"> 1066</span> <span class="keywordflow">return</span> num_hashes_per_seed;</div>
<div class="line"><a id="l01067" name="l01067"></a><span class="lineno"> 1067</span> }</div>
</div>
<div class="line"><a id="l01068" name="l01068"></a><span class="lineno"> 1068</span> </div>
<div class="line"><a id="l01073" name="l01073"></a><span class="lineno"><a class="line" href="classbtllib_1_1BlindSeedNtHash.html#a4e8501a1589980dd7747cc439f114bee"> 1073</a></span> hashing_internals::K_TYPE <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#a4e8501a1589980dd7747cc439f114bee">get_k</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> k; }</div>
<div class="line"><a id="l01074" name="l01074"></a><span class="lineno"> 1074</span> </div>
<div class="line"><a id="l01079" name="l01079"></a><span class="lineno"><a class="line" href="classbtllib_1_1BlindSeedNtHash.html#a2f9ed686ee9586b140f2fbffb2cfe3b9"> 1079</a></span> uint64_t* <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#a2f9ed686ee9586b140f2fbffb2cfe3b9">get_forward_hash</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> fwd_hash.get(); }</div>
<div class="line"><a id="l01080" name="l01080"></a><span class="lineno"> 1080</span> </div>
<div class="line"><a id="l01085" name="l01085"></a><span class="lineno"><a class="line" href="classbtllib_1_1BlindSeedNtHash.html#ad9ef4f3200b4df316275a407e82c3841"> 1085</a></span> uint64_t* <a class="code hl_function" href="classbtllib_1_1BlindSeedNtHash.html#ad9ef4f3200b4df316275a407e82c3841">get_reverse_hash</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> rev_hash.get(); }</div>
<div class="line"><a id="l01086" name="l01086"></a><span class="lineno"> 1086</span> </div>
<div class="line"><a id="l01087" name="l01087"></a><span class="lineno"> 1087</span><span class="keyword">private</span>:</div>
<div class="line"><a id="l01088" name="l01088"></a><span class="lineno"> 1088</span> std::deque<char> seq;</div>
<div class="line"><a id="l01089" name="l01089"></a><span class="lineno"> 1089</span> hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed;</div>
<div class="line"><a id="l01090" name="l01090"></a><span class="lineno"> 1090</span> hashing_internals::K_TYPE k;</div>
<div class="line"><a id="l01091" name="l01091"></a><span class="lineno"> 1091</span> <span class="keywordtype">long</span> pos;</div>
<div class="line"><a id="l01092" name="l01092"></a><span class="lineno"> 1092</span> std::vector<hashing_internals::SpacedSeedBlocks> blocks;</div>
<div class="line"><a id="l01093" name="l01093"></a><span class="lineno"> 1093</span> std::vector<hashing_internals::SpacedSeedMonomers> monomers;</div>
<div class="line"><a id="l01094" name="l01094"></a><span class="lineno"> 1094</span> std::unique_ptr<uint64_t[]> fwd_hash_nomonos;</div>
<div class="line"><a id="l01095" name="l01095"></a><span class="lineno"> 1095</span> std::unique_ptr<uint64_t[]> rev_hash_nomonos;</div>
<div class="line"><a id="l01096" name="l01096"></a><span class="lineno"> 1096</span> std::unique_ptr<uint64_t[]> fwd_hash;</div>
<div class="line"><a id="l01097" name="l01097"></a><span class="lineno"> 1097</span> std::unique_ptr<uint64_t[]> rev_hash;</div>
<div class="line"><a id="l01098" name="l01098"></a><span class="lineno"> 1098</span> std::unique_ptr<uint64_t[]> hash_arr;</div>
<div class="line"><a id="l01099" name="l01099"></a><span class="lineno"> 1099</span>};</div>
</div>
<div class="line"><a id="l01100" name="l01100"></a><span class="lineno"> 1100</span> </div>
<div class="line"><a id="l01101" name="l01101"></a><span class="lineno"> 1101</span>} <span class="comment">// namespace btllib</span></div>
<div class="ttc" id="aclassbtllib_1_1BlindSeedNtHash_html"><div class="ttname"><a href="classbtllib_1_1BlindSeedNtHash.html">btllib::BlindSeedNtHash</a></div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:919</div></div>
<div class="ttc" id="aclassbtllib_1_1BlindSeedNtHash_html_a18522427b5f52dcc4cec91cfc230ac5b"><div class="ttname"><a href="classbtllib_1_1BlindSeedNtHash.html#a18522427b5f52dcc4cec91cfc230ac5b">btllib::BlindSeedNtHash::roll_back</a></div><div class="ttdeci">void roll_back(char char_in)</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:1023</div></div>
<div class="ttc" id="aclassbtllib_1_1BlindSeedNtHash_html_a18ddf0bb63594daca7bce886579bf4a3"><div class="ttname"><a href="classbtllib_1_1BlindSeedNtHash.html#a18ddf0bb63594daca7bce886579bf4a3">btllib::BlindSeedNtHash::BlindSeedNtHash</a></div><div class="ttdeci">BlindSeedNtHash(const char *seq, const std::vector< std::string > &seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, long pos=0)</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:932</div></div>
<div class="ttc" id="aclassbtllib_1_1BlindSeedNtHash_html_a210be6425f3188dc373bb3fb6634ed01"><div class="ttname"><a href="classbtllib_1_1BlindSeedNtHash.html#a210be6425f3188dc373bb3fb6634ed01">btllib::BlindSeedNtHash::roll</a></div><div class="ttdeci">void roll(char char_in)</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:1002</div></div>
<div class="ttc" id="aclassbtllib_1_1BlindSeedNtHash_html_a2f9ed686ee9586b140f2fbffb2cfe3b9"><div class="ttname"><a href="classbtllib_1_1BlindSeedNtHash.html#a2f9ed686ee9586b140f2fbffb2cfe3b9">btllib::BlindSeedNtHash::get_forward_hash</a></div><div class="ttdeci">uint64_t * get_forward_hash() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:1079</div></div>
<div class="ttc" id="aclassbtllib_1_1BlindSeedNtHash_html_a4e8501a1589980dd7747cc439f114bee"><div class="ttname"><a href="classbtllib_1_1BlindSeedNtHash.html#a4e8501a1589980dd7747cc439f114bee">btllib::BlindSeedNtHash::get_k</a></div><div class="ttdeci">hashing_internals::K_TYPE get_k() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:1073</div></div>
<div class="ttc" id="aclassbtllib_1_1BlindSeedNtHash_html_a5cf5d88504d3f768bba2ab46ee01b6c7"><div class="ttname"><a href="classbtllib_1_1BlindSeedNtHash.html#a5cf5d88504d3f768bba2ab46ee01b6c7">btllib::BlindSeedNtHash::get_pos</a></div><div class="ttdeci">long get_pos() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:1052</div></div>
<div class="ttc" id="aclassbtllib_1_1BlindSeedNtHash_html_a958e1d781cba419320f451a85f094225"><div class="ttname"><a href="classbtllib_1_1BlindSeedNtHash.html#a958e1d781cba419320f451a85f094225">btllib::BlindSeedNtHash::get_hash_num_per_seed</a></div><div class="ttdeci">hashing_internals::NUM_HASHES_TYPE get_hash_num_per_seed() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:1064</div></div>
<div class="ttc" id="aclassbtllib_1_1BlindSeedNtHash_html_ab6968cfbfa0dea74bbd0fec5457154ee"><div class="ttname"><a href="classbtllib_1_1BlindSeedNtHash.html#ab6968cfbfa0dea74bbd0fec5457154ee">btllib::BlindSeedNtHash::get_hash_num</a></div><div class="ttdeci">unsigned get_hash_num() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:1058</div></div>
<div class="ttc" id="aclassbtllib_1_1BlindSeedNtHash_html_ad9ef4f3200b4df316275a407e82c3841"><div class="ttname"><a href="classbtllib_1_1BlindSeedNtHash.html#ad9ef4f3200b4df316275a407e82c3841">btllib::BlindSeedNtHash::get_reverse_hash</a></div><div class="ttdeci">uint64_t * get_reverse_hash() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:1085</div></div>
<div class="ttc" id="aclassbtllib_1_1BlindSeedNtHash_html_af253096d6159a23f5282672815f72ac7"><div class="ttname"><a href="classbtllib_1_1BlindSeedNtHash.html#af253096d6159a23f5282672815f72ac7">btllib::BlindSeedNtHash::hashes</a></div><div class="ttdeci">const uint64_t * hashes() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:1045</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html">btllib::SeedNtHash</a></div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:517</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_a0e8786dd693fd7da8ab6ffdfb5d39e1a"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#a0e8786dd693fd7da8ab6ffdfb5d39e1a">btllib::SeedNtHash::peek_back</a></div><div class="ttdeci">bool peek_back(char char_in)</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:788</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_a1eb3ee60193f3303309c794150192ec0"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#a1eb3ee60193f3303309c794150192ec0">btllib::SeedNtHash::get_forward_hash</a></div><div class="ttdeci">uint64_t * get_forward_hash() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:862</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_a293e694de84eafbb19bf7123749f9ba6"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#a293e694de84eafbb19bf7123749f9ba6">btllib::SeedNtHash::roll_back</a></div><div class="ttdeci">bool roll_back()</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:689</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_a2aec9116c2544ac084fbafedd30ece41"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#a2aec9116c2544ac084fbafedd30ece41">btllib::SeedNtHash::get_reverse_hash</a></div><div class="ttdeci">uint64_t * get_reverse_hash() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:868</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_a2db58d333504f97eaa807dbb4aaafc9d"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#a2db58d333504f97eaa807dbb4aaafc9d">btllib::SeedNtHash::peek_back</a></div><div class="ttdeci">bool peek_back()</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:736</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_a4931b3de033fadd4472bd934a44c5eaa"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#a4931b3de033fadd4472bd934a44c5eaa">btllib::SeedNtHash::get_pos</a></div><div class="ttdeci">size_t get_pos() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:835</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_a650de4cf7e6ed95ee9dead6e23171d44"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#a650de4cf7e6ed95ee9dead6e23171d44">btllib::SeedNtHash::SeedNtHash</a></div><div class="ttdeci">SeedNtHash(const std::string &seq, const std::vector< std::string > &seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos=0)</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:563</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_a8148bacf86867fb48d4bb61a61e505cb"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#a8148bacf86867fb48d4bb61a61e505cb">btllib::SeedNtHash::SeedNtHash</a></div><div class="ttdeci">SeedNtHash(const char *seq, size_t seq_len, const std::vector< std::vector< unsigned > > &seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos=0)</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:582</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_a876aa5a1a091d61b9155adaae7a0d889"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#a876aa5a1a091d61b9155adaae7a0d889">btllib::SeedNtHash::SeedNtHash</a></div><div class="ttdeci">SeedNtHash(const std::string &seq, const std::vector< std::vector< unsigned > > &seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos=0)</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:612</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_a9bbe1be0a6af592bc65fb5779f454029"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#a9bbe1be0a6af592bc65fb5779f454029">btllib::SeedNtHash::peek</a></div><div class="ttdeci">bool peek()</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:724</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_aa817b8acaf7c57d7be8ce47fcf5ac758"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#aa817b8acaf7c57d7be8ce47fcf5ac758">btllib::SeedNtHash::roll</a></div><div class="ttdeci">bool roll()</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:658</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_aafce9763427d377cd416880d1450cf9f"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#aafce9763427d377cd416880d1450cf9f">btllib::SeedNtHash::get_hash_num</a></div><div class="ttdeci">unsigned get_hash_num() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:841</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_abc4bcd67a4cb9b886665c07813d5b9e3"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#abc4bcd67a4cb9b886665c07813d5b9e3">btllib::SeedNtHash::peek</a></div><div class="ttdeci">bool peek(char char_in)</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:748</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_adc6e950dac4dbdd41190f1e1159c27a8"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#adc6e950dac4dbdd41190f1e1159c27a8">btllib::SeedNtHash::SeedNtHash</a></div><div class="ttdeci">SeedNtHash(const char *seq, size_t seq_len, const std::vector< std::string > &seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos=0)</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:530</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_ae18f9d65b17ccaa9457167ead16d4d75"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#ae18f9d65b17ccaa9457167ead16d4d75">btllib::SeedNtHash::get_k</a></div><div class="ttdeci">hashing_internals::K_TYPE get_k() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:856</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_ae28265c1630d54925a22b94d01dec9db"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#ae28265c1630d54925a22b94d01dec9db">btllib::SeedNtHash::hashes</a></div><div class="ttdeci">const uint64_t * hashes() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:828</div></div>
<div class="ttc" id="aclassbtllib_1_1SeedNtHash_html_ae992f944f85fb16b4956e74c7ccbe9e4"><div class="ttname"><a href="classbtllib_1_1SeedNtHash.html#ae992f944f85fb16b4956e74c7ccbe9e4">btllib::SeedNtHash::get_hash_num_per_seed</a></div><div class="ttdeci">hashing_internals::NUM_HASHES_TYPE get_hash_num_per_seed() const</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:847</div></div>
<div class="ttc" id="anamespacebtllib_html"><div class="ttname"><a href="namespacebtllib.html">btllib</a></div><div class="ttdef"><b>Definition</b> aahash.hpp:12</div></div>
<div class="ttc" id="anamespacebtllib_html_a540bce0213b7718e519ddc4466361bf7"><div class="ttname"><a href="namespacebtllib.html#a540bce0213b7718e519ddc4466361bf7">btllib::check_error</a></div><div class="ttdeci">void check_error(bool condition, const std::string &msg)</div></div>
<div class="ttc" id="anamespacebtllib_html_a60a36f4583a7eb03001f8bdb7b395507"><div class="ttname"><a href="namespacebtllib.html#a60a36f4583a7eb03001f8bdb7b395507">btllib::check_warning</a></div><div class="ttdeci">void check_warning(bool condition, const std::string &msg)</div></div>
<div class="ttc" id="anamespacebtllib_html_ac954d7c54d302d9f285beb797dbe84a5"><div class="ttname"><a href="namespacebtllib.html#ac954d7c54d302d9f285beb797dbe84a5">btllib::parse_seeds</a></div><div class="ttdeci">std::vector< std::vector< unsigned > > parse_seeds(const std::vector< std::string > &seed_strings)</div><div class="ttdef"><b>Definition</b> nthash_seed.hpp:496</div></div>