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<div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="comment">/*</span></div>
<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span><span class="comment"> * nthash_lowlevel.hpp</span></div>
<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="comment"> * Author: Hamid Mohamadi</span></div>
<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span><span class="comment"> * Genome Sciences Centre,</span></div>
<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span><span class="comment"> * British Columbia Cancer Agency</span></div>
<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="comment"> */</span></div>
<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span> </div>
<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span><span class="preprocessor">#ifndef BTLLIB_NTHASH_LOWLEVEL_HPP</span></div>
<div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span><span class="preprocessor">#define BTLLIB_NTHASH_LOWLEVEL_HPP</span></div>
<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span> </div>
<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span><span class="preprocessor">#include "btllib/nthash_consts.hpp"</span></div>
<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span><span class="preprocessor">#include <array></span></div>
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include <cstddef></span></div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#include <cstdint></span></div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include <ctime></span></div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="preprocessor">#include <iostream></span></div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="preprocessor">#include <limits></span></div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include <string></span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span><span class="preprocessor">#include <vector></span></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">namespace </span><a class="code hl_namespace" href="namespacebtllib.html">btllib</a> {</div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> </div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span><span class="keyword">template</span><<span class="keyword">typename</span> T></div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span><span class="keyword">inline</span> T</div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span>canonical(<span class="keyword">const</span> T fwd, <span class="keyword">const</span> T rev)</div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span>{</div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> <span class="keywordflow">return</span> fwd + rev;</div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span>}</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> </div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span><span class="keyword">static_assert</span>(std::numeric_limits<unsigned>::max() + 1 == 0,</div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span> <span class="stringliteral">"Integers don't overflow on this platform which is necessary for "</span></div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> <span class="stringliteral">"ntHash canonical hash computation."</span>);</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> </div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span><span class="comment">// Data structures for spaced seeds</span></div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> </div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span><span class="comment">// List of don't care positions</span></div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span><span class="keyword">using </span>SpacedSeed = std::vector<unsigned>;</div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> </div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span><span class="comment">// Bx2 array representing block start and end positions.</span></div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span><span class="keyword">using </span>SpacedSeedBlocks = std::vector<std::array<unsigned, 2>>;</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> </div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span><span class="comment">// List of blocks with sizes of one.</span></div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span><span class="keyword">using </span>SpacedSeedMonomers = std::vector<unsigned>;</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> </div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f"> 54</a></span><a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(<span class="keyword">const</span> uint64_t x)</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span>{</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> uint64_t m = ((x & 0x8000000000000000ULL) >> 30) | <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> ((x & 0x100000000ULL) >> 32); <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> <span class="keywordflow">return</span> ((x << 1) & 0xFFFFFFFDFFFFFFFFULL) | m; <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span>}</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> </div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a8adee205e2a9bc7509250a46f01a2c40"> 71</a></span><a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(<span class="keyword">const</span> uint64_t x, <span class="keyword">const</span> <span class="keywordtype">unsigned</span> d)</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span>{</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> uint64_t v = (x << d) | (x >> (64 - d)); <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> uint64_t y = (v ^ (v >> 33)) & <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> (std::numeric_limits<uint64_t>::max() >> (64 - d)); <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> <span class="keywordflow">return</span> v ^ (y | (y << 33)); <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span>}</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> </div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a731d4ddcd44c63f3b6bfa6c33a0eedb8"> 88</a></span><a class="code hl_function" href="namespacebtllib.html#a731d4ddcd44c63f3b6bfa6c33a0eedb8">sror</a>(<span class="keyword">const</span> uint64_t x)</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> uint64_t m = ((x & 0x200000000ULL) << 30) | ((x & 1ULL) << 32); <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> <span class="keywordflow">return</span> ((x >> 1) & 0xFFFFFFFEFFFFFFFFULL) | m; <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span>}</div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"><a class="line" href="namespacebtllib.html#adf40469a5081c357816a15ba2a7a158d"> 103</a></span><a class="code hl_function" href="namespacebtllib.html#adf40469a5081c357816a15ba2a7a158d">ntf64</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq, <span class="keywordtype">unsigned</span> k)</div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span>{</div>
<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> uint64_t h_val = 0;</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; i < k / 4; i++) {</div>
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span> h_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(h_val, 4);</div>
<div class="line"><a id="l00108" name="l00108"></a><span class="lineno"> 108</span> <span class="keyword">const</span> uint8_t curr_offset = 4 * i;</div>
<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</span> <span class="keyword">const</span> uint8_t tetramer_loc =</div>
<div class="line"><a id="l00110" name="l00110"></a><span class="lineno"> 110</span> 64 * CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[curr_offset]] + <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> 16 * CONVERT_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[curr_offset + 1]] + <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> 4 * CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[curr_offset + 2]] +</div>
<div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span> CONVERT_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[curr_offset + 3]];</div>
<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> h_val ^= TETRAMER_TAB[tetramer_loc];</div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> }</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> remainder = k % 4;</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> h_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(h_val, remainder);</div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> <span class="keywordflow">if</span> (remainder == 3) {</div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> <span class="keyword">const</span> uint8_t trimer_loc =</div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> 16 * CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 3]] + <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> 4 * CONVERT_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[k - 2]] +</div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 1]];</div>
<div class="line"><a id="l00123" name="l00123"></a><span class="lineno"> 123</span> h_val ^= TRIMER_TAB[trimer_loc];</div>
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (remainder == 2) {</div>
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> <span class="keyword">const</span> uint8_t dimer_loc = 4 * CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 2]] +</div>
<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span> CONVERT_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[k - 1]];</div>
<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> h_val ^= DIMER_TAB[dimer_loc];</div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (remainder == 1) {</div>
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> h_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 1]];</div>
<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> }</div>
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> <span class="keywordflow">return</span> h_val;</div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span>}</div>
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"><a class="line" href="namespacebtllib.html#aa2ad0c0e5b78e8db97508044ce9c1906"> 144</a></span><a class="code hl_function" href="namespacebtllib.html#aa2ad0c0e5b78e8db97508044ce9c1906">ntr64</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq, <span class="keywordtype">unsigned</span> k)</div>
<div class="line"><a id="l00145" name="l00145"></a><span class="lineno"> 145</span>{</div>
<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"> 146</span> uint64_t h_val = 0;</div>
<div class="line"><a id="l00147" name="l00147"></a><span class="lineno"> 147</span> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> remainder = k % 4;</div>
<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</span> <span class="keywordflow">if</span> (remainder == 3) {</div>
<div class="line"><a id="l00149" name="l00149"></a><span class="lineno"> 149</span> <span class="keyword">const</span> uint8_t trimer_loc =</div>
<div class="line"><a id="l00150" name="l00150"></a><span class="lineno"> 150</span> 16 * RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 1]] + <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00151" name="l00151"></a><span class="lineno"> 151</span> 4 * RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[k - 2]] +</div>
<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"> 152</span> RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 3]];</div>
<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</span> h_val ^= TRIMER_TAB[trimer_loc];</div>
<div class="line"><a id="l00154" name="l00154"></a><span class="lineno"> 154</span> } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (remainder == 2) {</div>
<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"> 155</span> <span class="keyword">const</span> uint8_t dimer_loc =</div>
<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span> 4 * RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 1]] +</div>
<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[k - 2]];</div>
<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> h_val ^= DIMER_TAB[dimer_loc];</div>
<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (remainder == 1) {</div>
<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> h_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 1] & CP_OFF];</div>
<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> }</div>
<div class="line"><a id="l00162" name="l00162"></a><span class="lineno"> 162</span> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; i < k / 4; i++) {</div>
<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"> 163</span> h_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(h_val, 4);</div>
<div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span> <span class="keyword">const</span> uint8_t curr_offset = 4 * (k / 4 - i) - 1;</div>
<div class="line"><a id="l00165" name="l00165"></a><span class="lineno"> 165</span> <span class="keyword">const</span> uint8_t tetramer_loc =</div>
<div class="line"><a id="l00166" name="l00166"></a><span class="lineno"> 166</span> 64 * RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[curr_offset]] + <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00167" name="l00167"></a><span class="lineno"> 167</span> 16 * RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[curr_offset - 1]] + <span class="comment">// NOLINT</span></div>
<div class="line"><a id="l00168" name="l00168"></a><span class="lineno"> 168</span> 4 * RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[curr_offset - 2]] +</div>
<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span> RC_CONVERT_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[curr_offset - 3]];</div>
<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> h_val ^= TETRAMER_TAB[tetramer_loc];</div>
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span> }</div>
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> <span class="keywordflow">return</span> h_val;</div>
<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span>}</div>
<div class="line"><a id="l00174" name="l00174"></a><span class="lineno"> 174</span> </div>
<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"> 186</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a236dfca51ded53acf1233b5333bba7c1"> 187</a></span><a class="code hl_function" href="namespacebtllib.html#adf40469a5081c357816a15ba2a7a158d">ntf64</a>(uint64_t fh_val,</div>
<div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00189" name="l00189"></a><span class="lineno"> 189</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_out,</div>
<div class="line"><a id="l00190" name="l00190"></a><span class="lineno"> 190</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_in)</div>
<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span>{</div>
<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</span> uint64_t h_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(fh_val);</div>
<div class="line"><a id="l00193" name="l00193"></a><span class="lineno"> 193</span> h_val ^= SEED_TAB[char_in];</div>
<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> h_val ^= MS_TAB(char_out, k);</div>
<div class="line"><a id="l00195" name="l00195"></a><span class="lineno"> 195</span> <span class="keywordflow">return</span> h_val;</div>
<div class="line"><a id="l00196" name="l00196"></a><span class="lineno"> 196</span>}</div>
<div class="line"><a id="l00197" name="l00197"></a><span class="lineno"> 197</span> </div>
<div class="line"><a id="l00210" name="l00210"></a><span class="lineno"> 210</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a2a930f0a7bfaeed6b8ca353dec5a8751"> 211</a></span><a class="code hl_function" href="namespacebtllib.html#aa2ad0c0e5b78e8db97508044ce9c1906">ntr64</a>(uint64_t rh_val,</div>
<div class="line"><a id="l00212" name="l00212"></a><span class="lineno"> 212</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_out,</div>
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_in)</div>
<div class="line"><a id="l00215" name="l00215"></a><span class="lineno"> 215</span>{</div>
<div class="line"><a id="l00216" name="l00216"></a><span class="lineno"> 216</span> uint64_t h_val = rh_val ^ MS_TAB(char_in & CP_OFF, k);</div>
<div class="line"><a id="l00217" name="l00217"></a><span class="lineno"> 217</span> h_val ^= SEED_TAB[char_out & CP_OFF];</div>
<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> h_val = <a class="code hl_function" href="namespacebtllib.html#a731d4ddcd44c63f3b6bfa6c33a0eedb8">sror</a>(h_val);</div>
<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"> 219</span> <span class="keywordflow">return</span> h_val;</div>
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span>}</div>
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> </div>
<div class="line"><a id="l00230" name="l00230"></a><span class="lineno"> 230</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00231" name="l00231"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a8ada92e6d8bdcf53b8985bb25a09738f"> 231</a></span><a class="code hl_function" href="namespacebtllib.html#a8ada92e6d8bdcf53b8985bb25a09738f">ntc64</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq, <span class="keywordtype">unsigned</span> k)</div>
<div class="line"><a id="l00232" name="l00232"></a><span class="lineno"> 232</span>{</div>
<div class="line"><a id="l00233" name="l00233"></a><span class="lineno"> 233</span> uint64_t fh_val = 0, rh_val = 0;</div>
<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span> fh_val = <a class="code hl_function" href="namespacebtllib.html#adf40469a5081c357816a15ba2a7a158d">ntf64</a>(kmer_seq, k);</div>
<div class="line"><a id="l00235" name="l00235"></a><span class="lineno"> 235</span> rh_val = <a class="code hl_function" href="namespacebtllib.html#aa2ad0c0e5b78e8db97508044ce9c1906">ntr64</a>(kmer_seq, k);</div>
<div class="line"><a id="l00236" name="l00236"></a><span class="lineno"> 236</span> <span class="keywordflow">return</span> canonical(fh_val, rh_val);</div>
<div class="line"><a id="l00237" name="l00237"></a><span class="lineno"> 237</span>}</div>
<div class="line"><a id="l00238" name="l00238"></a><span class="lineno"> 238</span> </div>
<div class="line"><a id="l00250" name="l00250"></a><span class="lineno"> 250</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a1a450d4a4b3c84db384b167ebb914498"> 251</a></span><a class="code hl_function" href="namespacebtllib.html#a8ada92e6d8bdcf53b8985bb25a09738f">ntc64</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq, <span class="keywordtype">unsigned</span> k, uint64_t& fh_val, uint64_t& rh_val)</div>
<div class="line"><a id="l00252" name="l00252"></a><span class="lineno"> 252</span>{</div>
<div class="line"><a id="l00253" name="l00253"></a><span class="lineno"> 253</span> fh_val = <a class="code hl_function" href="namespacebtllib.html#adf40469a5081c357816a15ba2a7a158d">ntf64</a>(kmer_seq, k);</div>
<div class="line"><a id="l00254" name="l00254"></a><span class="lineno"> 254</span> rh_val = <a class="code hl_function" href="namespacebtllib.html#aa2ad0c0e5b78e8db97508044ce9c1906">ntr64</a>(kmer_seq, k);</div>
<div class="line"><a id="l00255" name="l00255"></a><span class="lineno"> 255</span> <span class="keywordflow">return</span> canonical(fh_val, rh_val);</div>
<div class="line"><a id="l00256" name="l00256"></a><span class="lineno"> 256</span>}</div>
<div class="line"><a id="l00257" name="l00257"></a><span class="lineno"> 257</span> </div>
<div class="line"><a id="l00269" name="l00269"></a><span class="lineno"> 269</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00270" name="l00270"></a><span class="lineno"><a class="line" href="namespacebtllib.html#aebbb9de01e6cfa57a7735a963d030235"> 270</a></span><a class="code hl_function" href="namespacebtllib.html#a8ada92e6d8bdcf53b8985bb25a09738f">ntc64</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_out,</div>
<div class="line"><a id="l00271" name="l00271"></a><span class="lineno"> 271</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_in,</div>
<div class="line"><a id="l00272" name="l00272"></a><span class="lineno"> 272</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00273" name="l00273"></a><span class="lineno"> 273</span> uint64_t& fh_val,</div>
<div class="line"><a id="l00274" name="l00274"></a><span class="lineno"> 274</span> uint64_t& rh_val)</div>
<div class="line"><a id="l00275" name="l00275"></a><span class="lineno"> 275</span>{</div>
<div class="line"><a id="l00276" name="l00276"></a><span class="lineno"> 276</span> fh_val = <a class="code hl_function" href="namespacebtllib.html#adf40469a5081c357816a15ba2a7a158d">ntf64</a>(fh_val, k, char_out, char_in);</div>
<div class="line"><a id="l00277" name="l00277"></a><span class="lineno"> 277</span> rh_val = <a class="code hl_function" href="namespacebtllib.html#aa2ad0c0e5b78e8db97508044ce9c1906">ntr64</a>(rh_val, k, char_out, char_in);</div>
<div class="line"><a id="l00278" name="l00278"></a><span class="lineno"> 278</span> <span class="keywordflow">return</span> canonical(fh_val, rh_val);</div>
<div class="line"><a id="l00279" name="l00279"></a><span class="lineno"> 279</span>}</div>
<div class="line"><a id="l00280" name="l00280"></a><span class="lineno"> 280</span> </div>
<div class="line"><a id="l00291" name="l00291"></a><span class="lineno"> 291</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00292" name="l00292"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a26d4fe6e3d7e9a4bb3edfb4d51d9a7d2"> 292</a></span><a class="code hl_function" href="namespacebtllib.html#a26d4fe6e3d7e9a4bb3edfb4d51d9a7d2">ntf64l</a>(uint64_t rh_val,</div>
<div class="line"><a id="l00293" name="l00293"></a><span class="lineno"> 293</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00294" name="l00294"></a><span class="lineno"> 294</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_out,</div>
<div class="line"><a id="l00295" name="l00295"></a><span class="lineno"> 295</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_in)</div>
<div class="line"><a id="l00296" name="l00296"></a><span class="lineno"> 296</span>{</div>
<div class="line"><a id="l00297" name="l00297"></a><span class="lineno"> 297</span> uint64_t h_val = rh_val ^ MS_TAB(char_in, k);</div>
<div class="line"><a id="l00298" name="l00298"></a><span class="lineno"> 298</span> h_val ^= SEED_TAB[char_out];</div>
<div class="line"><a id="l00299" name="l00299"></a><span class="lineno"> 299</span> h_val = <a class="code hl_function" href="namespacebtllib.html#a731d4ddcd44c63f3b6bfa6c33a0eedb8">sror</a>(h_val);</div>
<div class="line"><a id="l00300" name="l00300"></a><span class="lineno"> 300</span> <span class="keywordflow">return</span> h_val;</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="l00313" name="l00313"></a><span class="lineno"> 313</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00314" name="l00314"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a2a43294ffe95420456953e3c2e674bdb"> 314</a></span><a class="code hl_function" href="namespacebtllib.html#a2a43294ffe95420456953e3c2e674bdb">ntr64l</a>(uint64_t fh_val,</div>
<div class="line"><a id="l00315" name="l00315"></a><span class="lineno"> 315</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00316" name="l00316"></a><span class="lineno"> 316</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_out,</div>
<div class="line"><a id="l00317" name="l00317"></a><span class="lineno"> 317</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_in)</div>
<div class="line"><a id="l00318" name="l00318"></a><span class="lineno"> 318</span>{</div>
<div class="line"><a id="l00319" name="l00319"></a><span class="lineno"> 319</span> uint64_t h_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(fh_val);</div>
<div class="line"><a id="l00320" name="l00320"></a><span class="lineno"> 320</span> h_val ^= SEED_TAB[char_in & CP_OFF];</div>
<div class="line"><a id="l00321" name="l00321"></a><span class="lineno"> 321</span> h_val ^= MS_TAB(char_out & CP_OFF, k);</div>
<div class="line"><a id="l00322" name="l00322"></a><span class="lineno"> 322</span> <span class="keywordflow">return</span> h_val;</div>
<div class="line"><a id="l00323" name="l00323"></a><span class="lineno"> 323</span>}</div>
<div class="line"><a id="l00324" name="l00324"></a><span class="lineno"> 324</span> </div>
<div class="line"><a id="l00337" name="l00337"></a><span class="lineno"> 337</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00338" name="l00338"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a624a7c9e6716eaa82f78785ac705c81a"> 338</a></span><a class="code hl_function" href="namespacebtllib.html#a624a7c9e6716eaa82f78785ac705c81a">ntc64l</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_out,</div>
<div class="line"><a id="l00339" name="l00339"></a><span class="lineno"> 339</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_in,</div>
<div class="line"><a id="l00340" name="l00340"></a><span class="lineno"> 340</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00341" name="l00341"></a><span class="lineno"> 341</span> uint64_t& fh_val,</div>
<div class="line"><a id="l00342" name="l00342"></a><span class="lineno"> 342</span> uint64_t& rh_val)</div>
<div class="line"><a id="l00343" name="l00343"></a><span class="lineno"> 343</span>{</div>
<div class="line"><a id="l00344" name="l00344"></a><span class="lineno"> 344</span> fh_val = <a class="code hl_function" href="namespacebtllib.html#a26d4fe6e3d7e9a4bb3edfb4d51d9a7d2">ntf64l</a>(fh_val, k, char_out, char_in);</div>
<div class="line"><a id="l00345" name="l00345"></a><span class="lineno"> 345</span> rh_val = <a class="code hl_function" href="namespacebtllib.html#a2a43294ffe95420456953e3c2e674bdb">ntr64l</a>(rh_val, k, char_out, char_in);</div>
<div class="line"><a id="l00346" name="l00346"></a><span class="lineno"> 346</span> <span class="keywordflow">return</span> canonical(fh_val, rh_val);</div>
<div class="line"><a id="l00347" name="l00347"></a><span class="lineno"> 347</span>}</div>
<div class="line"><a id="l00348" name="l00348"></a><span class="lineno"> 348</span> </div>
<div class="line"><a id="l00357" name="l00357"></a><span class="lineno"> 357</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00358" name="l00358"></a><span class="lineno"><a class="line" href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d"> 358</a></span><a class="code hl_function" href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d">nte64</a>(uint64_t bh_val, <span class="keywordtype">unsigned</span> k, <span class="keywordtype">unsigned</span> h, uint64_t* h_val)</div>
<div class="line"><a id="l00359" name="l00359"></a><span class="lineno"> 359</span>{</div>
<div class="line"><a id="l00360" name="l00360"></a><span class="lineno"> 360</span> uint64_t t_val;</div>
<div class="line"><a id="l00361" name="l00361"></a><span class="lineno"> 361</span> h_val[0] = bh_val;</div>
<div class="line"><a id="l00362" name="l00362"></a><span class="lineno"> 362</span> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 1; i < h; i++) {</div>
<div class="line"><a id="l00363" name="l00363"></a><span class="lineno"> 363</span> t_val = bh_val * (i ^ k * MULTISEED);</div>
<div class="line"><a id="l00364" name="l00364"></a><span class="lineno"> 364</span> t_val ^= t_val >> MULTISHIFT;</div>
<div class="line"><a id="l00365" name="l00365"></a><span class="lineno"> 365</span> h_val[i] = t_val;</div>
<div class="line"><a id="l00366" name="l00366"></a><span class="lineno"> 366</span> }</div>
<div class="line"><a id="l00367" name="l00367"></a><span class="lineno"> 367</span>}</div>
<div class="line"><a id="l00368" name="l00368"></a><span class="lineno"> 368</span> </div>
<div class="line"><a id="l00377" name="l00377"></a><span class="lineno"> 377</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00378" name="l00378"></a><span class="lineno"><a class="line" href="namespacebtllib.html#add27b36e36996d6a042932a4337d6e91"> 378</a></span>ntmc64(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq, <span class="keywordtype">unsigned</span> k, <span class="keywordtype">unsigned</span> m, uint64_t* h_val)</div>
<div class="line"><a id="l00379" name="l00379"></a><span class="lineno"> 379</span>{</div>
<div class="line"><a id="l00380" name="l00380"></a><span class="lineno"> 380</span> <span class="keyword">const</span> uint64_t b_val = <a class="code hl_function" href="namespacebtllib.html#a8ada92e6d8bdcf53b8985bb25a09738f">ntc64</a>(kmer_seq, k);</div>
<div class="line"><a id="l00381" name="l00381"></a><span class="lineno"> 381</span> <a class="code hl_function" href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d">nte64</a>(b_val, k, m, h_val);</div>
<div class="line"><a id="l00382" name="l00382"></a><span class="lineno"> 382</span>}</div>
<div class="line"><a id="l00383" name="l00383"></a><span class="lineno"> 383</span> </div>
<div class="line"><a id="l00395" name="l00395"></a><span class="lineno"> 395</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00396" name="l00396"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a30dcece8f00356f24359578ffb01915f"> 396</a></span>ntmc64(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00397" name="l00397"></a><span class="lineno"> 397</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00398" name="l00398"></a><span class="lineno"> 398</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00399" name="l00399"></a><span class="lineno"> 399</span> uint64_t& fh_val,</div>
<div class="line"><a id="l00400" name="l00400"></a><span class="lineno"> 400</span> uint64_t& rh_val,</div>
<div class="line"><a id="l00401" name="l00401"></a><span class="lineno"> 401</span> uint64_t* h_val)</div>
<div class="line"><a id="l00402" name="l00402"></a><span class="lineno"> 402</span>{</div>
<div class="line"><a id="l00403" name="l00403"></a><span class="lineno"> 403</span> <span class="keyword">const</span> uint64_t b_val = <a class="code hl_function" href="namespacebtllib.html#a8ada92e6d8bdcf53b8985bb25a09738f">ntc64</a>(kmer_seq, k, fh_val, rh_val);</div>
<div class="line"><a id="l00404" name="l00404"></a><span class="lineno"> 404</span> <a class="code hl_function" href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d">nte64</a>(b_val, k, m, h_val);</div>
<div class="line"><a id="l00405" name="l00405"></a><span class="lineno"> 405</span>}</div>
<div class="line"><a id="l00406" name="l00406"></a><span class="lineno"> 406</span> </div>
<div class="line"><a id="l00418" name="l00418"></a><span class="lineno"> 418</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00419" name="l00419"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a7ec16866e3ece0bd9a725cf74ce04707"> 419</a></span>ntmc64(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_out,</div>
<div class="line"><a id="l00420" name="l00420"></a><span class="lineno"> 420</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_in,</div>
<div class="line"><a id="l00421" name="l00421"></a><span class="lineno"> 421</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00422" name="l00422"></a><span class="lineno"> 422</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00423" name="l00423"></a><span class="lineno"> 423</span> uint64_t& fh_val,</div>
<div class="line"><a id="l00424" name="l00424"></a><span class="lineno"> 424</span> uint64_t& rh_val,</div>
<div class="line"><a id="l00425" name="l00425"></a><span class="lineno"> 425</span> uint64_t* h_val)</div>
<div class="line"><a id="l00426" name="l00426"></a><span class="lineno"> 426</span>{</div>
<div class="line"><a id="l00427" name="l00427"></a><span class="lineno"> 427</span> <span class="keyword">const</span> uint64_t b_val = <a class="code hl_function" href="namespacebtllib.html#a8ada92e6d8bdcf53b8985bb25a09738f">ntc64</a>(char_out, char_in, k, fh_val, rh_val);</div>
<div class="line"><a id="l00428" name="l00428"></a><span class="lineno"> 428</span> <a class="code hl_function" href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d">nte64</a>(b_val, k, m, h_val);</div>
<div class="line"><a id="l00429" name="l00429"></a><span class="lineno"> 429</span>}</div>
<div class="line"><a id="l00430" name="l00430"></a><span class="lineno"> 430</span> </div>
<div class="line"><a id="l00442" name="l00442"></a><span class="lineno"> 442</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00443" name="l00443"></a><span class="lineno"><a class="line" href="namespacebtllib.html#ac2c018914a37e61bd60d2bee577fd246"> 443</a></span>ntmc64l(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_out,</div>
<div class="line"><a id="l00444" name="l00444"></a><span class="lineno"> 444</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_in,</div>
<div class="line"><a id="l00445" name="l00445"></a><span class="lineno"> 445</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00446" name="l00446"></a><span class="lineno"> 446</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00447" name="l00447"></a><span class="lineno"> 447</span> uint64_t& fh_val,</div>
<div class="line"><a id="l00448" name="l00448"></a><span class="lineno"> 448</span> uint64_t& rh_val,</div>
<div class="line"><a id="l00449" name="l00449"></a><span class="lineno"> 449</span> uint64_t* h_val)</div>
<div class="line"><a id="l00450" name="l00450"></a><span class="lineno"> 450</span>{</div>
<div class="line"><a id="l00451" name="l00451"></a><span class="lineno"> 451</span> <span class="keyword">const</span> uint64_t b_val = <a class="code hl_function" href="namespacebtllib.html#a624a7c9e6716eaa82f78785ac705c81a">ntc64l</a>(char_out, char_in, k, fh_val, rh_val);</div>
<div class="line"><a id="l00452" name="l00452"></a><span class="lineno"> 452</span> <a class="code hl_function" href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d">nte64</a>(b_val, k, m, h_val);</div>
<div class="line"><a id="l00453" name="l00453"></a><span class="lineno"> 453</span>}</div>
<div class="line"><a id="l00454" name="l00454"></a><span class="lineno"> 454</span> </div>
<div class="line"><a id="l00467" name="l00467"></a><span class="lineno"> 467</span><span class="keyword">inline</span> <span class="keywordtype">bool</span></div>
<div class="line"><a id="l00468" name="l00468"></a><span class="lineno"><a class="line" href="namespacebtllib.html#ab3e9d3c79f52523e326b4a6a77988995"> 468</a></span><a class="code hl_function" href="namespacebtllib.html#a8ada92e6d8bdcf53b8985bb25a09738f">ntc64</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq, <span class="keywordtype">unsigned</span> k, uint64_t& h_val, <span class="keywordtype">unsigned</span>& loc_n)</div>
<div class="line"><a id="l00469" name="l00469"></a><span class="lineno"> 469</span>{</div>
<div class="line"><a id="l00470" name="l00470"></a><span class="lineno"> 470</span> h_val = 0;</div>
<div class="line"><a id="l00471" name="l00471"></a><span class="lineno"> 471</span> loc_n = 0;</div>
<div class="line"><a id="l00472" name="l00472"></a><span class="lineno"> 472</span> uint64_t fh_val = 0, rh_val = 0;</div>
<div class="line"><a id="l00473" name="l00473"></a><span class="lineno"> 473</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = <span class="keywordtype">int</span>(k - 1); i >= 0; i--) {</div>
<div class="line"><a id="l00474" name="l00474"></a><span class="lineno"> 474</span> <span class="keywordflow">if</span> (SEED_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[i]] == SEED_N) {</div>
<div class="line"><a id="l00475" name="l00475"></a><span class="lineno"> 475</span> loc_n = i;</div>
<div class="line"><a id="l00476" name="l00476"></a><span class="lineno"> 476</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</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> fh_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(fh_val);</div>
<div class="line"><a id="l00479" name="l00479"></a><span class="lineno"> 479</span> fh_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 1 - i]];</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> rh_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(rh_val);</div>
<div class="line"><a id="l00482" name="l00482"></a><span class="lineno"> 482</span> rh_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i] & CP_OFF];</div>
<div class="line"><a id="l00483" name="l00483"></a><span class="lineno"> 483</span> }</div>
<div class="line"><a id="l00484" name="l00484"></a><span class="lineno"> 484</span> h_val = canonical(fh_val, rh_val);</div>
<div class="line"><a id="l00485" name="l00485"></a><span class="lineno"> 485</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00486" name="l00486"></a><span class="lineno"> 486</span>}</div>
<div class="line"><a id="l00487" name="l00487"></a><span class="lineno"> 487</span> </div>
<div class="line"><a id="l00501" name="l00501"></a><span class="lineno"> 501</span><span class="keyword">inline</span> <span class="keywordtype">bool</span></div>
<div class="line"><a id="l00502" name="l00502"></a><span class="lineno"><a class="line" href="namespacebtllib.html#ad9d89881b66efe9b906433065314e015"> 502</a></span>ntmc64(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00503" name="l00503"></a><span class="lineno"> 503</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00504" name="l00504"></a><span class="lineno"> 504</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00505" name="l00505"></a><span class="lineno"> 505</span> <span class="keywordtype">unsigned</span>& loc_n,</div>
<div class="line"><a id="l00506" name="l00506"></a><span class="lineno"> 506</span> uint64_t* h_val)</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> uint64_t b_val = 0, fh_val = 0, rh_val = 0;</div>
<div class="line"><a id="l00509" name="l00509"></a><span class="lineno"> 509</span> loc_n = 0;</div>
<div class="line"><a id="l00510" name="l00510"></a><span class="lineno"> 510</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = <span class="keywordtype">int</span>(k - 1); i >= 0; i--) {</div>
<div class="line"><a id="l00511" name="l00511"></a><span class="lineno"> 511</span> <span class="keywordflow">if</span> (SEED_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[i]] == SEED_N) {</div>
<div class="line"><a id="l00512" name="l00512"></a><span class="lineno"> 512</span> loc_n = i;</div>
<div class="line"><a id="l00513" name="l00513"></a><span class="lineno"> 513</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00514" name="l00514"></a><span class="lineno"> 514</span> }</div>
<div class="line"><a id="l00515" name="l00515"></a><span class="lineno"> 515</span> fh_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(fh_val);</div>
<div class="line"><a id="l00516" name="l00516"></a><span class="lineno"> 516</span> fh_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 1 - i]];</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> rh_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(rh_val);</div>
<div class="line"><a id="l00519" name="l00519"></a><span class="lineno"> 519</span> rh_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i] & CP_OFF];</div>
<div class="line"><a id="l00520" name="l00520"></a><span class="lineno"> 520</span> }</div>
<div class="line"><a id="l00521" name="l00521"></a><span class="lineno"> 521</span> b_val = canonical(fh_val, rh_val);</div>
<div class="line"><a id="l00522" name="l00522"></a><span class="lineno"> 522</span> <a class="code hl_function" href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d">nte64</a>(b_val, k, m, h_val);</div>
<div class="line"><a id="l00523" name="l00523"></a><span class="lineno"> 523</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00524" name="l00524"></a><span class="lineno"> 524</span>}</div>
<div class="line"><a id="l00525" name="l00525"></a><span class="lineno"> 525</span> </div>
<div class="line"><a id="l00540" name="l00540"></a><span class="lineno"> 540</span><span class="keyword">inline</span> <span class="keywordtype">bool</span></div>
<div class="line"><a id="l00541" name="l00541"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a5fae0b8707ea6083163b98bcb806913b"> 541</a></span><a class="code hl_function" href="namespacebtllib.html#a8ada92e6d8bdcf53b8985bb25a09738f">ntc64</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00542" name="l00542"></a><span class="lineno"> 542</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00543" name="l00543"></a><span class="lineno"> 543</span> uint64_t& fh_val,</div>
<div class="line"><a id="l00544" name="l00544"></a><span class="lineno"> 544</span> uint64_t& rh_val,</div>
<div class="line"><a id="l00545" name="l00545"></a><span class="lineno"> 545</span> uint64_t& h_val,</div>
<div class="line"><a id="l00546" name="l00546"></a><span class="lineno"> 546</span> <span class="keywordtype">unsigned</span>& loc_n)</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> h_val = fh_val = rh_val = 0;</div>
<div class="line"><a id="l00549" name="l00549"></a><span class="lineno"> 549</span> loc_n = 0;</div>
<div class="line"><a id="l00550" name="l00550"></a><span class="lineno"> 550</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = <span class="keywordtype">int</span>(k - 1); i >= 0; i--) {</div>
<div class="line"><a id="l00551" name="l00551"></a><span class="lineno"> 551</span> <span class="keywordflow">if</span> (SEED_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[i]] == SEED_N) {</div>
<div class="line"><a id="l00552" name="l00552"></a><span class="lineno"> 552</span> loc_n = i;</div>
<div class="line"><a id="l00553" name="l00553"></a><span class="lineno"> 553</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00554" name="l00554"></a><span class="lineno"> 554</span> }</div>
<div class="line"><a id="l00555" name="l00555"></a><span class="lineno"> 555</span> fh_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(fh_val);</div>
<div class="line"><a id="l00556" name="l00556"></a><span class="lineno"> 556</span> fh_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 1 - i]];</div>
<div class="line"><a id="l00557" name="l00557"></a><span class="lineno"> 557</span> </div>
<div class="line"><a id="l00558" name="l00558"></a><span class="lineno"> 558</span> rh_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(rh_val);</div>
<div class="line"><a id="l00559" name="l00559"></a><span class="lineno"> 559</span> rh_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i] & CP_OFF];</div>
<div class="line"><a id="l00560" name="l00560"></a><span class="lineno"> 560</span> }</div>
<div class="line"><a id="l00561" name="l00561"></a><span class="lineno"> 561</span> h_val = canonical(fh_val, rh_val);</div>
<div class="line"><a id="l00562" name="l00562"></a><span class="lineno"> 562</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00563" name="l00563"></a><span class="lineno"> 563</span>}</div>
<div class="line"><a id="l00564" name="l00564"></a><span class="lineno"> 564</span> </div>
<div class="line"><a id="l00580" name="l00580"></a><span class="lineno"> 580</span><span class="keyword">inline</span> <span class="keywordtype">bool</span></div>
<div class="line"><a id="l00581" name="l00581"></a><span class="lineno"><a class="line" href="namespacebtllib.html#af1e944135aeae5fec1af3c96e928e256"> 581</a></span>ntmc64(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00582" name="l00582"></a><span class="lineno"> 582</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00583" name="l00583"></a><span class="lineno"> 583</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00584" name="l00584"></a><span class="lineno"> 584</span> uint64_t& fh_val,</div>
<div class="line"><a id="l00585" name="l00585"></a><span class="lineno"> 585</span> uint64_t& rh_val,</div>
<div class="line"><a id="l00586" name="l00586"></a><span class="lineno"> 586</span> <span class="keywordtype">unsigned</span>& loc_n,</div>
<div class="line"><a id="l00587" name="l00587"></a><span class="lineno"> 587</span> uint64_t* h_val)</div>
<div class="line"><a id="l00588" name="l00588"></a><span class="lineno"> 588</span>{</div>
<div class="line"><a id="l00589" name="l00589"></a><span class="lineno"> 589</span> fh_val = rh_val = 0;</div>
<div class="line"><a id="l00590" name="l00590"></a><span class="lineno"> 590</span> uint64_t b_val = 0;</div>
<div class="line"><a id="l00591" name="l00591"></a><span class="lineno"> 591</span> loc_n = 0;</div>
<div class="line"><a id="l00592" name="l00592"></a><span class="lineno"> 592</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = <span class="keywordtype">int</span>(k - 1); i >= 0; i--) {</div>
<div class="line"><a id="l00593" name="l00593"></a><span class="lineno"> 593</span> <span class="keywordflow">if</span> (SEED_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[i]] == SEED_N) {</div>
<div class="line"><a id="l00594" name="l00594"></a><span class="lineno"> 594</span> loc_n = i;</div>
<div class="line"><a id="l00595" name="l00595"></a><span class="lineno"> 595</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00596" name="l00596"></a><span class="lineno"> 596</span> }</div>
<div class="line"><a id="l00597" name="l00597"></a><span class="lineno"> 597</span> fh_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(fh_val);</div>
<div class="line"><a id="l00598" name="l00598"></a><span class="lineno"> 598</span> fh_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 1 - i]];</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> rh_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(rh_val);</div>
<div class="line"><a id="l00601" name="l00601"></a><span class="lineno"> 601</span> rh_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i] & CP_OFF];</div>
<div class="line"><a id="l00602" name="l00602"></a><span class="lineno"> 602</span> }</div>
<div class="line"><a id="l00603" name="l00603"></a><span class="lineno"> 603</span> b_val = canonical(fh_val, rh_val);</div>
<div class="line"><a id="l00604" name="l00604"></a><span class="lineno"> 604</span> <a class="code hl_function" href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d">nte64</a>(b_val, k, m, h_val);</div>
<div class="line"><a id="l00605" name="l00605"></a><span class="lineno"> 605</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00606" name="l00606"></a><span class="lineno"> 606</span>}</div>
<div class="line"><a id="l00607" name="l00607"></a><span class="lineno"> 607</span> </div>
<div class="line"><a id="l00625" name="l00625"></a><span class="lineno"> 625</span><span class="keyword">inline</span> <span class="keywordtype">bool</span></div>
<div class="line"><a id="l00626" name="l00626"></a><span class="lineno"><a class="line" href="namespacebtllib.html#ad1e06b1022676e280c1cbe7258034124"> 626</a></span>ntmc64(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00627" name="l00627"></a><span class="lineno"> 627</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00628" name="l00628"></a><span class="lineno"> 628</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00629" name="l00629"></a><span class="lineno"> 629</span> uint64_t& fh_val,</div>
<div class="line"><a id="l00630" name="l00630"></a><span class="lineno"> 630</span> uint64_t& rh_val,</div>
<div class="line"><a id="l00631" name="l00631"></a><span class="lineno"> 631</span> <span class="keywordtype">unsigned</span>& loc_n,</div>
<div class="line"><a id="l00632" name="l00632"></a><span class="lineno"> 632</span> uint64_t* h_val,</div>
<div class="line"><a id="l00633" name="l00633"></a><span class="lineno"> 633</span> <span class="keywordtype">bool</span>& h_stn)</div>
<div class="line"><a id="l00634" name="l00634"></a><span class="lineno"> 634</span>{</div>
<div class="line"><a id="l00635" name="l00635"></a><span class="lineno"> 635</span> fh_val = rh_val = 0;</div>
<div class="line"><a id="l00636" name="l00636"></a><span class="lineno"> 636</span> uint64_t b_val = 0;</div>
<div class="line"><a id="l00637" name="l00637"></a><span class="lineno"> 637</span> loc_n = 0;</div>
<div class="line"><a id="l00638" name="l00638"></a><span class="lineno"> 638</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = <span class="keywordtype">int</span>(k - 1); i >= 0; i--) {</div>
<div class="line"><a id="l00639" name="l00639"></a><span class="lineno"> 639</span> <span class="keywordflow">if</span> (SEED_TAB[(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[i]] == SEED_N) {</div>
<div class="line"><a id="l00640" name="l00640"></a><span class="lineno"> 640</span> loc_n = i;</div>
<div class="line"><a id="l00641" name="l00641"></a><span class="lineno"> 641</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00642" name="l00642"></a><span class="lineno"> 642</span> }</div>
<div class="line"><a id="l00643" name="l00643"></a><span class="lineno"> 643</span> fh_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(fh_val);</div>
<div class="line"><a id="l00644" name="l00644"></a><span class="lineno"> 644</span> fh_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[k - 1 - i]];</div>
<div class="line"><a id="l00645" name="l00645"></a><span class="lineno"> 645</span> </div>
<div class="line"><a id="l00646" name="l00646"></a><span class="lineno"> 646</span> rh_val = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(rh_val);</div>
<div class="line"><a id="l00647" name="l00647"></a><span class="lineno"> 647</span> rh_val ^= SEED_TAB[(<span class="keywordtype">unsigned</span> char)kmer_seq[i] & CP_OFF];</div>
<div class="line"><a id="l00648" name="l00648"></a><span class="lineno"> 648</span> }</div>
<div class="line"><a id="l00649" name="l00649"></a><span class="lineno"> 649</span> h_stn = rh_val < fh_val;</div>
<div class="line"><a id="l00650" name="l00650"></a><span class="lineno"> 650</span> b_val = canonical(fh_val, rh_val);</div>
<div class="line"><a id="l00651" name="l00651"></a><span class="lineno"> 651</span> <a class="code hl_function" href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d">nte64</a>(b_val, k, m, h_val);</div>
<div class="line"><a id="l00652" name="l00652"></a><span class="lineno"> 652</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00653" name="l00653"></a><span class="lineno"> 653</span>}</div>
<div class="line"><a id="l00654" name="l00654"></a><span class="lineno"> 654</span> </div>
<div class="line"><a id="l00668" name="l00668"></a><span class="lineno"> 668</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00669" name="l00669"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a681fcbc2a3469c0992304a05611cad8c"> 669</a></span>ntmc64(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_out,</div>
<div class="line"><a id="l00670" name="l00670"></a><span class="lineno"> 670</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> char_in,</div>
<div class="line"><a id="l00671" name="l00671"></a><span class="lineno"> 671</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00672" name="l00672"></a><span class="lineno"> 672</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00673" name="l00673"></a><span class="lineno"> 673</span> uint64_t& fh_val,</div>
<div class="line"><a id="l00674" name="l00674"></a><span class="lineno"> 674</span> uint64_t& rh_val,</div>
<div class="line"><a id="l00675" name="l00675"></a><span class="lineno"> 675</span> uint64_t* h_val,</div>
<div class="line"><a id="l00676" name="l00676"></a><span class="lineno"> 676</span> <span class="keywordtype">bool</span>& h_stn)</div>
<div class="line"><a id="l00677" name="l00677"></a><span class="lineno"> 677</span>{</div>
<div class="line"><a id="l00678" name="l00678"></a><span class="lineno"> 678</span> <span class="keyword">const</span> uint64_t b_val = <a class="code hl_function" href="namespacebtllib.html#a8ada92e6d8bdcf53b8985bb25a09738f">ntc64</a>(char_out, char_in, k, fh_val, rh_val);</div>
<div class="line"><a id="l00679" name="l00679"></a><span class="lineno"> 679</span> h_stn = rh_val < fh_val;</div>
<div class="line"><a id="l00680" name="l00680"></a><span class="lineno"> 680</span> <a class="code hl_function" href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d">nte64</a>(b_val, k, m, h_val);</div>
<div class="line"><a id="l00681" name="l00681"></a><span class="lineno"> 681</span>}</div>
<div class="line"><a id="l00682" name="l00682"></a><span class="lineno"> 682</span> </div>
<div class="line"><a id="l00696" name="l00696"></a><span class="lineno"> 696</span><span class="keyword">inline</span> uint64_t</div>
<div class="line"><a id="l00697" name="l00697"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a5f5f8a7e2bab90519461ed0f19a1963d"> 697</a></span><a class="code hl_function" href="namespacebtllib.html#a5f5f8a7e2bab90519461ed0f19a1963d">mask_hash</a>(uint64_t& fk_val,</div>
<div class="line"><a id="l00698" name="l00698"></a><span class="lineno"> 698</span> uint64_t& rk_val,</div>
<div class="line"><a id="l00699" name="l00699"></a><span class="lineno"> 699</span> <span class="keyword">const</span> <span class="keywordtype">char</span>* seed_seq,</div>
<div class="line"><a id="l00700" name="l00700"></a><span class="lineno"> 700</span> <span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00701" name="l00701"></a><span class="lineno"> 701</span> <span class="keywordtype">unsigned</span> k)</div>
<div class="line"><a id="l00702" name="l00702"></a><span class="lineno"> 702</span>{</div>
<div class="line"><a id="l00703" name="l00703"></a><span class="lineno"> 703</span> uint64_t fs_val = fk_val, rs_val = rk_val;</div>
<div class="line"><a id="l00704" name="l00704"></a><span class="lineno"> 704</span> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; i < k; i++) {</div>
<div class="line"><a id="l00705" name="l00705"></a><span class="lineno"> 705</span> <span class="keywordflow">if</span> (seed_seq[i] != <span class="charliteral">'1'</span>) {</div>
<div class="line"><a id="l00706" name="l00706"></a><span class="lineno"> 706</span> fs_val ^= MS_TAB((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[i], k - 1 - i);</div>
<div class="line"><a id="l00707" name="l00707"></a><span class="lineno"> 707</span> rs_val ^= MS_TAB((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[i] & CP_OFF, i);</div>
<div class="line"><a id="l00708" name="l00708"></a><span class="lineno"> 708</span> }</div>
<div class="line"><a id="l00709" name="l00709"></a><span class="lineno"> 709</span> }</div>
<div class="line"><a id="l00710" name="l00710"></a><span class="lineno"> 710</span> <span class="keywordflow">return</span> canonical(fs_val, rs_val);</div>
<div class="line"><a id="l00711" name="l00711"></a><span class="lineno"> 711</span>}</div>
<div class="line"><a id="l00712" name="l00712"></a><span class="lineno"> 712</span> </div>
<div class="line"><a id="l00727" name="l00727"></a><span class="lineno"> 727</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00728" name="l00728"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a28157a0a7a0364f94b8b1fec3a95bb40"> 728</a></span><a class="code hl_function" href="namespacebtllib.html#a28157a0a7a0364f94b8b1fec3a95bb40">sub_hash</a>(uint64_t fh_val,</div>
<div class="line"><a id="l00729" name="l00729"></a><span class="lineno"> 729</span> uint64_t rh_val,</div>
<div class="line"><a id="l00730" name="l00730"></a><span class="lineno"> 730</span> <span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00731" name="l00731"></a><span class="lineno"> 731</span> <span class="keyword">const</span> std::vector<unsigned>& positions,</div>
<div class="line"><a id="l00732" name="l00732"></a><span class="lineno"> 732</span> <span class="keyword">const</span> std::vector<unsigned char>& new_bases,</div>
<div class="line"><a id="l00733" name="l00733"></a><span class="lineno"> 733</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00734" name="l00734"></a><span class="lineno"> 734</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00735" name="l00735"></a><span class="lineno"> 735</span> uint64_t* h_val)</div>
<div class="line"><a id="l00736" name="l00736"></a><span class="lineno"> 736</span>{</div>
<div class="line"><a id="l00737" name="l00737"></a><span class="lineno"> 737</span> uint64_t b_val = 0;</div>
<div class="line"><a id="l00738" name="l00738"></a><span class="lineno"> 738</span> </div>
<div class="line"><a id="l00739" name="l00739"></a><span class="lineno"> 739</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < positions.size(); i++) {</div>
<div class="line"><a id="l00740" name="l00740"></a><span class="lineno"> 740</span> <span class="keyword">const</span> <span class="keyword">auto</span> pos = positions[i];</div>
<div class="line"><a id="l00741" name="l00741"></a><span class="lineno"> 741</span> <span class="keyword">const</span> <span class="keyword">auto</span> new_base = new_bases[i];</div>
<div class="line"><a id="l00742" name="l00742"></a><span class="lineno"> 742</span> </div>
<div class="line"><a id="l00743" name="l00743"></a><span class="lineno"> 743</span> fh_val ^= MS_TAB((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[pos], k - 1 - pos);</div>
<div class="line"><a id="l00744" name="l00744"></a><span class="lineno"> 744</span> fh_val ^= MS_TAB(new_base, k - 1 - pos);</div>
<div class="line"><a id="l00745" name="l00745"></a><span class="lineno"> 745</span> </div>
<div class="line"><a id="l00746" name="l00746"></a><span class="lineno"> 746</span> rh_val ^= MS_TAB((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[pos] & CP_OFF, pos);</div>
<div class="line"><a id="l00747" name="l00747"></a><span class="lineno"> 747</span> rh_val ^= MS_TAB(new_base & CP_OFF, pos);</div>
<div class="line"><a id="l00748" name="l00748"></a><span class="lineno"> 748</span> }</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> b_val = canonical(fh_val, rh_val);</div>
<div class="line"><a id="l00751" name="l00751"></a><span class="lineno"> 751</span> <a class="code hl_function" href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d">nte64</a>(b_val, k, m, h_val);</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> </div>
<div class="line"><a id="l00778" name="l00778"></a><span class="lineno"> 778</span><span class="keyword">inline</span> <span class="keywordtype">bool</span></div>
<div class="line"><a id="l00779" name="l00779"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a6313004e085d5c5002a57f261b4d83e5"> 779</a></span>ntmsm64(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00780" name="l00780"></a><span class="lineno"> 780</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l00781" name="l00781"></a><span class="lineno"> 781</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l00782" name="l00782"></a><span class="lineno"> 782</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00783" name="l00783"></a><span class="lineno"> 783</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00784" name="l00784"></a><span class="lineno"> 784</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l00785" name="l00785"></a><span class="lineno"> 785</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l00786" name="l00786"></a><span class="lineno"> 786</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l00787" name="l00787"></a><span class="lineno"> 787</span> uint64_t* fh_val,</div>
<div class="line"><a id="l00788" name="l00788"></a><span class="lineno"> 788</span> uint64_t* rh_val,</div>
<div class="line"><a id="l00789" name="l00789"></a><span class="lineno"> 789</span> <span class="keywordtype">unsigned</span>& loc_n,</div>
<div class="line"><a id="l00790" name="l00790"></a><span class="lineno"> 790</span> uint64_t* h_val)</div>
<div class="line"><a id="l00791" name="l00791"></a><span class="lineno"> 791</span>{</div>
<div class="line"><a id="l00792" name="l00792"></a><span class="lineno"> 792</span> <span class="keywordtype">unsigned</span> i_base;</div>
<div class="line"><a id="l00793" name="l00793"></a><span class="lineno"> 793</span> uint64_t fh_seed, rh_seed;</div>
<div class="line"><a id="l00794" name="l00794"></a><span class="lineno"> 794</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="l00795" name="l00795"></a><span class="lineno"> 795</span> fh_seed = 0;</div>
<div class="line"><a id="l00796" name="l00796"></a><span class="lineno"> 796</span> rh_seed = 0;</div>
<div class="line"><a id="l00797" name="l00797"></a><span class="lineno"> 797</span> </div>
<div class="line"><a id="l00798" name="l00798"></a><span class="lineno"> 798</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="l00799" name="l00799"></a><span class="lineno"> 799</span> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> pos = block[0]; pos < block[1]; pos++) {</div>
<div class="line"><a id="l00800" name="l00800"></a><span class="lineno"> 800</span> <span class="keywordflow">if</span> (kmer_seq[pos] == SEED_N) {</div>
<div class="line"><a id="l00801" name="l00801"></a><span class="lineno"> 801</span> loc_n = pos;</div>
<div class="line"><a id="l00802" name="l00802"></a><span class="lineno"> 802</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00803" name="l00803"></a><span class="lineno"> 803</span> }</div>
<div class="line"><a id="l00804" name="l00804"></a><span class="lineno"> 804</span> fh_seed ^= MS_TAB((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[pos], k - 1 - pos);</div>
<div class="line"><a id="l00805" name="l00805"></a><span class="lineno"> 805</span> rh_seed ^= MS_TAB((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[pos] & CP_OFF, pos);</div>
<div class="line"><a id="l00806" name="l00806"></a><span class="lineno"> 806</span> }</div>
<div class="line"><a id="l00807" name="l00807"></a><span class="lineno"> 807</span> }</div>
<div class="line"><a id="l00808" name="l00808"></a><span class="lineno"> 808</span> fh_nomonos[i_seed] = fh_seed;</div>
<div class="line"><a id="l00809" name="l00809"></a><span class="lineno"> 809</span> rh_nomonos[i_seed] = rh_seed;</div>
<div class="line"><a id="l00810" name="l00810"></a><span class="lineno"> 810</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keywordtype">unsigned</span> pos : seeds_monomers[i_seed]) {</div>
<div class="line"><a id="l00811" name="l00811"></a><span class="lineno"> 811</span> fh_seed ^= MS_TAB((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[pos], k - 1 - pos);</div>
<div class="line"><a id="l00812" name="l00812"></a><span class="lineno"> 812</span> rh_seed ^= MS_TAB((<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>)kmer_seq[pos] & CP_OFF, pos);</div>
<div class="line"><a id="l00813" name="l00813"></a><span class="lineno"> 813</span> }</div>
<div class="line"><a id="l00814" name="l00814"></a><span class="lineno"> 814</span> fh_val[i_seed] = fh_seed;</div>
<div class="line"><a id="l00815" name="l00815"></a><span class="lineno"> 815</span> rh_val[i_seed] = rh_seed;</div>
<div class="line"><a id="l00816" name="l00816"></a><span class="lineno"> 816</span> i_base = i_seed * m2;</div>
<div class="line"><a id="l00817" name="l00817"></a><span class="lineno"> 817</span> h_val[i_base] = canonical(fh_seed, rh_seed);</div>
<div class="line"><a id="l00818" name="l00818"></a><span class="lineno"> 818</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="l00819" name="l00819"></a><span class="lineno"> 819</span> h_val[i_base + i_hash] = h_val[i_base] * (i_hash ^ k * MULTISEED);</div>
<div class="line"><a id="l00820" name="l00820"></a><span class="lineno"> 820</span> h_val[i_base + i_hash] ^= h_val[i_base + i_hash] >> MULTISHIFT;</div>
<div class="line"><a id="l00821" name="l00821"></a><span class="lineno"> 821</span> }</div>
<div class="line"><a id="l00822" name="l00822"></a><span class="lineno"> 822</span> }</div>
<div class="line"><a id="l00823" name="l00823"></a><span class="lineno"> 823</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a id="l00824" name="l00824"></a><span class="lineno"> 824</span>}</div>
<div class="line"><a id="l00825" name="l00825"></a><span class="lineno"> 825</span> </div>
<div class="line"><a id="l00826" name="l00826"></a><span class="lineno"> 826</span><span class="preprocessor">#define NTMSM64(ROL_HANDLING, IN_HANDLING, OUT_HANDLING, ROR_HANDLING) \</span></div>
<div class="line"><a id="l00827" name="l00827"></a><span class="lineno"> 827</span><span class="preprocessor"> unsigned char char_out, char_in; \</span></div>
<div class="line"><a id="l00828" name="l00828"></a><span class="lineno"> 828</span><span class="preprocessor"> uint64_t fh_seed, rh_seed; \</span></div>
<div class="line"><a id="l00829" name="l00829"></a><span class="lineno"> 829</span><span class="preprocessor"> unsigned i_out, i_in, i_base; \</span></div>
<div class="line"><a id="l00830" name="l00830"></a><span class="lineno"> 830</span><span class="preprocessor"> for (unsigned i_seed = 0; i_seed < m; i_seed++) { \</span></div>
<div class="line"><a id="l00831" name="l00831"></a><span class="lineno"> 831</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="l00832" name="l00832"></a><span class="lineno"> 832</span><span class="preprocessor"> for (const auto& block : seeds_blocks[i_seed]) \</span></div>
<div class="line"><a id="l00833" name="l00833"></a><span class="lineno"> 833</span><span class="preprocessor"> { \</span></div>
<div class="line"><a id="l00834" name="l00834"></a><span class="lineno"> 834</span><span class="preprocessor"> IN_HANDLING \</span></div>
<div class="line"><a id="l00835" name="l00835"></a><span class="lineno"> 835</span><span class="preprocessor"> OUT_HANDLING \</span></div>
<div class="line"><a id="l00836" name="l00836"></a><span class="lineno"> 836</span><span class="preprocessor"> fh_seed ^= MS_TAB(char_out, k - i_out); \</span></div>
<div class="line"><a id="l00837" name="l00837"></a><span class="lineno"> 837</span><span class="preprocessor"> fh_seed ^= MS_TAB(char_in, k - i_in); \</span></div>
<div class="line"><a id="l00838" name="l00838"></a><span class="lineno"> 838</span><span class="preprocessor"> rh_seed ^= MS_TAB(char_out & CP_OFF, i_out); \</span></div>
<div class="line"><a id="l00839" name="l00839"></a><span class="lineno"> 839</span><span class="preprocessor"> rh_seed ^= MS_TAB(char_in & CP_OFF, i_in); \</span></div>
<div class="line"><a id="l00840" name="l00840"></a><span class="lineno"> 840</span><span class="preprocessor"> } \</span></div>
<div class="line"><a id="l00841" name="l00841"></a><span class="lineno"> 841</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="l00842" name="l00842"></a><span class="lineno"> 842</span><span class="preprocessor"> fh_nomonos[i_seed] = fh_seed; \</span></div>
<div class="line"><a id="l00843" name="l00843"></a><span class="lineno"> 843</span><span class="preprocessor"> rh_nomonos[i_seed] = rh_seed; \</span></div>
<div class="line"><a id="l00844" name="l00844"></a><span class="lineno"> 844</span><span class="preprocessor"> for (const auto& pos : seeds_monomers[i_seed]) { \</span></div>
<div class="line"><a id="l00845" name="l00845"></a><span class="lineno"> 845</span><span class="preprocessor"> fh_seed ^= MS_TAB((unsigned char)kmer_seq[pos + 1], k - 1 - pos); \</span></div>
<div class="line"><a id="l00846" name="l00846"></a><span class="lineno"> 846</span><span class="preprocessor"> rh_seed ^= MS_TAB((unsigned char)kmer_seq[pos + 1] & CP_OFF, pos); \</span></div>
<div class="line"><a id="l00847" name="l00847"></a><span class="lineno"> 847</span><span class="preprocessor"> } \</span></div>
<div class="line"><a id="l00848" name="l00848"></a><span class="lineno"> 848</span><span class="preprocessor"> fh_val[i_seed] = fh_seed; \</span></div>
<div class="line"><a id="l00849" name="l00849"></a><span class="lineno"> 849</span><span class="preprocessor"> rh_val[i_seed] = rh_seed; \</span></div>
<div class="line"><a id="l00850" name="l00850"></a><span class="lineno"> 850</span><span class="preprocessor"> i_base = i_seed * m2; \</span></div>
<div class="line"><a id="l00851" name="l00851"></a><span class="lineno"> 851</span><span class="preprocessor"> h_val[i_base] = canonical(fh_seed, rh_seed); \</span></div>
<div class="line"><a id="l00852" name="l00852"></a><span class="lineno"> 852</span><span class="preprocessor"> for (unsigned i_hash = 1; i_hash < m2; i_hash++) { \</span></div>
<div class="line"><a id="l00853" name="l00853"></a><span class="lineno"> 853</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="l00854" name="l00854"></a><span class="lineno"> 854</span><span class="preprocessor"> h_val[i_base + i_hash] ^= h_val[i_base + i_hash] >> MULTISHIFT; \</span></div>
<div class="line"><a id="l00855" name="l00855"></a><span class="lineno"> 855</span><span class="preprocessor"> } \</span></div>
<div class="line"><a id="l00856" name="l00856"></a><span class="lineno"> 856</span><span class="preprocessor"> }</span></div>
<div class="line"><a id="l00857" name="l00857"></a><span class="lineno"> 857</span> </div>
<div class="line"><a id="l00879" name="l00879"></a><span class="lineno"> 879</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00880" name="l00880"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a3f5acf04d8639fd2a87590aeb74624fe"> 880</a></span>ntmsm64(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00881" name="l00881"></a><span class="lineno"> 881</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l00882" name="l00882"></a><span class="lineno"> 882</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l00883" name="l00883"></a><span class="lineno"> 883</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00884" name="l00884"></a><span class="lineno"> 884</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00885" name="l00885"></a><span class="lineno"> 885</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l00886" name="l00886"></a><span class="lineno"> 886</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l00887" name="l00887"></a><span class="lineno"> 887</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l00888" name="l00888"></a><span class="lineno"> 888</span> uint64_t* fh_val,</div>
<div class="line"><a id="l00889" name="l00889"></a><span class="lineno"> 889</span> uint64_t* rh_val,</div>
<div class="line"><a id="l00890" name="l00890"></a><span class="lineno"> 890</span> uint64_t* h_val)</div>
<div class="line"><a id="l00891" name="l00891"></a><span class="lineno"> 891</span>{</div>
<div class="line"><a id="l00892" name="l00892"></a><span class="lineno"> 892</span> NTMSM64(fh_seed = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(fh_nomonos[i_seed]); rh_seed = rh_nomonos[i_seed];</div>
<div class="line"><a id="l00893" name="l00893"></a><span class="lineno"> 893</span> , i_in = block[1];</div>
<div class="line"><a id="l00894" name="l00894"></a><span class="lineno"> 894</span> char_in = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_in];</div>
<div class="line"><a id="l00895" name="l00895"></a><span class="lineno"> 895</span> , i_out = block[0];</div>
<div class="line"><a id="l00896" name="l00896"></a><span class="lineno"> 896</span> char_out = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_out];</div>
<div class="line"><a id="l00897" name="l00897"></a><span class="lineno"> 897</span> , rh_seed = <a class="code hl_function" href="namespacebtllib.html#a731d4ddcd44c63f3b6bfa6c33a0eedb8">sror</a>(rh_seed);)</div>
<div class="line"><a id="l00898" name="l00898"></a><span class="lineno"> 898</span>}</div>
<div class="line"><a id="l00899" name="l00899"></a><span class="lineno"> 899</span> </div>
<div class="line"><a id="l00921" name="l00921"></a><span class="lineno"> 921</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00922" name="l00922"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a9f26f832a1ae7fdb50c4ccbfcfda4740"> 922</a></span>ntmsm64l(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00923" name="l00923"></a><span class="lineno"> 923</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l00924" name="l00924"></a><span class="lineno"> 924</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l00925" name="l00925"></a><span class="lineno"> 925</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00926" name="l00926"></a><span class="lineno"> 926</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00927" name="l00927"></a><span class="lineno"> 927</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l00928" name="l00928"></a><span class="lineno"> 928</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l00929" name="l00929"></a><span class="lineno"> 929</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l00930" name="l00930"></a><span class="lineno"> 930</span> uint64_t* fh_val,</div>
<div class="line"><a id="l00931" name="l00931"></a><span class="lineno"> 931</span> uint64_t* rh_val,</div>
<div class="line"><a id="l00932" name="l00932"></a><span class="lineno"> 932</span> uint64_t* h_val)</div>
<div class="line"><a id="l00933" name="l00933"></a><span class="lineno"> 933</span>{</div>
<div class="line"><a id="l00934" name="l00934"></a><span class="lineno"> 934</span> NTMSM64(fh_seed = fh_nomonos[i_seed]; rh_seed = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(rh_nomonos[i_seed]);</div>
<div class="line"><a id="l00935" name="l00935"></a><span class="lineno"> 935</span> , i_in = block[0];</div>
<div class="line"><a id="l00936" name="l00936"></a><span class="lineno"> 936</span> char_in = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_in];</div>
<div class="line"><a id="l00937" name="l00937"></a><span class="lineno"> 937</span> , i_out = block[1];</div>
<div class="line"><a id="l00938" name="l00938"></a><span class="lineno"> 938</span> char_out = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_out];</div>
<div class="line"><a id="l00939" name="l00939"></a><span class="lineno"> 939</span> , fh_seed = <a class="code hl_function" href="namespacebtllib.html#a731d4ddcd44c63f3b6bfa6c33a0eedb8">sror</a>(fh_seed);)</div>
<div class="line"><a id="l00940" name="l00940"></a><span class="lineno"> 940</span>}</div>
<div class="line"><a id="l00941" name="l00941"></a><span class="lineno"> 941</span> </div>
<div class="line"><a id="l00963" name="l00963"></a><span class="lineno"> 963</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l00964" name="l00964"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a4223b68d52ad14567baed28f23538b27"> 964</a></span>ntmsm64(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l00965" name="l00965"></a><span class="lineno"> 965</span> <span class="keywordtype">char</span> in,</div>
<div class="line"><a id="l00966" name="l00966"></a><span class="lineno"> 966</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l00967" name="l00967"></a><span class="lineno"> 967</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l00968" name="l00968"></a><span class="lineno"> 968</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l00969" name="l00969"></a><span class="lineno"> 969</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l00970" name="l00970"></a><span class="lineno"> 970</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l00971" name="l00971"></a><span class="lineno"> 971</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l00972" name="l00972"></a><span class="lineno"> 972</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l00973" name="l00973"></a><span class="lineno"> 973</span> uint64_t* fh_val,</div>
<div class="line"><a id="l00974" name="l00974"></a><span class="lineno"> 974</span> uint64_t* rh_val,</div>
<div class="line"><a id="l00975" name="l00975"></a><span class="lineno"> 975</span> uint64_t* h_val)</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> NTMSM64(</div>
<div class="line"><a id="l00978" name="l00978"></a><span class="lineno"> 978</span> fh_seed = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(fh_nomonos[i_seed]); rh_seed = rh_nomonos[i_seed];</div>
<div class="line"><a id="l00979" name="l00979"></a><span class="lineno"> 979</span> , i_in = block[1];</div>
<div class="line"><a id="l00980" name="l00980"></a><span class="lineno"> 980</span> <span class="keywordflow">if</span> (i_in > k - 1) { char_in = in; } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00981" name="l00981"></a><span class="lineno"> 981</span> char_in = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_in];</div>
<div class="line"><a id="l00982" name="l00982"></a><span class="lineno"> 982</span> },</div>
<div class="line"><a id="l00983" name="l00983"></a><span class="lineno"> 983</span> i_out = block[0];</div>
<div class="line"><a id="l00984" name="l00984"></a><span class="lineno"> 984</span> char_out = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_out];</div>
<div class="line"><a id="l00985" name="l00985"></a><span class="lineno"> 985</span> , rh_seed = <a class="code hl_function" href="namespacebtllib.html#a731d4ddcd44c63f3b6bfa6c33a0eedb8">sror</a>(rh_seed);)</div>
<div class="line"><a id="l00986" name="l00986"></a><span class="lineno"> 986</span>}</div>
<div class="line"><a id="l00987" name="l00987"></a><span class="lineno"> 987</span> </div>
<div class="line"><a id="l01009" name="l01009"></a><span class="lineno"> 1009</span><span class="keyword">inline</span> <span class="keywordtype">void</span></div>
<div class="line"><a id="l01010" name="l01010"></a><span class="lineno"><a class="line" href="namespacebtllib.html#a9d6a992860a01379d2b67902a10ff275"> 1010</a></span>ntmsm64l(<span class="keyword">const</span> <span class="keywordtype">char</span>* kmer_seq,</div>
<div class="line"><a id="l01011" name="l01011"></a><span class="lineno"> 1011</span> <span class="keywordtype">char</span> in,</div>
<div class="line"><a id="l01012" name="l01012"></a><span class="lineno"> 1012</span> <span class="keyword">const</span> std::vector<SpacedSeedBlocks>& seeds_blocks,</div>
<div class="line"><a id="l01013" name="l01013"></a><span class="lineno"> 1013</span> <span class="keyword">const</span> std::vector<SpacedSeedMonomers>& seeds_monomers,</div>
<div class="line"><a id="l01014" name="l01014"></a><span class="lineno"> 1014</span> <span class="keywordtype">unsigned</span> k,</div>
<div class="line"><a id="l01015" name="l01015"></a><span class="lineno"> 1015</span> <span class="keywordtype">unsigned</span> m,</div>
<div class="line"><a id="l01016" name="l01016"></a><span class="lineno"> 1016</span> <span class="keywordtype">unsigned</span> m2,</div>
<div class="line"><a id="l01017" name="l01017"></a><span class="lineno"> 1017</span> uint64_t* fh_nomonos,</div>
<div class="line"><a id="l01018" name="l01018"></a><span class="lineno"> 1018</span> uint64_t* rh_nomonos,</div>
<div class="line"><a id="l01019" name="l01019"></a><span class="lineno"> 1019</span> uint64_t* fh_val,</div>
<div class="line"><a id="l01020" name="l01020"></a><span class="lineno"> 1020</span> uint64_t* rh_val,</div>
<div class="line"><a id="l01021" name="l01021"></a><span class="lineno"> 1021</span> uint64_t* h_val)</div>
<div class="line"><a id="l01022" name="l01022"></a><span class="lineno"> 1022</span>{</div>
<div class="line"><a id="l01023" name="l01023"></a><span class="lineno"> 1023</span> NTMSM64(</div>
<div class="line"><a id="l01024" name="l01024"></a><span class="lineno"> 1024</span> fh_seed = fh_nomonos[i_seed]; rh_seed = <a class="code hl_function" href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">srol</a>(rh_nomonos[i_seed]);</div>
<div class="line"><a id="l01025" name="l01025"></a><span class="lineno"> 1025</span> , i_in = block[0];</div>
<div class="line"><a id="l01026" name="l01026"></a><span class="lineno"> 1026</span> <span class="keywordflow">if</span> (i_in > k - 1) { char_in = in; } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l01027" name="l01027"></a><span class="lineno"> 1027</span> char_in = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_in];</div>
<div class="line"><a id="l01028" name="l01028"></a><span class="lineno"> 1028</span> },</div>
<div class="line"><a id="l01029" name="l01029"></a><span class="lineno"> 1029</span> i_out = block[1];</div>
<div class="line"><a id="l01030" name="l01030"></a><span class="lineno"> 1030</span> char_out = (<span class="keywordtype">unsigned</span> char)kmer_seq[i_out];</div>
<div class="line"><a id="l01031" name="l01031"></a><span class="lineno"> 1031</span> , fh_seed = <a class="code hl_function" href="namespacebtllib.html#a731d4ddcd44c63f3b6bfa6c33a0eedb8">sror</a>(fh_seed);)</div>
<div class="line"><a id="l01032" name="l01032"></a><span class="lineno"> 1032</span>}</div>
<div class="line"><a id="l01033" name="l01033"></a><span class="lineno"> 1033</span> </div>
<div class="line"><a id="l01034" name="l01034"></a><span class="lineno"> 1034</span>} <span class="comment">// namespace btllib</span></div>
<div class="line"><a id="l01035" name="l01035"></a><span class="lineno"> 1035</span> </div>
<div class="line"><a id="l01036" name="l01036"></a><span class="lineno"> 1036</span><span class="preprocessor">#endif</span></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:15</div></div>
<div class="ttc" id="anamespacebtllib_html_a26d4fe6e3d7e9a4bb3edfb4d51d9a7d2"><div class="ttname"><a href="namespacebtllib.html#a26d4fe6e3d7e9a4bb3edfb4d51d9a7d2">btllib::ntf64l</a></div><div class="ttdeci">uint64_t ntf64l(uint64_t rh_val, unsigned k, unsigned char char_out, unsigned char char_in)</div><div class="ttdef"><b>Definition</b> nthash_lowlevel.hpp:292</div></div>
<div class="ttc" id="anamespacebtllib_html_a28157a0a7a0364f94b8b1fec3a95bb40"><div class="ttname"><a href="namespacebtllib.html#a28157a0a7a0364f94b8b1fec3a95bb40">btllib::sub_hash</a></div><div class="ttdeci">void sub_hash(uint64_t fh_val, uint64_t rh_val, const char *kmer_seq, const std::vector< unsigned > &positions, const std::vector< unsigned char > &new_bases, unsigned k, unsigned m, uint64_t *h_val)</div><div class="ttdef"><b>Definition</b> nthash_lowlevel.hpp:728</div></div>
<div class="ttc" id="anamespacebtllib_html_a2a43294ffe95420456953e3c2e674bdb"><div class="ttname"><a href="namespacebtllib.html#a2a43294ffe95420456953e3c2e674bdb">btllib::ntr64l</a></div><div class="ttdeci">uint64_t ntr64l(uint64_t fh_val, unsigned k, unsigned char char_out, unsigned char char_in)</div><div class="ttdef"><b>Definition</b> nthash_lowlevel.hpp:314</div></div>
<div class="ttc" id="anamespacebtllib_html_a3d172327f4a061736fa3788a476da88f"><div class="ttname"><a href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">btllib::srol</a></div><div class="ttdeci">uint64_t srol(const uint64_t x)</div><div class="ttdef"><b>Definition</b> nthash_lowlevel.hpp:54</div></div>
<div class="ttc" id="anamespacebtllib_html_a5f5f8a7e2bab90519461ed0f19a1963d"><div class="ttname"><a href="namespacebtllib.html#a5f5f8a7e2bab90519461ed0f19a1963d">btllib::mask_hash</a></div><div class="ttdeci">uint64_t mask_hash(uint64_t &fk_val, uint64_t &rk_val, const char *seed_seq, const char *kmer_seq, unsigned k)</div><div class="ttdef"><b>Definition</b> nthash_lowlevel.hpp:697</div></div>
<div class="ttc" id="anamespacebtllib_html_a624a7c9e6716eaa82f78785ac705c81a"><div class="ttname"><a href="namespacebtllib.html#a624a7c9e6716eaa82f78785ac705c81a">btllib::ntc64l</a></div><div class="ttdeci">uint64_t ntc64l(unsigned char char_out, unsigned char char_in, unsigned k, uint64_t &fh_val, uint64_t &rh_val)</div><div class="ttdef"><b>Definition</b> nthash_lowlevel.hpp:338</div></div>
<div class="ttc" id="anamespacebtllib_html_a731d4ddcd44c63f3b6bfa6c33a0eedb8"><div class="ttname"><a href="namespacebtllib.html#a731d4ddcd44c63f3b6bfa6c33a0eedb8">btllib::sror</a></div><div class="ttdeci">uint64_t sror(const uint64_t x)</div><div class="ttdef"><b>Definition</b> nthash_lowlevel.hpp:88</div></div>
<div class="ttc" id="anamespacebtllib_html_a8ada92e6d8bdcf53b8985bb25a09738f"><div class="ttname"><a href="namespacebtllib.html#a8ada92e6d8bdcf53b8985bb25a09738f">btllib::ntc64</a></div><div class="ttdeci">uint64_t ntc64(const char *kmer_seq, unsigned k)</div><div class="ttdef"><b>Definition</b> nthash_lowlevel.hpp:231</div></div>
<div class="ttc" id="anamespacebtllib_html_aa2ad0c0e5b78e8db97508044ce9c1906"><div class="ttname"><a href="namespacebtllib.html#aa2ad0c0e5b78e8db97508044ce9c1906">btllib::ntr64</a></div><div class="ttdeci">uint64_t ntr64(const char *kmer_seq, unsigned k)</div><div class="ttdef"><b>Definition</b> nthash_lowlevel.hpp:144</div></div>
<div class="ttc" id="anamespacebtllib_html_aac394235878ae23a28e3d6eb152f5d6d"><div class="ttname"><a href="namespacebtllib.html#aac394235878ae23a28e3d6eb152f5d6d">btllib::nte64</a></div><div class="ttdeci">void nte64(uint64_t bh_val, unsigned k, unsigned h, uint64_t *h_val)</div><div class="ttdef"><b>Definition</b> nthash_lowlevel.hpp:358</div></div>
<div class="ttc" id="anamespacebtllib_html_adf40469a5081c357816a15ba2a7a158d"><div class="ttname"><a href="namespacebtllib.html#adf40469a5081c357816a15ba2a7a158d">btllib::ntf64</a></div><div class="ttdeci">uint64_t ntf64(const char *kmer_seq, unsigned k)</div><div class="ttdef"><b>Definition</b> nthash_lowlevel.hpp:103</div></div>
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