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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<div class="title">xsample06.cpp</div> </div>
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<p>Use of sparse vector for compressed DNA strings (2 bits per bp) Construction of comparison functions on bit-transposed compressed containers, benchmarking.</p><dl class="section see"><dt>See also</dt><dd><a class="el" href="classbm_1_1sparse__vector.html" title="sparse vector with runtime compression using bit transposition method">bm::sparse_vector</a> </dd>
<dd>
<a class="el" href="group__svalgo.html#ga5b8ca92c5fff30f5b741fc95fe2b3199" title="Find first mismatch (element which is different) between two sparse vectors (uses linear scan in bit-...">bm::sparse_vector_find_first_mismatch</a></dd></dl>
<div class="fragment"><div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment">Copyright(c) 2002-2019 Anatoliy Kuznetsov(anatoliy_kuznetsov at yahoo.com)</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">Licensed under the Apache License, Version 2.0 (the "License");</span></div>
<div class="line"><span class="comment">you may not use this file except in compliance with the License.</span></div>
<div class="line"><span class="comment">You may obtain a copy of the License at</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> http://www.apache.org/licenses/LICENSE-2.0</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">Unless required by applicable law or agreed to in writing, software</span></div>
<div class="line"><span class="comment">distributed under the License is distributed on an "AS IS" BASIS,</span></div>
<div class="line"><span class="comment">WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></div>
<div class="line"><span class="comment">See the License for the specific language governing permissions and</span></div>
<div class="line"><span class="comment">limitations under the License.</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">For more information please visit: http://bitmagic.io</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/** \example xsample06.cpp</span></div>
<div class="line"><span class="comment"> Use of sparse vector for compressed DNA strings (2 bits per bp)</span></div>
<div class="line"><span class="comment"> Construction of comparison functions on bit-transposed compressed</span></div>
<div class="line"><span class="comment"> containers, benchmarking.</span></div>
<div class="line"><span class="comment"> </span></div>
<div class="line"><span class="comment"> \sa bm::sparse_vector</span></div>
<div class="line"><span class="comment"> \sa bm::sparse_vector_find_first_mismatch</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/*! \file xsample06.cpp</span></div>
<div class="line"><span class="comment"> \brief Example: Use of sparse vector for compressed DNA strings</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"> </div>
<div class="line"><span class="preprocessor">#include <assert.h></span></div>
<div class="line"><span class="preprocessor">#include <stdlib.h></span></div>
<div class="line"> </div>
<div class="line"><span class="preprocessor">#include <iostream></span></div>
<div class="line"><span class="preprocessor">#include <vector></span></div>
<div class="line"><span class="preprocessor">#include <algorithm></span></div>
<div class="line"><span class="preprocessor">#include <utility></span></div>
<div class="line"> </div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bm_8h.html">bm.h</a>"</span></div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bmsparsevec_8h.html">bmsparsevec.h</a>"</span></div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bmsparsevec__algo_8h.html">bmsparsevec_algo.h</a>"</span></div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bmsparsevec__serial_8h.html">bmsparsevec_serial.h</a>"</span></div>
<div class="line"> </div>
<div class="line"><span class="comment">// BitMagic utilities for debug and timings</span></div>
<div class="line"><span class="preprocessor">#include "bmdbg.h"</span></div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bmtimer_8h.html">bmtimer.h</a>"</span></div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="keyword">using namespace </span>std;</div>
<div class="line"> </div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// Translate DNA letter to integer code</span></div>
<div class="line"><span class="comment">/// Please note this function uses extended alphabet ATGC plus 'N' and '$'</span></div>
<div class="line"><span class="comment">/// Ns are used to indicate ambiguity and $ is part of Burrows-Wheeler transform</span></div>
<div class="line"><span class="comment">/// </span></div>
<div class="line"><span class="comment"></span><span class="keyword">inline</span> <span class="keywordtype">unsigned</span> <a name="a0"></a><a class="code" href="xsample06_8cpp.html#aee3c4aa1382abf2f5e1615e23d906002">DNA2int</a>(<span class="keywordtype">char</span> DNA_bp)</div>
<div class="line">{</div>
<div class="line"> <span class="keywordflow">switch</span> (DNA_bp)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'A'</span>:</div>
<div class="line"> <span class="keywordflow">return</span> 0; <span class="comment">// 000</span></div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'T'</span>:</div>
<div class="line"> <span class="keywordflow">return</span> 1; <span class="comment">// 001</span></div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'G'</span>:</div>
<div class="line"> <span class="keywordflow">return</span> 2; <span class="comment">// 010</span></div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'C'</span>:</div>
<div class="line"> <span class="keywordflow">return</span> 3; <span class="comment">// 011</span></div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'N'</span>:</div>
<div class="line"> <span class="keywordflow">return</span> 4; <span class="comment">// 100</span></div>
<div class="line"> <span class="keywordflow">case</span> <span class="charliteral">'$'</span>:</div>
<div class="line"> <span class="keywordflow">return</span> 5; <span class="comment">// 101</span></div>
<div class="line"> <span class="keywordflow">default</span>:</div>
<div class="line"> assert(0);</div>
<div class="line"> <span class="keywordflow">return</span> 0;</div>
<div class="line"> }</div>
<div class="line">}<span class="comment"></span></div>
<div class="line"><span class="comment">/// Translate integer code to DNA letter</span></div>
<div class="line"><span class="comment">///</span></div>
<div class="line"><span class="comment"></span><span class="keyword">inline</span> <span class="keywordtype">char</span> <a name="a1"></a><a class="code" href="xsample06_8cpp.html#aa961816c64399d669effbc66f555da72">int2DNA</a>(<span class="keywordtype">unsigned</span> code)</div>
<div class="line">{</div>
<div class="line"> <span class="keyword">static</span> <span class="keywordtype">char</span> lut[] = { <span class="charliteral">'A'</span>, <span class="charliteral">'T'</span>, <span class="charliteral">'G'</span>, <span class="charliteral">'C'</span>, <span class="charliteral">'N'</span>, <span class="charliteral">'$'</span> };</div>
<div class="line"> <span class="keywordflow">if</span> (code < 5)</div>
<div class="line"> <span class="keywordflow">return</span> lut[code];</div>
<div class="line"> assert(0);</div>
<div class="line"> <span class="keywordflow">return</span> <span class="charliteral">'N'</span>;</div>
<div class="line">}</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// Print sparse vector </span></div>
<div class="line"><span class="comment"></span><span class="keyword">template</span><<span class="keyword">typename</span> SV> <span class="keywordtype">void</span> <a name="a2"></a><a class="code" href="xsample06_8cpp.html#ab6a4303cab1279938d0d2a2d74645336">PrintSV</a>(<span class="keyword">const</span> SV& sv)</div>
<div class="line">{</div>
<div class="line"> cout << <span class="stringliteral">"size() = "</span> << sv.size() << <span class="stringliteral">" : "</span>;</div>
<div class="line"> <span class="keyword">auto</span> it = sv.begin(); <span class="keyword">auto</span> it_end = sv.end();</div>
<div class="line"> <span class="keywordflow">for</span> (; it != it_end; ++it)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> v = *it;</div>
<div class="line"> <span class="keywordtype">char</span> bp = <a class="code" href="xsample06_8cpp.html#aa961816c64399d669effbc66f555da72">int2DNA</a>(v);</div>
<div class="line"> cout << bp;</div>
<div class="line"> }</div>
<div class="line"> cout << endl;</div>
<div class="line">}</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// Test sparse vector against reference vector </span></div>
<div class="line"><span class="comment">/// (for QA purposes)</span></div>
<div class="line"><span class="comment">///</span></div>
<div class="line"><span class="comment"></span><span class="keyword">template</span><<span class="keyword">typename</span> SV, <span class="keyword">typename</span> VECT> </div>
<div class="line"><span class="keywordtype">void</span> <a name="a3"></a><a class="code" href="xsample06_8cpp.html#a07dc7dee7d605233aa81eb421999ab48">TestSV</a>(<span class="keyword">const</span> SV& sv, <span class="keyword">const</span> VECT& vect)</div>
<div class="line">{</div>
<div class="line"> <span class="keyword">auto</span> it = sv.begin(); <span class="keyword">auto</span> it_end = sv.end();</div>
<div class="line"> <span class="keyword">auto</span> itv = vect.begin(); <span class="keyword">auto</span> itv_end = vect.end();</div>
<div class="line"> <span class="keywordflow">for</span> (; it != it_end && itv != itv_end; ++it, ++itv)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> v = *it;</div>
<div class="line"> <span class="keywordtype">char</span> bp = <a class="code" href="xsample06_8cpp.html#aa961816c64399d669effbc66f555da72">int2DNA</a>(v);</div>
<div class="line"> <span class="keywordtype">char</span> bpv = *itv;</div>
<div class="line"> assert(bp == bpv);</div>
<div class="line"> <span class="keywordflow">if</span> (bp != bpv)</div>
<div class="line"> {</div>
<div class="line"> cerr << <span class="stringliteral">"Error: reference vector mismatch!"</span> << endl;</div>
<div class="line"> exit(1);</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">if</span> (it != it_end || itv != itv_end)</div>
<div class="line"> {</div>
<div class="line"> cerr << <span class="stringliteral">"Error: reference size mismatch!"</span> << endl;</div>
<div class="line"> exit(1);</div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="keyword">typedef</span> <a name="_a4"></a><a class="code" href="classbm_1_1sparse__vector.html">bm::sparse_vector<unsigned, bm::bvector<></a> > <a name="a5"></a><a class="code" href="xsample06_8cpp.html#a0d169ec2ee5a4e5265f850f56a3b3452">svector_u32</a>;</div>
<div class="line"><span class="keyword">typedef</span> std::vector<char> <a name="a6"></a><a class="code" href="xsample06_8cpp.html#a9eb066bc7179fb40780c2160bc69a52d">vector_char_type</a>;</div>
<div class="line"><span class="keyword">typedef</span> std::vector<std::pair<unsigned, unsigned> > <a name="a7"></a><a class="code" href="xsample06_8cpp.html#ad6d970bc3ae404c9ac3efae8a8506f7d">vector_pairs_type</a>;</div>
<div class="line"> </div>
<div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment"> Lexicographical compare of two sparse vectors using bit-plane</span></div>
<div class="line"><span class="comment"> mismatch search</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">int</span> <a name="a8"></a><a class="code" href="xsample06_8cpp.html#a3208f2f2bba3589b2477bbd5e3c7170a">compare_sv</a>(<span class="keyword">const</span> <a name="_a9"></a><a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a>& sv1, <span class="keyword">const</span> <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a>& sv2)</div>
<div class="line">{</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> pos;</div>
<div class="line"> <span class="keywordtype">bool</span> found = <a name="a10"></a><a class="code" href="group__svalgo.html#ga5b8ca92c5fff30f5b741fc95fe2b3199">bm::sparse_vector_find_first_mismatch</a>(sv1, sv2, pos);</div>
<div class="line"> <span class="keywordflow">if</span> (found)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> v1 = sv1[pos];</div>
<div class="line"> <span class="keyword">auto</span> v2 = sv2[pos];</div>
<div class="line"> <span class="keywordflow">if</span> (v1 < v2)</div>
<div class="line"> <span class="keywordflow">return</span> -1;</div>
<div class="line"> <span class="keywordflow">return</span> 1;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">return</span> 0; <span class="comment">// EQ</span></div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment"> Lexicographical compare of two sparse vectors using</span></div>
<div class="line"><span class="comment"> iterators. This variant is quite slow, because sparse vector iterators</span></div>
<div class="line"><span class="comment"> are heavy classes doing reverse transformation on the fly</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">int</span> <a name="a11"></a><a class="code" href="xsample06_8cpp.html#a1a5902071feb95fdde2858e0fb94d862">compare_sv_it</a>(<span class="keyword">const</span> <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a>& sv1, <span class="keyword">const</span> <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a>& sv2)</div>
<div class="line">{</div>
<div class="line"> <a name="a12"></a><a class="code" href="classbm_1_1sparse__vector.html#a73134a0c2f6d595d3cf165236622f5da">svector_u32::const_iterator</a> it1 = sv1.<a name="a13"></a><a class="code" href="classbm_1_1sparse__vector.html#ae60eed242dd6ca5ac13a046f3f75b2f7">begin</a>();</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#a73134a0c2f6d595d3cf165236622f5da">svector_u32::const_iterator</a> it2 = sv2.<a class="code" href="classbm_1_1sparse__vector.html#ae60eed242dd6ca5ac13a046f3f75b2f7">begin</a>();</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> sz = sv1.<a name="a14"></a><a class="code" href="classbm_1_1sparse__vector.html#a468ddeec517a36a4a9333008703acfab">size</a>();</div>
<div class="line"> <span class="keywordflow">for</span> (<a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> i = 0; i < sz; ++i, ++it1, ++it2)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> v1 = *it1; <span class="keyword">auto</span> v2 = *it2;</div>
<div class="line"> <span class="keywordflow">if</span> (v1 == v2)</div>
<div class="line"> <span class="keywordflow">continue</span>;</div>
<div class="line"> <span class="keywordflow">if</span> (v1 < v2)</div>
<div class="line"> <span class="keywordflow">return</span> -1;</div>
<div class="line"> <span class="keywordflow">return</span> 1;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">return</span> 0;</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment"> Utility function to generate random vector of DNA chars (4 letters)</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a15"></a><a class="code" href="xsample06_8cpp.html#ad6ab9ffe5164e9acc8b4b5a8aff26cbb">generate_DNA_vector</a>(<a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a>& sv, <a class="code" href="xsample06_8cpp.html#a9eb066bc7179fb40780c2160bc69a52d">vector_char_type</a>& vect, <span class="keywordtype">unsigned</span> sz)</div>
<div class="line">{</div>
<div class="line"> <a name="a16"></a><a class="code" href="classbm_1_1sparse__vector.html#a7362aaf921cee882e08cb349677d51de">svector_u32::back_insert_iterator</a> bi = sv.<a name="a17"></a><a class="code" href="classbm_1_1sparse__vector.html#a664bc1422f5a71c93c09d809b3d1ec3f">get_back_inserter</a>();</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; i < sz; ++i)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordtype">unsigned</span> code = rand() % 4; <span class="comment">// generate code between 0 and 3</span></div>
<div class="line"> <span class="keywordtype">char</span> bp = <a class="code" href="xsample06_8cpp.html#aa961816c64399d669effbc66f555da72">int2DNA</a>(code);</div>
<div class="line"> assert(bp == <span class="charliteral">'A'</span> || bp == <span class="charliteral">'T'</span> || bp == <span class="charliteral">'G'</span> || bp == <span class="charliteral">'C'</span>);</div>
<div class="line"> vect.push_back(bp);</div>
<div class="line"> bi = code;</div>
<div class="line"> }</div>
<div class="line"> bi.flush();</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment"> Utility function to add symulated centromer (block of Ns in the middle)</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">static</span> </div>
<div class="line"><span class="keywordtype">void</span> <a name="a18"></a><a class="code" href="xsample06_8cpp.html#a7b352930d74556561bdc3c91e4c47493">add_centromer_Ns</a>(<a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a>& sv, <a class="code" href="xsample06_8cpp.html#a9eb066bc7179fb40780c2160bc69a52d">vector_char_type</a>& vect, <span class="keywordtype">unsigned</span> csz)</div>
<div class="line">{</div>
<div class="line"> assert(csz);</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> sz = sv.<a class="code" href="classbm_1_1sparse__vector.html#a468ddeec517a36a4a9333008703acfab">size</a>();</div>
<div class="line"> assert(sz == <a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a>(vect.size()));</div>
<div class="line"> assert(csz < sz);</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> half = sz / 2; <span class="comment">// center position</span></div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> c_half = csz / 2; </div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> c_start = half - c_half; <span class="comment">// simulated centromere start</span></div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> c_end = half + c_half; <span class="comment">// simulated centromere end</span></div>
<div class="line"> </div>
<div class="line"> <span class="comment">// fill-in simulated centromere 'NNNNNN...NNNN' </span></div>
<div class="line"> <span class="keywordflow">for</span> (<a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> i = c_start; i < c_end; ++i)</div>
<div class="line"> {</div>
<div class="line"> vect[i] = <span class="charliteral">'N'</span>;</div>
<div class="line"> sv[i] = <a class="code" href="xsample06_8cpp.html#aee3c4aa1382abf2f5e1615e23d906002">DNA2int</a>(<span class="charliteral">'N'</span>); <span class="comment">// 4</span></div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment"> Generate large vectors to simulate human chr1</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a19"></a><a class="code" href="xsample06_8cpp.html#aedf5a6cd535b91488b8fda0fd2b5b569">generate_big_case</a>(<a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a>& sv, <a class="code" href="xsample06_8cpp.html#a9eb066bc7179fb40780c2160bc69a52d">vector_char_type</a>& vect)</div>
<div class="line">{</div>
<div class="line"> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> case_size = 200000000; <span class="comment">// 200M bps</span></div>
<div class="line"> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> centr_size = 7000000; <span class="comment">// 7M centromere Ns</span></div>
<div class="line"> </div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#ad6ab9ffe5164e9acc8b4b5a8aff26cbb">generate_DNA_vector</a>(sv, vect, case_size);</div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#a7b352930d74556561bdc3c91e4c47493">add_centromer_Ns</a>(sv, vect, centr_size);</div>
<div class="line"> </div>
<div class="line"> sv.<a name="a20"></a><a class="code" href="classbm_1_1sparse__vector.html#af9f218aa3af25cdfc9088cc0affdaa8f">optimize</a>(); <span class="comment">// this will compress the sparse (N) plane</span></div>
<div class="line"> </div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#a07dc7dee7d605233aa81eb421999ab48">TestSV</a>(sv, vect); <span class="comment">// paranoiya check</span></div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment"> Generate benchmark set of mismatches</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a21"></a><a class="code" href="xsample06_8cpp.html#ae2de67cf9952fc46565d1c9d5cfbc1ec">generate_mismatches</a>(<a class="code" href="xsample06_8cpp.html#ad6d970bc3ae404c9ac3efae8a8506f7d">vector_pairs_type</a>& vect_m,</div>
<div class="line"> <span class="keyword">const</span> <a class="code" href="xsample06_8cpp.html#a9eb066bc7179fb40780c2160bc69a52d">vector_char_type</a>& vect,</div>
<div class="line"> <span class="keywordtype">unsigned</span> m_count)</div>
<div class="line">{</div>
<div class="line"> vect_m.resize(0);</div>
<div class="line"> <span class="keywordflow">if</span> (!vect.size())</div>
<div class="line"> <span class="keywordflow">return</span>;</div>
<div class="line"> </div>
<div class="line"> vector_char_type::size_type sz = vect.size();</div>
<div class="line"> vector_char_type::size_type delta = sz / m_count;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">for</span> (vector_char_type::size_type i = 0; i < sz; i += delta)</div>
<div class="line"> {</div>
<div class="line"> vector_char_type::value_type v1 = vect[i];</div>
<div class="line"> <span class="keywordtype">unsigned</span> code = rand() % 4;</div>
<div class="line"> vector_char_type::value_type v2 = <a class="code" href="xsample06_8cpp.html#aa961816c64399d669effbc66f555da72">int2DNA</a>(code);</div>
<div class="line"> <span class="keywordflow">if</span> (v2 == v1)</div>
<div class="line"> <span class="keywordflow">continue</span>;</div>
<div class="line"> vect_m.push_back(vector_pairs_type::value_type(i, code));</div>
<div class="line"> } <span class="comment">// for i</span></div>
<div class="line"> </div>
<div class="line"> <span class="comment">// add some extra with a distrubution skewed to the beginning</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> <span class="keywordflow">for</span> (vector_char_type::size_type i = 1; i < sz / 4; i += (rand()%(1024 * 10)))</div>
<div class="line"> {</div>
<div class="line"> vector_char_type::value_type v1 = vect[i];</div>
<div class="line"> <span class="keywordtype">unsigned</span> code = rand() % 4;</div>
<div class="line"> vector_char_type::value_type v2 = <a class="code" href="xsample06_8cpp.html#aa961816c64399d669effbc66f555da72">int2DNA</a>(code);</div>
<div class="line"> <span class="keywordflow">if</span> (v2 == v1)</div>
<div class="line"> <span class="keywordflow">continue</span>;</div>
<div class="line"> vect_m.push_back(vector_pairs_type::value_type(i, code));</div>
<div class="line"> } <span class="comment">// for i</span></div>
<div class="line"> </div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment">// -------------------------------------------------------------------</span></div>
<div class="line"> </div>
<div class="line"><a class="code" href="classbm_1_1chrono__taker.html#add1676592117ed0eaa2fa6279a71b46a">bm::chrono_taker::duration_map_type</a> <a name="a22"></a><a class="code" href="xsample06_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>;</div>
<div class="line"><span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a name="a23"></a><a class="code" href="xsample06_8cpp.html#a8746daf93f54845307d786389e3bd9dc">repeats</a> = 20000;</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment"> Mismatch search benchmark for bm::sparse_vector_find_first_mismatch</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a24"></a><a class="code" href="xsample06_8cpp.html#a8793686d965cb50f06824fbac060db1e">test_mismatch_search</a>(<span class="keyword">const</span> <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a>& sv, <span class="keyword">const</span> <a class="code" href="xsample06_8cpp.html#ad6d970bc3ae404c9ac3efae8a8506f7d">vector_pairs_type</a>& vect_m)</div>
<div class="line">{</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a> sv1(sv); <span class="comment">// copy sv</span></div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> sz = (<a name="a25"></a><a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a>)vect_m.size();</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">unsigned</span> cnt = 0;</div>
<div class="line"> </div>
<div class="line"> <a name="_a26"></a><a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"1. SV mismatch"</span>, sz, &<a class="code" href="xsample06_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> k = 0; k < sz; ++k)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordtype">unsigned</span> i = vect_m[k].first;</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#afb9b294f2f1fcaed3e4828eb218c4ea4">svector_u32::value_type</a> v1 = sv1[i];</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#afb9b294f2f1fcaed3e4828eb218c4ea4">svector_u32::value_type</a> v2 = vect_m[k].second;</div>
<div class="line"> assert(v1 != v2);</div>
<div class="line"> </div>
<div class="line"> sv1.<a name="a27"></a><a class="code" href="classbm_1_1sparse__vector.html#a56101ce9a559b30f8e14153133063ca7">set</a>(i, v2); <span class="comment">// change the copy vector</span></div>
<div class="line"> </div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">svector_u32::size_type</a> pos;</div>
<div class="line"> <span class="keywordtype">bool</span> found = <a class="code" href="group__svalgo.html#ga5b8ca92c5fff30f5b741fc95fe2b3199">bm::sparse_vector_find_first_mismatch</a>(sv, sv1, pos);</div>
<div class="line"> cnt += found;</div>
<div class="line"> assert(found);</div>
<div class="line"> assert(pos == i);</div>
<div class="line"> </div>
<div class="line"> sv1.<a class="code" href="classbm_1_1sparse__vector.html#a56101ce9a559b30f8e14153133063ca7">set</a>(pos, v1); <span class="comment">// restore old value</span></div>
<div class="line"> } <span class="comment">// for</span></div>
<div class="line"> assert(cnt == vect_m.size());</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment"> Mismatch search benchmark for std::vector::const_iterator</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a28"></a><a class="code" href="xsample06_8cpp.html#aa7c73426e0ebcd551ffca7214a5ac8bf">test_vect_mismatch_search</a>(<span class="keyword">const</span> <a class="code" href="xsample06_8cpp.html#a9eb066bc7179fb40780c2160bc69a52d">vector_char_type</a>& vect,</div>
<div class="line"> <span class="keyword">const</span> <a class="code" href="xsample06_8cpp.html#ad6d970bc3ae404c9ac3efae8a8506f7d">vector_pairs_type</a>& vect_m)</div>
<div class="line">{</div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#a9eb066bc7179fb40780c2160bc69a52d">vector_char_type</a> vect1(vect);</div>
<div class="line"> <span class="keywordtype">unsigned</span> sz = (unsigned)vect_m.size();</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">unsigned</span> cnt = 0;</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"2. STL iterator"</span>, sz, &<a class="code" href="xsample06_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> k = 0; k < sz; ++k)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordtype">unsigned</span> i = vect_m[k].first;</div>
<div class="line"> vector_char_type::value_type v1 = vect[i];</div>
<div class="line"> vector_char_type::value_type v2 = <a class="code" href="xsample06_8cpp.html#aa961816c64399d669effbc66f555da72">int2DNA</a>(vect_m[k].second);</div>
<div class="line"> assert(v1 != v2);</div>
<div class="line"> </div>
<div class="line"> vect1[i] = v2; <span class="comment">// change the copy vector</span></div>
<div class="line"> </div>
<div class="line"> <span class="comment">// possible to use std::mismatch() here</span></div>
<div class="line"> <span class="keywordtype">bool</span> found = <span class="keyword">false</span>;</div>
<div class="line"> vector_char_type::size_type pos;</div>
<div class="line"> <span class="keyword">auto</span> it = vect.begin(); <span class="keyword">auto</span> it_end = vect.end();</div>
<div class="line"> <span class="keyword">auto</span> it1 = vect1.begin();</div>
<div class="line"> <span class="keywordflow">for</span> (; it != it_end; ++it, ++it1)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">if</span> (*it != *it1)</div>
<div class="line"> {</div>
<div class="line"> found = <span class="keyword">true</span>; </div>
<div class="line"> pos = vector_char_type::size_type(it - vect.begin());</div>
<div class="line"> <span class="keywordflow">break</span>;</div>
<div class="line"> }</div>
<div class="line"> } <span class="comment">// for it</span></div>
<div class="line"> cnt += found;</div>
<div class="line"> assert(found);</div>
<div class="line"> assert(pos == i);</div>
<div class="line"> vect1[i] = v1; <span class="comment">// restore old value</span></div>
<div class="line"> } <span class="comment">// for</span></div>
<div class="line"> assert(cnt == vect_m.size());</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment"> Mismatch search benchmark for std::vector using strncmp()</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a29"></a><a class="code" href="xsample06_8cpp.html#a52e4343830affee94b4a308b978f2ce3">test_strcmp</a>(<span class="keyword">const</span> <a class="code" href="xsample06_8cpp.html#a9eb066bc7179fb40780c2160bc69a52d">vector_char_type</a>& vect, <span class="keyword">const</span> <a class="code" href="xsample06_8cpp.html#ad6d970bc3ae404c9ac3efae8a8506f7d">vector_pairs_type</a>& vect_m)</div>
<div class="line">{</div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#a9eb066bc7179fb40780c2160bc69a52d">vector_char_type</a> vect1(vect);</div>
<div class="line"> <span class="keywordtype">unsigned</span> sz = (unsigned)vect_m.size();</div>
<div class="line"> <span class="keywordtype">unsigned</span> cnt = 0;</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"3. strcmp() test "</span>, sz, &<a class="code" href="xsample06_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">unsigned</span> vs = unsigned(vect.size());</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> k = 0; k < sz; ++k)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordtype">unsigned</span> i = vect_m[k].first;</div>
<div class="line"> vector_char_type::value_type v1 = vect[i];</div>
<div class="line"> assert(vect_m[k].second < 4);</div>
<div class="line"> vector_char_type::value_type v2 = <a class="code" href="xsample06_8cpp.html#aa961816c64399d669effbc66f555da72">int2DNA</a>(vect_m[k].second);</div>
<div class="line"> assert(v1 != v2);</div>
<div class="line"> </div>
<div class="line"> vect1[i] = v2; <span class="comment">// change the copy vector</span></div>
<div class="line"> </div>
<div class="line"> <span class="keyword">const</span> <span class="keywordtype">char</span>* s1 = vect.data();</div>
<div class="line"> <span class="keyword">const</span> <span class="keywordtype">char</span>* s2 = vect1.data();</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">int</span> res = ::strncmp(s1, s2, vs);</div>
<div class="line"> cnt += bool(res);</div>
<div class="line"> assert(res);</div>
<div class="line"> vect1[i] = v1; <span class="comment">// restore</span></div>
<div class="line"> } <span class="comment">// for</span></div>
<div class="line"> assert(cnt == vect_m.size());</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment"> Sparse vector compare benchmark</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">static</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a30"></a><a class="code" href="xsample06_8cpp.html#a035f44ada932750cb4089348b4b646af">test_sv_cmp</a>(<span class="keyword">const</span> <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a>& sv, <span class="keyword">const</span> <a class="code" href="xsample06_8cpp.html#ad6d970bc3ae404c9ac3efae8a8506f7d">vector_pairs_type</a>& vect_m)</div>
<div class="line">{</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a> sv1(sv);</div>
<div class="line"> <span class="keywordtype">unsigned</span> sz = (unsigned)vect_m.size();</div>
<div class="line"> <span class="keywordtype">unsigned</span> cnt = 0;</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"4. sv compare"</span>, sz, &<a class="code" href="xsample06_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> k = 0; k < sz; ++k)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordtype">unsigned</span> i = vect_m[k].first;</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#afb9b294f2f1fcaed3e4828eb218c4ea4">svector_u32::value_type</a> v1 = sv1[i];</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#afb9b294f2f1fcaed3e4828eb218c4ea4">svector_u32::value_type</a> v2 = vect_m[k].second;</div>
<div class="line"> assert(v1 != v2);</div>
<div class="line"> </div>
<div class="line"> sv1.<a class="code" href="classbm_1_1sparse__vector.html#a56101ce9a559b30f8e14153133063ca7">set</a>(i, v2); <span class="comment">// change the copy vector</span></div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">int</span> res = <a class="code" href="xsample06_8cpp.html#a3208f2f2bba3589b2477bbd5e3c7170a">compare_sv</a>(sv, sv1);</div>
<div class="line"> assert(res != 0);</div>
<div class="line"> cnt += bool(res);</div>
<div class="line"> </div>
<div class="line"> sv1.<a class="code" href="classbm_1_1sparse__vector.html#a56101ce9a559b30f8e14153133063ca7">set</a>(i, v1); <span class="comment">// restore</span></div>
<div class="line"> } <span class="comment">// for</span></div>
<div class="line"> assert(cnt == vect_m.size());</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment"> Sparse vector compare benchmark using iterators (very slow)</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="keyword">inline</span></div>
<div class="line"><span class="keywordtype">void</span> <a name="a31"></a><a class="code" href="xsample06_8cpp.html#a5c98d21dcab8fdaf6b082bc0d9f9ab35">test_sv_cmp_it</a>(<span class="keyword">const</span> <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a>& sv, <span class="keyword">const</span> <a class="code" href="xsample06_8cpp.html#ad6d970bc3ae404c9ac3efae8a8506f7d">vector_pairs_type</a>& vect_m)</div>
<div class="line">{</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a> sv1(sv);</div>
<div class="line"> <span class="keywordtype">unsigned</span> sz = (unsigned)vect_m.size();</div>
<div class="line"> <span class="keywordtype">unsigned</span> cnt = 0;</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="classbm_1_1chrono__taker.html">bm::chrono_taker</a> tt1(<span class="stringliteral">"4. sv-cmp-it()"</span>, sz, &<a class="code" href="xsample06_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>);</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> k = 0; k < sz; ++k)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordtype">unsigned</span> i = vect_m[k].first;</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#afb9b294f2f1fcaed3e4828eb218c4ea4">svector_u32::value_type</a> v1 = sv1[i];</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#afb9b294f2f1fcaed3e4828eb218c4ea4">svector_u32::value_type</a> v2 = vect_m[k].second;</div>
<div class="line"> assert(v1 != v2);</div>
<div class="line"> </div>
<div class="line"> sv1.<a class="code" href="classbm_1_1sparse__vector.html#a56101ce9a559b30f8e14153133063ca7">set</a>(i, v2); <span class="comment">// change the copy vector</span></div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">int</span> res = <a class="code" href="xsample06_8cpp.html#a1a5902071feb95fdde2858e0fb94d862">compare_sv_it</a>(sv, sv1);</div>
<div class="line"> cnt += bool(res);</div>
<div class="line"> </div>
<div class="line"> assert(res != 0);</div>
<div class="line"> </div>
<div class="line"> sv1.<a class="code" href="classbm_1_1sparse__vector.html#a56101ce9a559b30f8e14153133063ca7">set</a>(i, v1); <span class="comment">// restore</span></div>
<div class="line"> } <span class="comment">// for</span></div>
<div class="line"> assert(cnt == vect_m.size());</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment">// -------------------------------------------------------------------</span></div>
<div class="line"> </div>
<div class="line"><span class="keywordtype">int</span> <a name="a32"></a><a class="code" href="xsample06_8cpp.html#a840291bc02cba5474a4cb46a9b9566fe">main</a>(<span class="keywordtype">void</span>)</div>
<div class="line">{</div>
<div class="line"> <span class="keywordflow">try</span></div>
<div class="line"> {</div>
<div class="line"> <span class="comment">// generate short DNA vector as STL vector and BitMagic </span></div>
<div class="line"> <span class="comment">// bit-transposed container, print the results (as a demo)</span></div>
<div class="line"> <span class="comment">// we don't have to re-load it every time,</span></div>
<div class="line"> <span class="comment">// bit transposed container is serializable</span></div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">const</span> <span class="keywordtype">char</span>* s = <span class="stringliteral">"ATGTCNNNNNTATA"</span>;</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a> sv;</div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html#a7362aaf921cee882e08cb349677d51de">svector_u32::back_insert_iterator</a> bi = sv.<a class="code" href="classbm_1_1sparse__vector.html#a664bc1422f5a71c93c09d809b3d1ec3f">get_back_inserter</a>();</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> i = 0; s[i]; ++i)</div>
<div class="line"> {</div>
<div class="line"> bi = <a class="code" href="xsample06_8cpp.html#aee3c4aa1382abf2f5e1615e23d906002">DNA2int</a>(s[i]);</div>
<div class="line"> }</div>
<div class="line"> bi.flush();</div>
<div class="line"> }</div>
<div class="line"> sv.<a class="code" href="classbm_1_1sparse__vector.html#af9f218aa3af25cdfc9088cc0affdaa8f">optimize</a>(); <span class="comment">// this will compress the sparse (N) plane</span></div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#ab6a4303cab1279938d0d2a2d74645336">PrintSV</a>(sv);</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// run a battery of benchmarks for variants of mismatch searches</span></div>
<div class="line"> <span class="comment">// and compare functions</span></div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="classbm_1_1sparse__vector.html">svector_u32</a> sv1;</div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#a9eb066bc7179fb40780c2160bc69a52d">vector_char_type</a> dna_vect;</div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#ad6d970bc3ae404c9ac3efae8a8506f7d">vector_pairs_type</a> vect_m;</div>
<div class="line"> </div>
<div class="line"> cout << <span class="stringliteral">"Generate benchmark test data."</span> << endl;</div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#aedf5a6cd535b91488b8fda0fd2b5b569">generate_big_case</a>(sv1, dna_vect);</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#ae2de67cf9952fc46565d1c9d5cfbc1ec">generate_mismatches</a>(vect_m, dna_vect, <a class="code" href="xsample06_8cpp.html#a8746daf93f54845307d786389e3bd9dc">repeats</a>);</div>
<div class="line"> cout << <span class="stringliteral">"generated mismatches="</span> << vect_m.size() << endl;</div>
<div class="line"> </div>
<div class="line"> cout << <span class="stringliteral">"SV mismatch search test"</span> << endl;</div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#a8793686d965cb50f06824fbac060db1e">test_mismatch_search</a>(sv1, vect_m);</div>
<div class="line"> </div>
<div class="line"> cout << <span class="stringliteral">"STL interator mismatch test"</span> << endl;</div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#aa7c73426e0ebcd551ffca7214a5ac8bf">test_vect_mismatch_search</a>(dna_vect, vect_m);</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// test compare functions</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> </div>
<div class="line"> cout << <span class="stringliteral">"strncmp() test"</span> << endl;</div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#a52e4343830affee94b4a308b978f2ce3">test_strcmp</a>(dna_vect, vect_m);</div>
<div class="line"> </div>
<div class="line"> cout << <span class="stringliteral">"SV compare test"</span> << endl;</div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#a035f44ada932750cb4089348b4b646af">test_sv_cmp</a>(sv1, vect_m);</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// really sow, not worth testing</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"><span class="preprocessor"> #if 0</span></div>
<div class="line"> cout << <span class="stringliteral">"SV compare iterators test"</span> << endl;</div>
<div class="line"> <a class="code" href="xsample06_8cpp.html#a5c98d21dcab8fdaf6b082bc0d9f9ab35">test_sv_cmp_it</a>(sv1, vect_m);</div>
<div class="line"><span class="preprocessor"> #endif</span></div>
<div class="line"> </div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> std::cout << std::endl << <span class="stringliteral">"Performance:"</span> << std::endl;</div>
<div class="line"> <a name="a33"></a><a class="code" href="classbm_1_1chrono__taker.html#a30b45453d952d14afe56c29087970899">bm::chrono_taker::print_duration_map</a>(<a class="code" href="xsample06_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a>, <a name="a34"></a><a class="code" href="classbm_1_1chrono__taker.html#a9a41e5f2fe48ba472fd77a1dbd86457da82bf0167445f7cec0bb401145e8b0a5d">bm::chrono_taker::ct_time</a>);</div>
<div class="line"> </div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">catch</span>(std::exception& ex)</div>
<div class="line"> {</div>
<div class="line"> std::cerr << ex.what() << std::endl;</div>
<div class="line"> <span class="keywordflow">return</span> 1;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">return</span> 0;</div>
<div class="line">}</div>
<div class="line"> </div>
</div><!-- fragment --> </div><!-- contents -->
<div class="ttc" id="axsample06_8cpp_html_a07dc7dee7d605233aa81eb421999ab48"><div class="ttname"><a href="xsample06_8cpp.html#a07dc7dee7d605233aa81eb421999ab48">TestSV</a></div><div class="ttdeci">void TestSV(const SV &sv, const VECT &vect)</div><div class="ttdoc">Test sparse vector against reference vector (for QA purposes)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00108">xsample06.cpp:108</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_aa7c73426e0ebcd551ffca7214a5ac8bf"><div class="ttname"><a href="xsample06_8cpp.html#aa7c73426e0ebcd551ffca7214a5ac8bf">test_vect_mismatch_search</a></div><div class="ttdeci">static void test_vect_mismatch_search(const vector_char_type &vect, const vector_pairs_type &vect_m)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00321">xsample06.cpp:321</a></div></div>
<div class="ttc" id="abmsparsevec__algo_8h_html"><div class="ttname"><a href="bmsparsevec__algo_8h.html">bmsparsevec_algo.h</a></div><div class="ttdoc">Algorithms for bm::sparse_vector.</div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_af9f218aa3af25cdfc9088cc0affdaa8f"><div class="ttname"><a href="classbm_1_1sparse__vector.html#af9f218aa3af25cdfc9088cc0affdaa8f">bm::sparse_vector::optimize</a></div><div class="ttdeci">void optimize(bm::word_t *temp_block=0, typename bvector_type::optmode opt_mode=bvector_type::opt_compress, typename sparse_vector< Val, BV >::statistics *stat=0)</div><div class="ttdoc">run memory optimization for all vector plains</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l01728">bmsparsevec.h:1728</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a7362aaf921cee882e08cb349677d51de"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a7362aaf921cee882e08cb349677d51de">bm::sparse_vector< unsigned, bm::bvector<> >::back_insert_iterator</a></div><div class="ttdeci">friend back_insert_iterator</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00349">bmsparsevec.h:349</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a73134a0c2f6d595d3cf165236622f5da"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a73134a0c2f6d595d3cf165236622f5da">bm::sparse_vector< unsigned, bm::bvector<> >::const_iterator</a></div><div class="ttdeci">friend const_iterator</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00348">bmsparsevec.h:348</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html"><div class="ttname"><a href="classbm_1_1sparse__vector.html">bm::sparse_vector</a></div><div class="ttdoc">sparse vector with runtime compression using bit transposition method</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00081">bmsparsevec.h:81</a></div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html"><div class="ttname"><a href="classbm_1_1chrono__taker.html">bm::chrono_taker</a></div><div class="ttdoc">Utility class to collect performance measurements and statistics.</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00039">bmtimer.h:39</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_ab6a4303cab1279938d0d2a2d74645336"><div class="ttname"><a href="xsample06_8cpp.html#ab6a4303cab1279938d0d2a2d74645336">PrintSV</a></div><div class="ttdeci">void PrintSV(const SV &sv)</div><div class="ttdoc">Print sparse vector.</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00091">xsample06.cpp:91</a></div></div>
<div class="ttc" id="abmsparsevec_8h_html"><div class="ttname"><a href="bmsparsevec_8h.html">bmsparsevec.h</a></div><div class="ttdoc">Sparse constainer sparse_vector<> for integer types using bit-transposition transform.</div></div>
<div class="ttc" id="axsample06_8cpp_html_a3208f2f2bba3589b2477bbd5e3c7170a"><div class="ttname"><a href="xsample06_8cpp.html#a3208f2f2bba3589b2477bbd5e3c7170a">compare_sv</a></div><div class="ttdeci">static int compare_sv(const svector_u32 &sv1, const svector_u32 &sv2)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00141">xsample06.cpp:141</a></div></div>
<div class="ttc" id="abmsparsevec__serial_8h_html"><div class="ttname"><a href="bmsparsevec__serial_8h.html">bmsparsevec_serial.h</a></div><div class="ttdoc">Serialization for sparse_vector<></div></div>
<div class="ttc" id="axsample06_8cpp_html_a5c98d21dcab8fdaf6b082bc0d9f9ab35"><div class="ttname"><a href="xsample06_8cpp.html#a5c98d21dcab8fdaf6b082bc0d9f9ab35">test_sv_cmp_it</a></div><div class="ttdeci">void test_sv_cmp_it(const svector_u32 &sv, const vector_pairs_type &vect_m)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00432">xsample06.cpp:432</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_a7b352930d74556561bdc3c91e4c47493"><div class="ttname"><a href="xsample06_8cpp.html#a7b352930d74556561bdc3c91e4c47493">add_centromer_Ns</a></div><div class="ttdeci">static void add_centromer_Ns(svector_u32 &sv, vector_char_type &vect, unsigned csz)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00201">xsample06.cpp:201</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_a6cb51d150528a5d2d87acb3e88f450bc"><div class="ttname"><a href="xsample06_8cpp.html#a6cb51d150528a5d2d87acb3e88f450bc">timing_map</a></div><div class="ttdeci">bm::chrono_taker::duration_map_type timing_map</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00280">xsample06.cpp:280</a></div></div>
<div class="ttc" id="agroup__svalgo_html_ga5b8ca92c5fff30f5b741fc95fe2b3199"><div class="ttname"><a href="group__svalgo.html#ga5b8ca92c5fff30f5b741fc95fe2b3199">bm::sparse_vector_find_first_mismatch</a></div><div class="ttdeci">bool sparse_vector_find_first_mismatch(const SV &sv1, const SV &sv2, typename SV::size_type &midx, bm::null_support null_proc=bm::use_null)</div><div class="ttdoc">Find first mismatch (element which is different) between two sparse vectors (uses linear scan in bit-...</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__algo_8h_source.html#l00170">bmsparsevec_algo.h:170</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_aee3c4aa1382abf2f5e1615e23d906002"><div class="ttname"><a href="xsample06_8cpp.html#aee3c4aa1382abf2f5e1615e23d906002">DNA2int</a></div><div class="ttdeci">unsigned DNA2int(char DNA_bp)</div><div class="ttdoc">Translate DNA letter to integer code Please note this function uses extended alphabet ATGC plus 'N' a...</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00058">xsample06.cpp:58</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_ad6ab9ffe5164e9acc8b4b5a8aff26cbb"><div class="ttname"><a href="xsample06_8cpp.html#ad6ab9ffe5164e9acc8b4b5a8aff26cbb">generate_DNA_vector</a></div><div class="ttdeci">static void generate_DNA_vector(svector_u32 &sv, vector_char_type &vect, unsigned sz)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00183">xsample06.cpp:183</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_a8793686d965cb50f06824fbac060db1e"><div class="ttname"><a href="xsample06_8cpp.html#a8793686d965cb50f06824fbac060db1e">test_mismatch_search</a></div><div class="ttdeci">static void test_mismatch_search(const svector_u32 &sv, const vector_pairs_type &vect_m)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00288">xsample06.cpp:288</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_afb9b294f2f1fcaed3e4828eb218c4ea4"><div class="ttname"><a href="classbm_1_1sparse__vector.html#afb9b294f2f1fcaed3e4828eb218c4ea4">bm::sparse_vector< unsigned, bm::bvector<> >::value_type</a></div><div class="ttdeci">unsigned value_type</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00084">bmsparsevec.h:84</a></div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html_a9a41e5f2fe48ba472fd77a1dbd86457da82bf0167445f7cec0bb401145e8b0a5d"><div class="ttname"><a href="classbm_1_1chrono__taker.html#a9a41e5f2fe48ba472fd77a1dbd86457da82bf0167445f7cec0bb401145e8b0a5d">bm::chrono_taker::ct_time</a></div><div class="ttdeci">@ ct_time</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00058">bmtimer.h:58</a></div></div>
<div class="ttc" id="abmtimer_8h_html"><div class="ttname"><a href="bmtimer_8h.html">bmtimer.h</a></div><div class="ttdoc">Timing utilities for benchmarking (internal)</div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a468ddeec517a36a4a9333008703acfab"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a468ddeec517a36a4a9333008703acfab">bm::sparse_vector::size</a></div><div class="ttdeci">size_type size() const BMNOEXCEPT</div><div class="ttdoc">return size of the vector</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00644">bmsparsevec.h:644</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_ae60eed242dd6ca5ac13a046f3f75b2f7"><div class="ttname"><a href="classbm_1_1sparse__vector.html#ae60eed242dd6ca5ac13a046f3f75b2f7">bm::sparse_vector::begin</a></div><div class="ttdeci">const_iterator begin() const BMNOEXCEPT</div><div class="ttdoc">Provide const iterator access to container content</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l01900">bmsparsevec.h:1900</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_a52e4343830affee94b4a308b978f2ce3"><div class="ttname"><a href="xsample06_8cpp.html#a52e4343830affee94b4a308b978f2ce3">test_strcmp</a></div><div class="ttdeci">static void test_strcmp(const vector_char_type &vect, const vector_pairs_type &vect_m)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00367">xsample06.cpp:367</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_ae2de67cf9952fc46565d1c9d5cfbc1ec"><div class="ttname"><a href="xsample06_8cpp.html#ae2de67cf9952fc46565d1c9d5cfbc1ec">generate_mismatches</a></div><div class="ttdeci">static void generate_mismatches(vector_pairs_type &vect_m, const vector_char_type &vect, unsigned m_count)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00243">xsample06.cpp:243</a></div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html_add1676592117ed0eaa2fa6279a71b46a"><div class="ttname"><a href="classbm_1_1chrono__taker.html#add1676592117ed0eaa2fa6279a71b46a">bm::chrono_taker::duration_map_type</a></div><div class="ttdeci">std::map< std::string, statistics > duration_map_type</div><div class="ttdoc">test name to duration map</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00065">bmtimer.h:65</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a664bc1422f5a71c93c09d809b3d1ec3f"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a664bc1422f5a71c93c09d809b3d1ec3f">bm::sparse_vector::get_back_inserter</a></div><div class="ttdeci">back_insert_iterator get_back_inserter()</div><div class="ttdoc">Provide back insert iterator Back insert iterator implements buffered insertion, which is faster,...</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00506">bmsparsevec.h:506</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_aa961816c64399d669effbc66f555da72"><div class="ttname"><a href="xsample06_8cpp.html#aa961816c64399d669effbc66f555da72">int2DNA</a></div><div class="ttdeci">char int2DNA(unsigned code)</div><div class="ttdoc">Translate integer code to DNA letter.</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00081">xsample06.cpp:81</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_a035f44ada932750cb4089348b4b646af"><div class="ttname"><a href="xsample06_8cpp.html#a035f44ada932750cb4089348b4b646af">test_sv_cmp</a></div><div class="ttdeci">static void test_sv_cmp(const svector_u32 &sv, const vector_pairs_type &vect_m)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00402">xsample06.cpp:402</a></div></div>
<div class="ttc" id="aclassbm_1_1chrono__taker_html_a30b45453d952d14afe56c29087970899"><div class="ttname"><a href="classbm_1_1chrono__taker.html#a30b45453d952d14afe56c29087970899">bm::chrono_taker::print_duration_map</a></div><div class="ttdeci">static void print_duration_map(const duration_map_type &dmap, format fmt=ct_time)</div><div class="ttdef"><b>Definition:</b> <a href="bmtimer_8h_source.html#l00127">bmtimer.h:127</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_a840291bc02cba5474a4cb46a9b9566fe"><div class="ttname"><a href="xsample06_8cpp.html#a840291bc02cba5474a4cb46a9b9566fe">main</a></div><div class="ttdeci">int main(void)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00461">xsample06.cpp:461</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_a8746daf93f54845307d786389e3bd9dc"><div class="ttname"><a href="xsample06_8cpp.html#a8746daf93f54845307d786389e3bd9dc">repeats</a></div><div class="ttdeci">const unsigned repeats</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00281">xsample06.cpp:281</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_a0d169ec2ee5a4e5265f850f56a3b3452"><div class="ttname"><a href="xsample06_8cpp.html#a0d169ec2ee5a4e5265f850f56a3b3452">svector_u32</a></div><div class="ttdeci">bm::sparse_vector< unsigned, bm::bvector<> > svector_u32</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00132">xsample06.cpp:132</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_aedf5a6cd535b91488b8fda0fd2b5b569"><div class="ttname"><a href="xsample06_8cpp.html#aedf5a6cd535b91488b8fda0fd2b5b569">generate_big_case</a></div><div class="ttdeci">static void generate_big_case(svector_u32 &sv, vector_char_type &vect)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00226">xsample06.cpp:226</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_a9eb066bc7179fb40780c2160bc69a52d"><div class="ttname"><a href="xsample06_8cpp.html#a9eb066bc7179fb40780c2160bc69a52d">vector_char_type</a></div><div class="ttdeci">std::vector< char > vector_char_type</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00133">xsample06.cpp:133</a></div></div>
<div class="ttc" id="abm_8h_html"><div class="ttname"><a href="bm_8h.html">bm.h</a></div><div class="ttdoc">Compressed bit-vector bvector<> container, set algebraic methods, traversal iterators.</div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a56101ce9a559b30f8e14153133063ca7"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a56101ce9a559b30f8e14153133063ca7">bm::sparse_vector::set</a></div><div class="ttdeci">void set(size_type idx, value_type v)</div><div class="ttdoc">set specified element with bounds checking and automatic resize</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l01469">bmsparsevec.h:1469</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_ad6d970bc3ae404c9ac3efae8a8506f7d"><div class="ttname"><a href="xsample06_8cpp.html#ad6d970bc3ae404c9ac3efae8a8506f7d">vector_pairs_type</a></div><div class="ttdeci">std::vector< std::pair< unsigned, unsigned > > vector_pairs_type</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00134">xsample06.cpp:134</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html_a0ce76a1e2cec9034664fb7ce4d5c23ae"><div class="ttname"><a href="classbm_1_1sparse__vector.html#a0ce76a1e2cec9034664fb7ce4d5c23ae">bm::sparse_vector< unsigned, bm::bvector<> >::size_type</a></div><div class="ttdeci">bvector_type::size_type size_type</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00087">bmsparsevec.h:87</a></div></div>
<div class="ttc" id="axsample06_8cpp_html_a1a5902071feb95fdde2858e0fb94d862"><div class="ttname"><a href="xsample06_8cpp.html#a1a5902071feb95fdde2858e0fb94d862">compare_sv_it</a></div><div class="ttdeci">static int compare_sv_it(const svector_u32 &sv1, const svector_u32 &sv2)</div><div class="ttdef"><b>Definition:</b> <a href="xsample06_8cpp_source.html#l00162">xsample06.cpp:162</a></div></div>
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