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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/commit/84ec4ca84ee105c86dce52bff966125257947cf4">84ec4ca8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-04-26T22:27:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 932</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/commit/01411f7523595dc7704feb0948ceb22df2f857bd">01411f75</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-04-26T22:27:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/932'
Update to upstream version '932'
with Debian dir ca55603e5f6bfad4fafbad60ea034882fa3de4f9</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/commit/317550679901b69830947e30d66f7b588c7866f9">31755067</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-04-26T22:27:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/commit/8316de431996441b620c54352430503b15507616">8316de43</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-04-26T22:27:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/commit/7c2a5450a7ca9883cb391e92a3c82edbc8bc9898">7c2a5450</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-04-26T22:27:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/commit/041dbcfce9f072a318f56c6f30d1b682d512abb5">041dbcfc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-04-26T22:30:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>25 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#57bf262130f956caf76c405086f0815caf4e0a89">
ChangeLog.txt
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#c86c7a6d9a7bc77f1c375315f47ff6952729ba5b">
doc/Makefile
</a>
</li>
<li class="file-stats">
<a href="#1d2db1d5c1263541e178e5c6d1a664dcaee43e97">
doc/lastal.html
</a>
</li>
<li class="file-stats">
<a href="#30d864ed8925787ee70643db49814772753a5f2c">
doc/lastal.txt
</a>
</li>
<li class="file-stats">
<a href="#0bf0c2b9afb77a75953faf3468b6707da7098872">
doc/lastdb.html
</a>
</li>
<li class="file-stats">
<a href="#485665224376f8470c80c62ef464a2a01e61c7e7">
doc/lastdb.txt
</a>
</li>
<li class="file-stats">
<a href="#58da1cd416cde68a946aa59fca29adab0c429965">
<span class="new-file">
+
doc/maf-cut.html
</span>
</a>
</li>
<li class="file-stats">
<a href="#a3726766a594e96c014f2e423263f9133696bd04">
<span class="new-file">
+
doc/maf-cut.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#d6f8248b8a5e868eac831cf1a35c8543f1fff6a8">
scripts/last-dotplot
</a>
</li>
<li class="file-stats">
<a href="#177815a02f622695617613b9dc8023a958d68f7b">
<span class="new-file">
+
scripts/maf-cut
</span>
</a>
</li>
<li class="file-stats">
<a href="#ab919b3eb596acbd0affb15613fb99fee03165d8">
src/Alphabet.cc
</a>
</li>
<li class="file-stats">
<a href="#e478528f9c99e8adc6fafff10d008edf048f9c32">
src/QualityPssmMaker.cc
</a>
</li>
<li class="file-stats">
<a href="#7e02f07907d04e1c14dd8cbe36e5ca852897fb6b">
src/ScoreMatrix.cc
</a>
</li>
<li class="file-stats">
<a href="#1abcf9a223f6f347de8e1e1bd3495e4900285b34">
src/ScoreMatrix.hh
</a>
</li>
<li class="file-stats">
<a href="#bb715be022c826aae5cd901677082c4701d4254f">
src/SubsetSuffixArray.hh
</a>
</li>
<li class="file-stats">
<a href="#2a1679fed6b9ef7f99d78c180fd4a4c60fc9f422">
src/SubsetSuffixArraySort.cc
</a>
</li>
<li class="file-stats">
<a href="#7b0830ebdd6062603b37b87c1a3b81a77a1b9578">
src/TantanMasker.cc
</a>
</li>
<li class="file-stats">
<a href="#606e6941b339f000d86394f6a0e1d0b6790c48b6">
src/alp/sls_alignment_evaluer.cpp
</a>
</li>
<li class="file-stats">
<a href="#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">
src/lastal.cc
</a>
</li>
<li class="file-stats">
<a href="#de4252990d12a909e50ff0b994d1715eae0ea5fd">
src/lastdb.cc
</a>
</li>
<li class="file-stats">
<a href="#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">
src/makefile
</a>
</li>
<li class="file-stats">
<a href="#8db93325f61aa7d617ad4cbce8b11461c573f871">
src/qualityScoreUtil.hh
</a>
</li>
<li class="file-stats">
<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">
src/version.hh
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="57bf262130f956caf76c405086f0815caf4e0a89">
<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2018-04-20 Martin C. Frith <Martin C. Frith></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * doc/Makefile, doc/lastal.txt, doc/maf-cut.txt, scripts/maf-cut:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Add maf-cut utility</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> [482845444bcd] [tip]</span>
</pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">2018-04-18 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * src/ScoreMatrix.cc, src/ScoreMatrix.hh, src/lastal.cc, src/makefile,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> test/last-test.out:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> Use appropriate scores for ambiguous DNA letters</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> [75785542d5a0]</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">2018-04-17 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * src/ScoreMatrix.cc, src/ScoreMatrix.hh, test/last-test.out:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Prettify the score matrix in lastal's header</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> [68bd00d2faff]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> * src/ScoreMatrix.cc, src/lastal.cc:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> [d1aa91889332]</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> * src/ScoreMatrix.cc, src/ScoreMatrix.hh, src/TantanMasker.cc,</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> src/lastal.cc:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> [e22cac29168c]</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">2018-04-16 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> * src/QualityPssmMaker.cc, src/ScoreMatrix.cc, src/ScoreMatrix.hh,</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> src/qualityScoreUtil.hh:</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> [fb851b8892a5]</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">2018-03-05 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> * scripts/last-dotplot, test/last-dotplot-test.out, test/last-dotplot-</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> test.sh:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> Fix dotplot --strands bug with cut sequences</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> [bc08832db1a1]</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> * scripts/last-dotplot, test/last-dotplot-test.out, test/last-dotplot-</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> test.sh:</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> Fix dotplot crash for sorting by sequence length</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> [e1861f956f60]</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">2018-02-26 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> * doc/lastdb.txt, src/Alphabet.cc, test/last-test.out, test/last-</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> test.sh:</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> Convert Us in RNA to Ts</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> [e7d7cb7db0a7]</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">2018-02-13 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> * doc/lastdb.txt, src/SubsetSuffixArray.hh,</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> src/SubsetSuffixArraySort.cc, src/lastdb.cc:</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> Multi-thread lastdb's main sort</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> [77d8757028c2]</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> * src/alp/sls_alignment_evaluer.cpp, test/last-test.out:</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> Fix some E-value & last-train fails</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> [2c57015b1e89]</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">2018-01-05 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> * src/Alignment.cc, src/Alignment.hh, src/Centroid.cc,</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> src/Centroid.hh:</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> [8430dbf5abe7]<span class="idiff left right"> [tip]</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> [8430dbf5abe7]</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"> * src/Centroid.cc:</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> Try to calculate lastal probs a tiny bit faster</span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">last-align (932-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.1.4</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 26 Apr 2018 22:27:19 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">last-align (921-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,9 +8,9 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> help2man,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python-pil,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">3</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/last-align.git</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/last-align.git</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/last-align</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/last-align.git</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: http://last.cbrc.jp/</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Package: last-align</span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#c86c7a6d9a7bc77f1c375315f47ff6952729ba5b"><strong>doc/Makefile</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ last-map-probs.html last-matrices.html last-pair-probs.html \</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make">last-papers.html last-parallel.html last-postmask.html <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make">last-repeats.html last-seeds.html last-split.html last-train.html <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make">last-tuning.html last-tutorial.html last.html lastal.html lastdb.html <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="make">maf-convert.html</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make">maf-convert.html<span class="idiff left right"> maf-cut.html</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">${DOCS}</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -462,14 +462,18 @@ value of -e, so if you specify -e then -E has no effect.</td></tr></td>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="html"><span class="nt" style="color: navy;"><td><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: navy;">></span>Specify a match/mismatch score matrix. Options -r and -q will</span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="html">be ignored. The built-in matrices are described in</span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="html"><span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"last-matrices.html"</span><span class="nt" style="color: navy;">></span>last-matrices.html<span class="nt" style="color: navy;"></a></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="html"><span class="nt" style="color: navy;"><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: navy;">></span>Any other NAME is assumed to be a file name. For an example of</span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="html">the format, see the matrix files in the data directory. Any</span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="html">letters that aren't in the matrix will get the lowest score in</span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="html">the matrix when aligned to anything. Asymmetric scores are</span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="html">allowed: query letters correspond to columns and reference</span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="html">letters correspond to rows. Other options can be specified on</span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="html">lines starting with <span class="ni" style="color: purple;">"</span>#last<span class="ni" style="color: purple;">"</span>, but command line options override</span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="html">them.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Any other NAME is assumed to be a file name. For an example of</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="html">the format, see the matrix files in the data directory.</span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="html">Asymmetric scores are allowed: query letters correspond to</span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="html">columns and reference letters correspond to rows.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Any letters that aren't in the matrix get default match/mismatch</span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="html">scores. For doubly- and triply-ambiguous bases (such as <span class="ni" style="color: purple;">"</span>W<span class="ni" style="color: purple;">"</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="html">meaning A or T), these default scores are derived from the ACGT</span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="html">scores, and are shown in the header of lastal's output. Any</span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="html">other letters get the lowest score in the matrix when aligned to</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="html">anything.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="html"><span class="nt" style="color: navy;"><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: navy;">></span>Other options can be specified on lines starting with <span class="ni" style="color: purple;">"</span>#last<span class="ni" style="color: purple;">"</span>,</span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="html">but command line options override them.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-a <span class="nt" style="color: navy;"><var></span>COST<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>
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<li id="30d864ed8925787ee70643db49814772753a5f2c">
<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#30d864ed8925787ee70643db49814772753a5f2c"><strong>doc/lastal.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,13 +130,19 @@ Score options</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext"> `<last-matrices.html>`_.</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext"> Any other NAME is assumed to be a file name. For an example of</span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext"> the format, see the matrix files in the data directory. Any</span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext"> letters that aren't in the matrix will get the lowest score in</span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext"> the matrix when aligned to anything. Asymmetric scores are</span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext"> allowed: query letters correspond to columns and reference</span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext"> letters correspond to rows. Other options can be specified on</span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext"> lines starting with "#last", but command line options override</span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext"> them.</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> the format, see the matrix files in the data directory.</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> Asymmetric scores are allowed: query letters correspond to</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> columns and reference letters correspond to rows.</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> Any letters that aren't in the matrix get default match/mismatch</span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> scores. For doubly- and triply-ambiguous bases (such as "W"</span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> meaning A or T), these default scores are derived from the ACGT</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> scores, and are shown in the header of lastal's output. Any</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> other letters get the lowest score in the matrix when aligned to</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> anything.</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"> Other options can be specified on lines starting with "#last",</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> but command line options override them.</span>
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140
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext"></span>
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141
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext"> -a COST</span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext"> Gap existence cost.</span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#0bf0c2b9afb77a75953faf3468b6707da7098872"><strong>doc/lastdb.html</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -461,8 +461,7 @@ lastdb and then used by lastal. These formats are described in</td>
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461
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-P <span class="nt" style="color: navy;"><var></span>THREADS<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>Divide the work between this number of threads running in</span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="html">parallel. 0 means use as many threads as your computer claims</span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="html">it can handle simultaneously. Currently, multi-threading is</span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="html">used for tantan masking only.<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="html">it can handle simultaneously.<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-m <span class="nt" style="color: navy;"><var></span>PATTERN<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="html"><span class="nt" style="color: navy;"><td><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: navy;">></span>Specify a spaced seed pattern, for example <span class="ni" style="color: purple;">"</span>-m 110101<span class="ni" style="color: purple;">"</span>. In this</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -490,7 +489,8 @@ alphabet is equivalent to "-a ACGT". The protein alphabet (-p)</td>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="html">is equivalent to <span class="ni" style="color: purple;">"</span>-a ACDEFGHIKLMNPQRSTVWY<span class="ni" style="color: purple;">"</span>. Non-alphabet</span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="html">letters are allowed in sequences, but by default they are</span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="html">excluded from initial matches and get the mismatch score when</span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="html">aligned to anything. If -a is specified, -p is ignored.<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="html">aligned to anything. As a special case, for the DNA alphabet,</span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="html">Us are converted to Ts. If -a is specified, -p is ignored.<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-i <span class="nt" style="color: navy;"><var></span>MATCHES<span class="nt" style="color: navy;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>This option makes lastdb faster, at the expense of limiting your</span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#485665224376f8470c80c62ef464a2a01e61c7e7"><strong>doc/lastdb.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -129,8 +129,7 @@ Advanced Options</td>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext"> -P THREADS</span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext"> Divide the work between this number of threads running in</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext"> parallel. 0 means use as many threads as your computer claims</span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext"> it can handle simultaneously. Currently, multi-threading is</span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext"> used for tantan masking only.</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> it can handle simultaneously.</span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext"> -m PATTERN</span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext"> Specify a spaced seed pattern, for example "-m 110101". In this</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -161,7 +160,8 @@ Advanced Options</td>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"> is equivalent to "-a ACDEFGHIKLMNPQRSTVWY". Non-alphabet</span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext"> letters are allowed in sequences, but by default they are</span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext"> excluded from initial matches and get the mismatch score when</span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext"> aligned to anything. If -a is specified, -p is ignored.</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> aligned to anything. As a special case, for the DNA alphabet,</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> Us are converted to Ts. If -a is specified, -p is ignored.</span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext"> -i MATCHES</span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext"> This option makes lastdb faster, at the expense of limiting your</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="html"><span class="nt" style="color: navy;"><title></span>maf-cut<span class="nt" style="color: navy;"></title></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">/*</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">:Author: David Goodger (goodger@python.org)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">:Id: $Id: html4css1.css 5951 2009-05-18 18:03:10Z milde $</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">:Copyright: This stylesheet has been placed in the public domain.</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="html"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">Default cascading style sheet for the HTML output of Docutils.</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="html"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">See http://docutils.sf.net/docs/howto/html-stylesheets.html for how to</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">customize this style sheet.</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">*/</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="html"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">/* used to remove borders from tables and images */</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="html"><span class="nc" style="color: #458; font-weight: 600;">.borderless</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.borderless</span> <span class="nt" style="color: navy;">td</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.borderless</span> <span class="nt" style="color: navy;">th</span> <span class="p">{</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="html"> <span class="nl">border</span><span class="p">:</span> <span class="m" style="color: #099;">0</span> <span class="p">}</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="html"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="html"><span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.borderless</span> <span class="nt" style="color: navy;">td</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.borderless</span> <span class="nt" style="color: navy;">th</span> <span class="p">{</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="html"> <span class="c" style="color: #998; font-style: italic;">/* Override padding for "table.docutils td" with "! important".</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> The right padding separates the table cells. */</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="html"> <span class="nl">padding</span><span class="p">:</span> <span class="m" style="color: #099;">0</span> <span class="m" style="color: #099;">0.5em</span> <span class="m" style="color: #099;">0</span> <span class="m" style="color: #099;">0</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">!</span> <span class="n" style="color: #333;">important</span> <span class="p">}</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="html"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="html"><span class="nc" style="color: #458; font-weight: 600;">.first</span> <span class="p">{</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="html"> <span class="c" style="color: #998; font-style: italic;">/* Override more specific margin styles with "! important". */</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="html"> <span class="nl">margin-top</span><span class="p">:</span> <span class="m" style="color: #099;">0</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">!</span> <span class="n" style="color: #333;">important</span> <span class="p">}</span></span>
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33
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="html"><span class="nc" style="color: #458; font-weight: 600;">.last</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">.with-subtitle</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="html"> <span class="nl">margin-bottom</span><span class="p">:</span> <span class="m" style="color: #099;">0</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">!</span> <span class="n" style="color: #333;">important</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="html"><span class="nc" style="color: #458; font-weight: 600;">.hidden</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="html"> <span class="nl">display</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">none</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="html"><span class="nt" style="color: navy;">a</span><span class="nc" style="color: #458; font-weight: 600;">.toc-backref</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="html"> <span class="nl">text-decoration</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">none</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="html"> <span class="nl">color</span><span class="p">:</span> <span class="no" style="color: teal;">black</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="html"><span class="nt" style="color: navy;">blockquote</span><span class="nc" style="color: #458; font-weight: 600;">.epigraph</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="html"> <span class="nl">margin</span><span class="p">:</span> <span class="m" style="color: #099;">2em</span> <span class="m" style="color: #099;">5em</span> <span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="html"><span class="nt" style="color: navy;">dl</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span> <span class="nt" style="color: navy;">dd</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="html"> <span class="nl">margin-bottom</span><span class="p">:</span> <span class="m" style="color: #099;">0.5em</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">/* Uncomment (and remove this text!) to get bold-faced definition list terms</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">dl.docutils dt {</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> font-weight: bold }</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.abstract</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="html"> <span class="nl">margin</span><span class="p">:</span> <span class="m" style="color: #099;">2em</span> <span class="m" style="color: #099;">5em</span> <span class="p">}</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.abstract</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.topic-title</span> <span class="p">{</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span> <span class="p">;</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="html"> <span class="nl">text-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">center</span> <span class="p">}</span></span>
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61
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.admonition</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.attention</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.caution</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.danger</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.error</span><span class="o" style="font-weight: 600;">,</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.hint</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.important</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.note</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.tip</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.warning</span> <span class="p">{</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="html"> <span class="nl">margin</span><span class="p">:</span> <span class="m" style="color: #099;">2em</span> <span class="p">;</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="html"> <span class="nl">border</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">medium</span> <span class="nb" style="color: #0086b3;">outset</span> <span class="p">;</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="html"> <span class="nl">padding</span><span class="p">:</span> <span class="m" style="color: #099;">1em</span> <span class="p">}</span></span>
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67
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.admonition</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.admonition-title</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.hint</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.admonition-title</span><span class="o" style="font-weight: 600;">,</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.important</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.admonition-title</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.note</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.admonition-title</span><span class="o" style="font-weight: 600;">,</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.tip</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.admonition-title</span> <span class="p">{</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span> <span class="p">;</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="html"> <span class="nl">font-family</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">sans-serif</span> <span class="p">}</span></span>
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73
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.attention</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.admonition-title</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.caution</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.admonition-title</span><span class="o" style="font-weight: 600;">,</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.danger</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.admonition-title</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.error</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.admonition-title</span><span class="o" style="font-weight: 600;">,</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.warning</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.admonition-title</span> <span class="p">{</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="html"> <span class="nl">color</span><span class="p">:</span> <span class="no" style="color: teal;">red</span> <span class="p">;</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span> <span class="p">;</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="html"> <span class="nl">font-family</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">sans-serif</span> <span class="p">}</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">/* Uncomment (and remove this text!) to get reduced vertical space in</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> compound paragraphs.</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">div.compound .compound-first, div.compound .compound-middle {</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> margin-bottom: 0.5em }</span></span>
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85
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">div.compound .compound-last, div.compound .compound-middle {</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> margin-top: 0.5em }</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">*/</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="html"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.dedication</span> <span class="p">{</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="html"> <span class="nl">margin</span><span class="p">:</span> <span class="m" style="color: #099;">2em</span> <span class="m" style="color: #099;">5em</span> <span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="html"> <span class="nl">text-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">center</span> <span class="p">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="html"> <span class="nl">font-style</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">italic</span> <span class="p">}</span></span>
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94
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.dedication</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.topic-title</span> <span class="p">{</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span> <span class="p">;</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="html"> <span class="nl">font-style</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">normal</span> <span class="p">}</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="html"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.figure</span> <span class="p">{</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="html"> <span class="nl">margin-left</span><span class="p">:</span> <span class="m" style="color: #099;">2em</span> <span class="p">;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="html"> <span class="nl">margin-right</span><span class="p">:</span> <span class="m" style="color: #099;">2em</span> <span class="p">}</span></span>
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102
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.footer</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.header</span> <span class="p">{</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="html"> <span class="nl">clear</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">both</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="html"> <span class="nl">font-size</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">smaller</span> <span class="p">}</span></span>
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106
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.line-block</span> <span class="p">{</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="html"> <span class="nl">display</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">block</span> <span class="p">;</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="html"> <span class="nl">margin-top</span><span class="p">:</span> <span class="m" style="color: #099;">1em</span> <span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="html"> <span class="nl">margin-bottom</span><span class="p">:</span> <span class="m" style="color: #099;">1em</span> <span class="p">}</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="html"></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.line-block</span> <span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.line-block</span> <span class="p">{</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="html"> <span class="nl">margin-top</span><span class="p">:</span> <span class="m" style="color: #099;">0</span> <span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="html"> <span class="nl">margin-bottom</span><span class="p">:</span> <span class="m" style="color: #099;">0</span> <span class="p">;</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="html"> <span class="nl">margin-left</span><span class="p">:</span> <span class="m" style="color: #099;">1.5em</span> <span class="p">}</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="html"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.sidebar</span> <span class="p">{</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="html"> <span class="nl">margin</span><span class="p">:</span> <span class="m" style="color: #099;">0</span> <span class="m" style="color: #099;">0</span> <span class="m" style="color: #099;">0.5em</span> <span class="m" style="color: #099;">1em</span> <span class="p">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="html"> <span class="nl">border</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">medium</span> <span class="nb" style="color: #0086b3;">outset</span> <span class="p">;</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="html"> <span class="nl">padding</span><span class="p">:</span> <span class="m" style="color: #099;">1em</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="html"> <span class="nl">background-color</span><span class="p">:</span> <span class="m" style="color: #099;">#ffffee</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="html"> <span class="nl">width</span><span class="p">:</span> <span class="m" style="color: #099;">40%</span> <span class="p">;</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="html"> <span class="nl">float</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">right</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="html"> <span class="nl">clear</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">right</span> <span class="p">}</span></span>
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125
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.sidebar</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.rubric</span> <span class="p">{</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="html"> <span class="nl">font-family</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">sans-serif</span> <span class="p">;</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="html"> <span class="nl">font-size</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">medium</span> <span class="p">}</span></span>
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129
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.system-messages</span> <span class="p">{</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="html"> <span class="nl">margin</span><span class="p">:</span> <span class="m" style="color: #099;">5em</span> <span class="p">}</span></span>
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132
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.system-messages</span> <span class="nt" style="color: navy;">h1</span> <span class="p">{</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="html"> <span class="nl">color</span><span class="p">:</span> <span class="no" style="color: teal;">red</span> <span class="p">}</span></span>
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135
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.system-message</span> <span class="p">{</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="html"> <span class="nl">border</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">medium</span> <span class="nb" style="color: #0086b3;">outset</span> <span class="p">;</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="html"> <span class="nl">padding</span><span class="p">:</span> <span class="m" style="color: #099;">1em</span> <span class="p">}</span></span>
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139
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.system-message</span> <span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.system-message-title</span> <span class="p">{</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="html"> <span class="nl">color</span><span class="p">:</span> <span class="no" style="color: teal;">red</span> <span class="p">;</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span> <span class="p">}</span></span>
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143
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.topic</span> <span class="p">{</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="html"> <span class="nl">margin</span><span class="p">:</span> <span class="m" style="color: #099;">2em</span> <span class="p">}</span></span>
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146
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="html"><span class="nt" style="color: navy;">h1</span><span class="nc" style="color: #458; font-weight: 600;">.section-subtitle</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">h2</span><span class="nc" style="color: #458; font-weight: 600;">.section-subtitle</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">h3</span><span class="nc" style="color: #458; font-weight: 600;">.section-subtitle</span><span class="o" style="font-weight: 600;">,</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="html"><span class="nt" style="color: navy;">h4</span><span class="nc" style="color: #458; font-weight: 600;">.section-subtitle</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">h5</span><span class="nc" style="color: #458; font-weight: 600;">.section-subtitle</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">h6</span><span class="nc" style="color: #458; font-weight: 600;">.section-subtitle</span> <span class="p">{</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="html"> <span class="nl">margin-top</span><span class="p">:</span> <span class="m" style="color: #099;">0.4em</span> <span class="p">}</span></span>
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150
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="html"><span class="nt" style="color: navy;">h1</span><span class="nc" style="color: #458; font-weight: 600;">.title</span> <span class="p">{</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="html"> <span class="nl">text-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">center</span> <span class="p">}</span></span>
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153
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="html"><span class="nt" style="color: navy;">h2</span><span class="nc" style="color: #458; font-weight: 600;">.subtitle</span> <span class="p">{</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="html"> <span class="nl">text-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">center</span> <span class="p">}</span></span>
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156
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="html"><span class="nt" style="color: navy;">hr</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span> <span class="p">{</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="html"> <span class="nl">width</span><span class="p">:</span> <span class="m" style="color: #099;">75%</span> <span class="p">}</span></span>
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159
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="html"><span class="nt" style="color: navy;">img</span><span class="nc" style="color: #458; font-weight: 600;">.align-left</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">.figure.align-left</span><span class="p">{</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="html"> <span class="nl">clear</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">left</span> <span class="p">;</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="html"> <span class="nl">float</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">left</span> <span class="p">;</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="html"> <span class="nl">margin-right</span><span class="p">:</span> <span class="m" style="color: #099;">1em</span> <span class="p">}</span></span>
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164
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="html"><span class="nt" style="color: navy;">img</span><span class="nc" style="color: #458; font-weight: 600;">.align-right</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">.figure.align-right</span> <span class="p">{</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="html"> <span class="nl">clear</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">right</span> <span class="p">;</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="html"> <span class="nl">float</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">right</span> <span class="p">;</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="html"> <span class="nl">margin-left</span><span class="p">:</span> <span class="m" style="color: #099;">1em</span> <span class="p">}</span></span>
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169
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="html"><span class="nc" style="color: #458; font-weight: 600;">.align-left</span> <span class="p">{</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="html"> <span class="nl">text-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">left</span> <span class="p">}</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="html"></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="html"><span class="nc" style="color: #458; font-weight: 600;">.align-center</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="html"> <span class="nl">clear</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">both</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="html"> <span class="nl">text-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">center</span> <span class="p">}</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="html"></span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="html"><span class="nc" style="color: #458; font-weight: 600;">.align-right</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="html"> <span class="nl">text-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">right</span> <span class="p">}</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="html"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">/* reset inner alignment in figures */</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.align-right</span> <span class="p">{</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="html"> <span class="nl">text-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">left</span> <span class="p">}</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="html"></span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">/* div.align-center * { */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">/* text-align: left } */</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="html"></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="html"><span class="nt" style="color: navy;">ol</span><span class="nc" style="color: #458; font-weight: 600;">.simple</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">ul</span><span class="nc" style="color: #458; font-weight: 600;">.simple</span> <span class="p">{</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="html"> <span class="nl">margin-bottom</span><span class="p">:</span> <span class="m" style="color: #099;">1em</span> <span class="p">}</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="html"></span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="html"><span class="nt" style="color: navy;">ol</span><span class="nc" style="color: #458; font-weight: 600;">.arabic</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="html"> <span class="nl">list-style</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">decimal</span> <span class="p">}</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="html"></span>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="html"><span class="nt" style="color: navy;">ol</span><span class="nc" style="color: #458; font-weight: 600;">.loweralpha</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="html"> <span class="nl">list-style</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">lower-alpha</span> <span class="p">}</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="html"></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="html"><span class="nt" style="color: navy;">ol</span><span class="nc" style="color: #458; font-weight: 600;">.upperalpha</span> <span class="p">{</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="html"> <span class="nl">list-style</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">upper-alpha</span> <span class="p">}</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="html"></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="html"><span class="nt" style="color: navy;">ol</span><span class="nc" style="color: #458; font-weight: 600;">.lowerroman</span> <span class="p">{</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="html"> <span class="nl">list-style</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">lower-roman</span> <span class="p">}</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="html"></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="html"><span class="nt" style="color: navy;">ol</span><span class="nc" style="color: #458; font-weight: 600;">.upperroman</span> <span class="p">{</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="html"> <span class="nl">list-style</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">upper-roman</span> <span class="p">}</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="html"></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="html"><span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.attribution</span> <span class="p">{</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="html"> <span class="nl">text-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">right</span> <span class="p">;</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="html"> <span class="nl">margin-left</span><span class="p">:</span> <span class="m" style="color: #099;">50%</span> <span class="p">}</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="html"></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="html"><span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.caption</span> <span class="p">{</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="html"> <span class="nl">font-style</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">italic</span> <span class="p">}</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="html"></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="html"><span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.credits</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="html"> <span class="nl">font-style</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">italic</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="html"> <span class="nl">font-size</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">smaller</span> <span class="p">}</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="html"></span>
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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="html"><span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.label</span> <span class="p">{</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="html"> <span class="nl">white-space</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">nowrap</span> <span class="p">}</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="html"></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="html"><span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.rubric</span> <span class="p">{</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span> <span class="p">;</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="html"> <span class="nl">font-size</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">larger</span> <span class="p">;</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="html"> <span class="nl">color</span><span class="p">:</span> <span class="no" style="color: teal;">maroon</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="html"> <span class="nl">text-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">center</span> <span class="p">}</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="html"></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="html"><span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.sidebar-title</span> <span class="p">{</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="html"> <span class="nl">font-family</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">sans-serif</span> <span class="p">;</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span> <span class="p">;</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="html"> <span class="nl">font-size</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">larger</span> <span class="p">}</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="html"></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="html"><span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.sidebar-subtitle</span> <span class="p">{</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="html"> <span class="nl">font-family</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">sans-serif</span> <span class="p">;</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span> <span class="p">}</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="html"></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="html"><span class="nt" style="color: navy;">p</span><span class="nc" style="color: #458; font-weight: 600;">.topic-title</span> <span class="p">{</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span> <span class="p">}</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="html"></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="html"><span class="nt" style="color: navy;">pre</span><span class="nc" style="color: #458; font-weight: 600;">.address</span> <span class="p">{</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="html"> <span class="nl">margin-bottom</span><span class="p">:</span> <span class="m" style="color: #099;">0</span> <span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="html"> <span class="nl">margin-top</span><span class="p">:</span> <span class="m" style="color: #099;">0</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="html"> <span class="nl">font</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">inherit</span> <span class="p">}</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="html"><span class="nt" style="color: navy;">pre</span><span class="nc" style="color: #458; font-weight: 600;">.literal-block</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">pre</span><span class="nc" style="color: #458; font-weight: 600;">.doctest-block</span> <span class="p">{</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="html"> <span class="nl">margin-left</span><span class="p">:</span> <span class="m" style="color: #099;">2em</span> <span class="p">;</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="html"> <span class="nl">margin-right</span><span class="p">:</span> <span class="m" style="color: #099;">2em</span> <span class="p">}</span></span>
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245
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="html"><span class="nt" style="color: navy;">span</span><span class="nc" style="color: #458; font-weight: 600;">.classifier</span> <span class="p">{</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="html"> <span class="nl">font-family</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">sans-serif</span> <span class="p">;</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="html"> <span class="nl">font-style</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">oblique</span> <span class="p">}</span></span>
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249
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="html"><span class="nt" style="color: navy;">span</span><span class="nc" style="color: #458; font-weight: 600;">.classifier-delimiter</span> <span class="p">{</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="html"> <span class="nl">font-family</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">sans-serif</span> <span class="p">;</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span> <span class="p">}</span></span>
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253
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="html"><span class="nt" style="color: navy;">span</span><span class="nc" style="color: #458; font-weight: 600;">.interpreted</span> <span class="p">{</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="html"> <span class="nl">font-family</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">sans-serif</span> <span class="p">}</span></span>
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256
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="html"><span class="nt" style="color: navy;">span</span><span class="nc" style="color: #458; font-weight: 600;">.option</span> <span class="p">{</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="html"> <span class="nl">white-space</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">nowrap</span> <span class="p">}</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="html"></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="html"><span class="nt" style="color: navy;">span</span><span class="nc" style="color: #458; font-weight: 600;">.pre</span> <span class="p">{</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="html"> <span class="nl">white-space</span><span class="p">:</span> <span class="n" style="color: #333;">pre</span> <span class="p">}</span></span>
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262
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="html"><span class="nt" style="color: navy;">span</span><span class="nc" style="color: #458; font-weight: 600;">.problematic</span> <span class="p">{</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="html"> <span class="nl">color</span><span class="p">:</span> <span class="no" style="color: teal;">red</span> <span class="p">}</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="html"></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="html"><span class="nt" style="color: navy;">span</span><span class="nc" style="color: #458; font-weight: 600;">.section-subtitle</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="html"> <span class="c" style="color: #998; font-style: italic;">/* font-size relative to parent (h1..h6 element) */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="html"> <span class="nl">font-size</span><span class="p">:</span> <span class="m" style="color: #099;">80%</span> <span class="p">}</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="html"></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="html"><span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.citation</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="html"> <span class="nl">border-left</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">solid</span> <span class="m" style="color: #099;">1px</span> <span class="no" style="color: teal;">gray</span><span class="p">;</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="html"> <span class="nl">margin-left</span><span class="p">:</span> <span class="m" style="color: #099;">1px</span> <span class="p">}</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="html"></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="html"><span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.docinfo</span> <span class="p">{</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="html"> <span class="nl">margin</span><span class="p">:</span> <span class="m" style="color: #099;">2em</span> <span class="m" style="color: #099;">4em</span> <span class="p">}</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="html"></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="html"><span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span> <span class="p">{</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="html"> <span class="nl">margin-top</span><span class="p">:</span> <span class="m" style="color: #099;">0.5em</span> <span class="p">;</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="html"> <span class="nl">margin-bottom</span><span class="p">:</span> <span class="m" style="color: #099;">0.5em</span> <span class="p">}</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="html"></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="html"><span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.footnote</span> <span class="p">{</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="html"> <span class="nl">border-left</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">solid</span> <span class="m" style="color: #099;">1px</span> <span class="no" style="color: teal;">black</span><span class="p">;</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="html"> <span class="nl">margin-left</span><span class="p">:</span> <span class="m" style="color: #099;">1px</span> <span class="p">}</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="html"></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="html"><span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span> <span class="nt" style="color: navy;">td</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span> <span class="nt" style="color: navy;">th</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="html"><span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.docinfo</span> <span class="nt" style="color: navy;">td</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.docinfo</span> <span class="nt" style="color: navy;">th</span> <span class="p">{</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="html"> <span class="nl">padding-left</span><span class="p">:</span> <span class="m" style="color: #099;">0.5em</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="html"> <span class="nl">padding-right</span><span class="p">:</span> <span class="m" style="color: #099;">0.5em</span> <span class="p">;</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="html"> <span class="nl">vertical-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">top</span> <span class="p">}</span></span>
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290
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<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="html"><span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span> <span class="nt" style="color: navy;">th</span><span class="nc" style="color: #458; font-weight: 600;">.field-name</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.docinfo</span> <span class="nt" style="color: navy;">th</span><span class="nc" style="color: #458; font-weight: 600;">.docinfo-name</span> <span class="p">{</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span> <span class="p">;</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="html"> <span class="nl">text-align</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">left</span> <span class="p">;</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="html"> <span class="nl">white-space</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">nowrap</span> <span class="p">;</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="html"> <span class="nl">padding-left</span><span class="p">:</span> <span class="m" style="color: #099;">0</span> <span class="p">}</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="html"></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="html"><span class="nt" style="color: navy;">h1</span> <span class="nt" style="color: navy;">tt</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">h2</span> <span class="nt" style="color: navy;">tt</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">h3</span> <span class="nt" style="color: navy;">tt</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="html"><span class="nt" style="color: navy;">h4</span> <span class="nt" style="color: navy;">tt</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">h5</span> <span class="nt" style="color: navy;">tt</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span><span class="o" style="font-weight: 600;">,</span> <span class="nt" style="color: navy;">h6</span> <span class="nt" style="color: navy;">tt</span><span class="nc" style="color: #458; font-weight: 600;">.docutils</span> <span class="p">{</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="html"> <span class="nl">font-size</span><span class="p">:</span> <span class="m" style="color: #099;">100%</span> <span class="p">}</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="html"></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="html"><span class="nt" style="color: navy;">ul</span><span class="nc" style="color: #458; font-weight: 600;">.auto-toc</span> <span class="p">{</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="html"> <span class="nl">list-style-type</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">none</span> <span class="p">}</span></span>
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303
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="html"><span class="nt" style="color: navy;"></style></span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="html"><span class="nt" style="color: navy;"><style </span><span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"text/css"</span><span class="nt" style="color: navy;">></span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="html"></span>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">/* Style sheet for LAST HTML documents */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="html"><span class="nt" style="color: navy;">h1</span> <span class="p">{</span> <span class="nl">color</span><span class="p">:</span> <span class="no" style="color: teal;">navy</span> <span class="p">}</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="html"><span class="nt" style="color: navy;">h2</span> <span class="p">{</span> <span class="nl">color</span><span class="p">:</span> <span class="no" style="color: teal;">teal</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="html"><span class="nt" style="color: navy;">div</span><span class="nc" style="color: #458; font-weight: 600;">.document</span> <span class="p">{</span> <span class="nl">margin-left</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">auto</span><span class="p">;</span> <span class="nl">margin-right</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">auto</span><span class="p">;</span> <span class="nl">max-width</span><span class="p">:</span> <span class="m" style="color: #099;">45em</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="html"><span class="nt" style="color: navy;">strong</span> <span class="p">{</span> <span class="nl">color</span><span class="p">:</span> <span class="no" style="color: teal;">red</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="html"><span class="nc" style="color: #458; font-weight: 600;">.option-list</span> <span class="nt" style="color: navy;">td</span> <span class="p">{</span> <span class="nl">padding-bottom</span><span class="p">:</span> <span class="m" style="color: #099;">1em</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="html"><span class="nt" style="color: navy;">table</span><span class="nc" style="color: #458; font-weight: 600;">.field-list</span> <span class="p">{</span> <span class="nl">border</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">thin</span> <span class="nb" style="color: #0086b3;">solid</span> <span class="no" style="color: teal;">green</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"document"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"maf-cut"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="html"><span class="nt" style="color: navy;"><h1</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: navy;">></span>maf-cut<span class="nt" style="color: navy;"></h1></span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="html"><span class="nt" style="color: navy;"><p><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: navy;">></span>maf-cut<span class="nt" style="color: navy;"></span></tt></span> cuts out parts of <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://genome.ucsc.edu/FAQ/FAQformat.html#format5"</span><span class="nt" style="color: navy;">></span>MAF<span class="nt" style="color: navy;"></a></span> format alignments. For example:<span class="nt" style="color: navy;"></p></span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="html">maf-cut chr7:1234000-1235000 alignments.maf</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>This gets alignment parts within the range 1234000-1235000 of the</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="html">sequence named <span class="ni" style="color: purple;">"</span>chr7<span class="ni" style="color: purple;">"</span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The ranges are zero-based. For example, <span class="nt" style="color: navy;"><tt</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: navy;">></span>chr7:0-1000<span class="nt" style="color: navy;"></span></tt></span> means the</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="html">first 1000 bases of chr7.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>You can omit the sequence name:<span class="nt" style="color: navy;"></p></span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="html">maf-cut 1234000-1235000 alignments.maf</span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Then, the range applies to the topmost sequence in each alignment.<span class="nt" style="color: navy;"></p></span></span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#a3726766a594e96c014f2e423263f9133696bd04"><strong>doc/maf-cut.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">maf-cut</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">=======</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">``maf-cut`` cuts out parts of MAF_ format alignments. For example::</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> maf-cut chr7:1234000-1235000 alignments.maf</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">This gets alignment parts within the range 1234000-1235000 of the</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">sequence named "chr7".</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">The ranges are zero-based. For example, ``chr7:0-1000`` means the</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">first 1000 bases of chr7.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">You can omit the sequence name::</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> maf-cut 1234000-1235000 alignments.maf</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Then, the range applies to the topmost sequence in each alignment.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.. _MAF: http://genome.ucsc.edu/FAQ/FAQformat.html#format5</span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#d6f8248b8a5e868eac831cf1a35c8543f1fff6a8"><strong>scripts/last-dotplot</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -285,7 +285,7 @@ def nameKey(oneSeqRanges):</td>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">natural_sort_key</span><span class="p">(</span><span class="n" style="color: #333;">oneSeqRanges</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sizeKey</span><span class="p">(</span><span class="n" style="color: #333;">oneSeqRanges</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">e</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">oneSeqRanges</span><span class="p">),</span> <span class="n" style="color: #333;">nameKey</span><span class="p">(</span><span class="n" style="color: #333;">oneSeqRanges</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">e</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">s</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">oneSeqRanges</span><span class="p">),</span> <span class="n" style="color: #333;">nameKey</span><span class="p">(</span><span class="n" style="color: #333;">oneSeqRanges</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">alignmentKey</span><span class="p">(</span><span class="n" style="color: #333;">seqNamesToLists</span><span class="p">,</span> <span class="n" style="color: #333;">oneSeqRanges</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oneSeqRanges</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -479,7 +479,7 @@ def strandAndOrigin(ranges, beg, size):</td>
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479
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isReverseStrand</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="p">(</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">size</span><span class="p">)</span></span>
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481
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rangeBeg</span><span class="p">,</span> <span class="n" style="color: #333;">rangeEnd</span><span class="p">,</span> <span class="n" style="color: #333;">isReverseRange</span><span class="p">,</span> <span class="n" style="color: #333;">origin</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ranges</span><span class="p">:</span></span>
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482
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rangeEnd</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">beg</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rangeEnd</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">beg</span><span class="p">:</span><span class="idiff left"> </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right"># assumes the ranges are sorted</span></span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">isReverseStrand</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">isReverseRange</span><span class="p">),</span> <span class="n" style="color: #333;">origin</span></span>
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">alignmentPixels</span><span class="p">(</span><span class="n" style="color: #333;">width</span><span class="p">,</span> <span class="n" style="color: #333;">height</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span><span class="p">,</span> <span class="n" style="color: #333;">bp_per_pix</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -698,7 +698,7 @@ def rangesWithOrigins(sortedRanges, rangePixBegs, rangePixLens, bpPerPix):</td>
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rangesPerSeq</span><span class="p">(</span><span class="n" style="color: #333;">sortedRanges</span><span class="p">,</span> <span class="n" style="color: #333;">rangePixBegs</span><span class="p">,</span> <span class="n" style="color: #333;">rangePixLens</span><span class="p">,</span> <span class="n" style="color: #333;">bpPerPix</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rangesWithOrigins</span><span class="p">(</span><span class="n" style="color: #333;">sortedRanges</span><span class="p">,</span> <span class="n" style="color: #333;">rangePixBegs</span><span class="p">,</span> <span class="n" style="color: #333;">rangePixLens</span><span class="p">,</span> <span class="n" style="color: #333;">bpPerPix</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getFont</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fontfile</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#! /usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">optparse</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">signal</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">):</span> <span class="c" style="color: #998; font-style: italic;"># faster than fileinput</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">alnBegFromSeqBeg</span><span class="p">(</span><span class="n" style="color: #333;">gappedSequence</span><span class="p">,</span> <span class="n" style="color: #333;">seqBeg</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">gappedSequence</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqBeg</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">i</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">seqBeg</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">alnEndFromSeqEnd</span><span class="p">(</span><span class="n" style="color: #333;">gappedSequence</span><span class="p">,</span> <span class="n" style="color: #333;">seqEnd</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">gappedSequence</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">seqEnd</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">alignmentRange</span><span class="p">(</span><span class="n" style="color: #333;">cutBeg</span><span class="p">,</span> <span class="n" style="color: #333;">cutEnd</span><span class="p">,</span> <span class="n" style="color: #333;">sLineFields</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">sLineFields</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">cutEnd</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">sequenceWithGaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sLineFields</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">span</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequenceWithGaps</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sequenceWithGaps</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">span</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">cutBeg</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">seqBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">cutBeg</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">alnBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnBegFromSeqBeg</span><span class="p">(</span><span class="n" style="color: #333;">sequenceWithGaps</span><span class="p">,</span> <span class="n" style="color: #333;">seqBeg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">seqEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">cutEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">span</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">alnEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnEndFromSeqEnd</span><span class="p">(</span><span class="n" style="color: #333;">sequenceWithGaps</span><span class="p">,</span> <span class="n" style="color: #333;">seqEnd</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">findTheSpecifiedSequence</span><span class="p">(</span><span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mafLines</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"s"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqName</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seqName</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fields</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cutMafRecords</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">,</span> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mafLines</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"s"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">oldSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">newSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldSeq</span><span class="p">[</span><span class="n" style="color: #333;">alnBeg</span><span class="p">:</span><span class="n" style="color: #333;">alnEnd</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alnBeg</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">oldSeq</span><span class="p">[:</span><span class="n" style="color: #333;">alnBeg</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">span</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">newSeq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">newSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">fields</span><span class="p">[:</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">beg</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">span</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">:</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">newSeq</span><span class="p">]</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"q"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">fields</span><span class="p">[:</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="n" style="color: #333;">alnBeg</span><span class="p">:</span><span class="n" style="color: #333;">alnEnd</span><span class="p">]]</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"p"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">fields</span><span class="p">[:</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">alnBeg</span><span class="p">:</span><span class="n" style="color: #333;">alnEnd</span><span class="p">]]</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">fields</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mafFieldWidths</span><span class="p">(</span><span class="n" style="color: #333;">mafRecords</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">sRecords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mafRecords</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"s"</span><span class="p">)</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">sColumns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sRecords</span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sColumns</span><span class="p">:</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printMafLine</span><span class="p">(</span><span class="n" style="color: #333;">fieldWidths</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">formatParams</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chain</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_iterable</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">fieldWidths</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="p">))</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%*</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%-*</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%*</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%*</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%*</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%*</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%*</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">formatParams</span><span class="p">))</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cutOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">):</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">cutBeg</span><span class="p">,</span> <span class="n" style="color: #333;">cutEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutRange</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">sLineFields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findTheSpecifiedSequence</span><span class="p">(</span><span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">)</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">sLineFields</span><span class="p">:</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignmentRange</span><span class="p">(</span><span class="n" style="color: #333;">cutBeg</span><span class="p">,</span> <span class="n" style="color: #333;">cutEnd</span><span class="p">,</span> <span class="n" style="color: #333;">sLineFields</span><span class="p">)</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alnBeg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">alnEnd</span><span class="p">:</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">mafRecords</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">cutMafRecords</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">,</span> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span><span class="p">))</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">fieldWidths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">mafFieldWidths</span><span class="p">(</span><span class="n" style="color: #333;">mafRecords</span><span class="p">))</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fields</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mafRecords</span><span class="p">:</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"s"</span><span class="p">:</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">printMafLine</span><span class="p">(</span><span class="n" style="color: #333;">fieldWidths</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="p">)</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"q"</span><span class="p">:</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">printMafLine</span><span class="p">(</span><span class="n" style="color: #333;">fieldWidths</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="p">[:</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">""</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"p"</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">printMafLine</span><span class="p">(</span><span class="n" style="color: #333;">fieldWidths</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="p">[:</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">""</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">))</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mafCutOneFile</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">mafLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isspace</span><span class="p">():</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">cutOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">)</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">mafLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"#"</span><span class="p">:</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">mafLines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">cutOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">)</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">wantedRange</span><span class="p">(</span><span class="n" style="color: #333;">cutSpecification</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">":"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cutSpecification</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">cutSpecification</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">beg</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mafCut</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">cutRange</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wantedRange</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]:</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">mafCutOneFile</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">mafCutOneFile</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span><span class="p">)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">signal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SIGPIPE</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SIG_DFL</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># avoid silly error message</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">usage</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">prog chrN:start-end alignments.maf"</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Get parts of MAF-format alignments."</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OptionParser</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">usage</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"please give me a cut specification and MAF alignments"</span><span class="p">)</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">mafCut</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#ab919b3eb596acbd0affb15613fb99fee03165d8"><strong>src/Alphabet.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -96,6 +96,11 @@ void Alphabet::initCaseConversions( unsigned codeEnd ) {</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">numbersToLowercase</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">letters</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">dna</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// kludge for RNA:</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">encode</span><span class="p">[</span><span class="sc" style="color: #d14;">'U'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">encode</span><span class="p">[</span><span class="sc" style="color: #d14;">'T'</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">encode</span><span class="p">[</span><span class="sc" style="color: #d14;">'u'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">encode</span><span class="p">[</span><span class="sc" style="color: #d14;">'t'</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">capacity</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">lettersToUppercase</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numbersToUppercase</span><span class="p">[</span> <span class="n" style="color: #333;">encode</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">];</span></span>
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101
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#e478528f9c99e8adc6fafff10d008edf048f9c32"><strong>src/QualityPssmMaker.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,8 +29,8 @@ void QualityPssmMaker::init(const ScoreMatrixRow *scoreMatrix,</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isMatchMismatchMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isMatchMismatchMatrix</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">toUnmasked</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toUnmasked</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchExp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">exp</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span> <span class="n" style="color: #333;">matchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mismatchExp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">exp</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span> <span class="n" style="color: #333;">mismatchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchExp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">probFromScore</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lambda</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">matchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mismatchExp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">probFromScore</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lambda</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">mismatchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qualityCapacity</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">errorProbFromQual</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">qualityOffset</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,12 +40,12 @@ void QualityPssmMaker::init(const ScoreMatrixRow *scoreMatrix,</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">expScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matchExp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mismatchExp</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">expScore</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">qualityToMatchScore</span><span class="p">[</span><span class="n" style="color: #333;">q</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">nearestInt</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">log</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">expScore</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">lambda</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">qualityToMatchScore</span><span class="p">[</span><span class="n" style="color: #333;">q</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">scoreFromProb</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lambda</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">expScore</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">expMatrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">exp</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// can be 0</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">expMatrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">probFromScore</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lambda</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// can be 0</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This function is a wee bit slow, even if isMatchMismatchMatrix and</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,7 +88,7 @@ void QualityPssmMaker::make(const uchar *sequenceBeg,</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">expScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">inner_product</span><span class="p">(</span><span class="n" style="color: #333;">letterProbs</span><span class="p">,</span> <span class="n" style="color: #333;">letterProbsEnd</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">expMatrix</span><span class="p">[</span><span class="n" style="color: #333;">unmasked1</span><span class="p">],</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">expScore</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">nearestInt</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">log</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">expScore</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">lambda</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">scoreFromProb</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lambda</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">expScore</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#7e02f07907d04e1c14dd8cbe36e5ca852897fb6b"><strong>src/ScoreMatrix.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ScoreMatrix.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ScoreMatrixData.hh"</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "qualityScoreUtil.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "zio.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sstream></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iomanip></span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,17 +10,24 @@</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdexcept></span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cassert></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cctype> // toupper, tolower</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <<span class="idiff left right">cstddef</span>> // size_t</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <<span class="idiff left right">stddef.h</span>> // size_t</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#include <iostream> // for debugging</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define ERR(x) throw std::runtime_error(x)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define COUNTOF(a) (sizeof (a) / sizeof *(a))</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">makeUppercase</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">canonicalName</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">name</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">s</span>ize_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">COUNTOF</span><span class="p">(</span><span class="n" style="color: #333;">scoreMatrixNicknames</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">COUNTOF</span><span class="p">(</span><span class="n" style="color: #333;">scoreMatrixNicknames</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>
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23
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">scoreMatrixNicknames</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">nickname</span> <span class="p">)</span></span>
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24
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">scoreMatrixNicknames</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">realname</span><span class="p">;</span></span>
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25
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,24 +36,24 @@ const char *ScoreMatrix::canonicalName( const std::string& name ){</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringFromName</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">name</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">canonicalName</span><span class="p">(</span> <span class="n" style="color: #333;">name</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">s</span>ize_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">COUNTOF</span><span class="p">(</span><span class="n" style="color: #333;">scoreMatrices</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">COUNTOF</span><span class="p">(</span><span class="n" style="color: #333;">scoreMatrices</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">scoreMatrices</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">scoreMatrices</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">text</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">slurp</span><span class="p">(</span> <span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">matchMismatch</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">letters</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">letters</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">letters</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">letters</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setMatchMismatch</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">matchScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mismatchCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">symbols</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">rowSymbols</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">symbols</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">symbols</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">colSymbols</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">symbols</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">symbols</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">cells</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span> <span class="n" style="color: #333;">size</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">symbols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">cells</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">)</span>{</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">mismatch</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">size</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff right">mismatchCost</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match<span class="idiff left right">Score</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -55,20 +63,31 @@ void ScoreMatrix::fromString( const std::string& matString ){</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">iss</span> <span class="p">)</span> <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"can't read the score matrix"</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">init</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">encode</span><span class="p">[]</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">rows</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">cols</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">s2i</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">[],</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">upperAndLowerIndex</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">tooBig</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">[],</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">symbol</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">upper</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">lower</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">symbol</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">upper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">lower</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">[</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tolower</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)];</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">upper</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">tooBig</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">lower</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">tooBig</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"bad letter in score matrix: "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">symbol</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">iterator</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rows</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">begin</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rows</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">toupper</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span></span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ScoreMatrix</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">init</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">uchar</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">symbolToIndex</span></span><span class="p"><span class="idiff">[])</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">assert</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">rowSymbols</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">colSymbols</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff right">()</span></span> <span class="p">);</span></span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">iterator</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cols</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">begin</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cols</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"> <span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">toupper</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">makeUppercase</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rowSymbols</span></span><span class="p"><span class="idiff right">);</span></span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">makeUppercase</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">colSymbols</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">maxScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">row</span>s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">c</span>ols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">s<span class="idiff left">ize_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">rowSymbol</span>s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">s<span class="idiff left">ize_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">colSymb</span>ols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span> <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">maxScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span> <span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,30 +101,25 @@ void ScoreMatrix::init( const uchar encode[] ){</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rows</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">encode</span><span class="p">[</span> <span class="n" style="color: #333;">uchar</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">encode</span><span class="p">[</span> <span class="n" style="color: #333;">uchar</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">encode</span><span class="p">[</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tolower</span><span class="p">(</span> <span class="n" style="color: #333;">rows</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">)</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">encode</span><span class="p">[</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tolower</span><span class="p">(</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">)</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">MAT</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"bad letter in score matrix: "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rows</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">MAT</span> <span class="p">)</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"bad letter in score matrix: "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">caseSensitive</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">][</span><span class="n" style="color: #333;">b</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">caseSensitive</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">][</span><span class="n" style="color: #333;">y</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">caseSensitive</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">][</span><span class="n" style="color: #333;">b</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">caseSensitive</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">][</span><span class="n" style="color: #333;">y</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// careful: maybe a==x or b==y</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">caseInsensitive</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">][</span><span class="n" style="color: #333;">y</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">caseInsensitive</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">][</span><span class="n" style="color: #333;">b</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">caseInsensitive</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">][</span><span class="n" style="color: #333;">y</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">caseInsensitive</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">][</span><span class="n" style="color: #333;">b</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rowSymbols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">colSymbols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="p">){</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">iu</span><span class="p">,</span> <span class="n" style="color: #333;">il</span><span class="p">,</span> <span class="n" style="color: #333;">ju</span><span class="p">,</span> <span class="n" style="color: #333;">jl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">upperAndLowerIndex</span><span class="p">(</span><span class="n" style="color: #333;">MAT</span><span class="p">,</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">,</span> <span class="n" style="color: #333;">rowSymbols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">iu</span><span class="p">,</span> <span class="n" style="color: #333;">il</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">upperAndLowerIndex</span><span class="p">(</span><span class="n" style="color: #333;">MAT</span><span class="p">,</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">,</span> <span class="n" style="color: #333;">colSymbols</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">ju</span><span class="p">,</span> <span class="n" style="color: #333;">jl</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">caseSensitive</span><span class="p">[</span><span class="n" style="color: #333;">iu</span><span class="p">][</span><span class="n" style="color: #333;">jl</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">caseSensitive</span><span class="p">[</span><span class="n" style="color: #333;">il</span><span class="p">][</span><span class="n" style="color: #333;">ju</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">caseSensitive</span><span class="p">[</span><span class="n" style="color: #333;">il</span><span class="p">][</span><span class="n" style="color: #333;">jl</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">caseSensitive</span><span class="p">[</span><span class="n" style="color: #333;">iu</span><span class="p">][</span><span class="n" style="color: #333;">ju</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// careful: maybe il==iu or jl==ju</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">caseInsensitive</span><span class="p">[</span><span class="n" style="color: #333;">iu</span><span class="p">][</span><span class="n" style="color: #333;">ju</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">caseInsensitive</span><span class="p">[</span><span class="n" style="color: #333;">iu</span><span class="p">][</span><span class="n" style="color: #333;">jl</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">caseInsensitive</span><span class="p">[</span><span class="n" style="color: #333;">il</span><span class="p">][</span><span class="n" style="color: #333;">ju</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">caseInsensitive</span><span class="p">[</span><span class="n" style="color: #333;">il</span><span class="p">][</span><span class="n" style="color: #333;">jl</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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103
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="p">}</span></span>
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104
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="p">}</span></span>
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105
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"></span>
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106
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// set a hugely negative score for the delimiter symbol:</span></span>
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107
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">delimiter</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">' '</span><span class="p">;</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">encode</span></span><span class="p">[</span><span class="n" style="color: #333;">delimiter</span><span class="p">];</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">symbolToIndex</span></span><span class="p">[</span><span class="n" style="color: #333;">delimiter</span><span class="p">];</span></span>
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109
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MAT</span> <span class="p">);</span></span>
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110
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MAT</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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111
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">caseSensitive</span><span class="p">[</span><span class="n" style="color: #333;">z</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INF</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,24 +130,26 @@ void ScoreMatrix::init( const uchar encode[] ){</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"><span class="p">}</span></span>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"></span>
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeCommented</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">colWidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">colSymbols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">20</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"></span>
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"# "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">' '</span><span class="p">;</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">c</span>ols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">OUTPAD</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">c</span>ols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">s<span class="idiff left">ize_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">colSymb</span>ols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">colWidth</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">colSymb</span>ols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="p">}</span></span>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">row</span>s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"# "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">rows</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">c</span>ols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">OUTPAD</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">s<span class="idiff left">ize_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">rowSymbol</span>s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"# "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">row<span class="idiff left right">Symbol</span>s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">s<span class="idiff left">ize_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">colSymb</span>ols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="p">){</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">colWidth</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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129
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="p">}</span></span>
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130
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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131
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="p">}</span></span>
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132
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"><span class="p">}</span></span>
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133
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"></span>
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134
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">>></span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">m</span> <span class="p">){</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmpRows</span><span class="p">;</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmpCols</span><span class="p">;</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmpRow<span class="idiff left right">Symbol</span>s</span><span class="p">;</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmpCol<span class="idiff left right">Symbol</span>s</span><span class="p">;</span></span>
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137
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmpCells</span><span class="p">;</span></span>
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138
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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139
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -145,46 +161,131 @@ std::istream& operator>>( std::istream& stream, ScoreMatrix& m ){</td>
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145
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">){</span></span>
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146
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'#'</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// skip comment lines at the top</span></span>
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147
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span><span class="p">{</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">tmpCols</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">tmpCol<span class="idiff left right">Symbol</span>s</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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149
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="n" style="color: #333;">iss</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">c</span> <span class="p">);</span></span>
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150
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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151
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
152
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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">tmpRows</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">tmpRow<span class="idiff left right">Symbol</span>s</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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154
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">tmpCells</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span> <span class="n" style="color: #333;">tmpCells</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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155
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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156
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="n" style="color: #333;">iss</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">score</span> <span class="p">){</span></span>
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157
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">tmpCells</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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158
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
159
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<td class="diff-line-num new_line old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">tmpCells</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">tmpCols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">)</span> <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"bad score matrix"</span> <span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmpCells</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">tmpColSymbols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="s" style="color: #d14;">"bad score matrix"</span><span class="p">);</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="p">}</span></span>
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160
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="p">}</span></span>
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161
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"> <span class="p">}</span></span>
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162
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">stream</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">stream</span><span class="p">.</span><span class="n" style="color: #333;">bad</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">tmpRows</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">){</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">stream</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">stream</span><span class="p">.</span><span class="n" style="color: #333;">bad</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">tmpRow<span class="idiff left right">Symbol</span>s</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">){</span></span>
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164
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<td class="diff-line-num new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">row<span class="idiff left">s</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">swap</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">tmpRow</span>s</span><span class="p">);</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">col<span class="idiff left">s</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">swap</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">tmpC</span>ols</span><span class="p">);</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">row<span class="idiff left">Symbols</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">swap</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">tmpRowSymbol</span>s</span><span class="p">);</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">col<span class="idiff left">Symbols</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">swap</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">tmpColSymb</span>ols</span><span class="p">);</span></span>
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167
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">cells</span><span class="p">.</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">tmpCells</span><span class="p">);</span></span>
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168
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"> <span class="p">}</span></span>
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169
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"></span>
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170
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">stream</span><span class="p">;</span></span>
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171
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"><span class="p">}</span></span>
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172
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;"><<</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">m</span> <span class="p">){</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">cols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">OUTPAD</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ambiguities</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="s" style="color: #d14;">"M"</span> <span class="s" style="color: #d14;">"AC"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="s" style="color: #d14;">"S"</span> <span class="s" style="color: #d14;">"CG"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"> <span class="s" style="color: #d14;">"K"</span> <span class="s" style="color: #d14;">"GT"</span><span class="p">,</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="s" style="color: #d14;">"W"</span> <span class="s" style="color: #d14;">"TA"</span><span class="p">,</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="s" style="color: #d14;">"R"</span> <span class="s" style="color: #d14;">"AG"</span><span class="p">,</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Y"</span> <span class="s" style="color: #d14;">"CT"</span><span class="p">,</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="s" style="color: #d14;">"B"</span> <span class="s" style="color: #d14;">"CGT"</span><span class="p">,</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="s" style="color: #d14;">"D"</span> <span class="s" style="color: #d14;">"AGT"</span><span class="p">,</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="s" style="color: #d14;">"H"</span> <span class="s" style="color: #d14;">"ACT"</span><span class="p">,</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="s" style="color: #d14;">"V"</span> <span class="s" style="color: #d14;">"ACG"</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"><span class="p">};</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfAmbiguousSymbols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">COUNTOF</span><span class="p">(</span><span class="n" style="color: #333;">ambiguities</span><span class="p">);</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">isIn</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"><span class="p">}</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">ambiguityList</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">symbol</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">scratch</span><span class="p">[])</span> <span class="p">{</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfAmbiguousSymbols</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ambiguities</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">symbol</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ambiguities</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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176
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <span class="p">}</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="n" style="color: #333;">scratch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">symbol</span><span class="p">;</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">scratch</span><span class="p">;</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"><span class="p">}</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">symbolProbSum</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">[],</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">symbols</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probs</span><span class="p">[])</span> <span class="p">{</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">symbols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">symbols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s2i</span><span class="p">(</span><span class="n" style="color: #333;">symbolToIndex</span><span class="p">,</span> <span class="n" style="color: #333;">symbols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">probs</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">];</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="p">}</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"><span class="p">}</span></span>
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178
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">rows</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">rows</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">cols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="p">){</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">OUTPAD</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">jointScore</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">fastMatrix</span><span class="p">,</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span><span class="p">,</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rowSymbolProbs</span><span class="p">[],</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">colSymbolProbs</span><span class="p">[],</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rSymbols</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cSymbols</span><span class="p">)</span> <span class="p">{</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isOneRowSymbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rSymbols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isOneColSymbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">cSymbols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">rSymbols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">cSymbols</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s2i</span><span class="p">(</span><span class="n" style="color: #333;">symbolToIndex</span><span class="p">,</span> <span class="n" style="color: #333;">rSymbols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s2i</span><span class="p">(</span><span class="n" style="color: #333;">symbolToIndex</span><span class="p">,</span> <span class="n" style="color: #333;">cSymbols</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isOneRowSymbol</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">rowSymbolProbs</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">];</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isOneColSymbol</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">colSymbolProbs</span><span class="p">[</span><span class="n" style="color: #333;">y</span><span class="p">];</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">probFromScore</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">fastMatrix</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">][</span><span class="n" style="color: #333;">y</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"> <span class="p">}</span></span>
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186
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">stream</span><span class="p">;</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rowProbSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">symbolProbSum</span><span class="p">(</span><span class="n" style="color: #333;">symbolToIndex</span><span class="p">,</span> <span class="n" style="color: #333;">rSymbols</span><span class="p">,</span> <span class="n" style="color: #333;">rowSymbolProbs</span><span class="p">);</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">colProbSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">symbolProbSum</span><span class="p">(</span><span class="n" style="color: #333;">symbolToIndex</span><span class="p">,</span> <span class="n" style="color: #333;">cSymbols</span><span class="p">,</span> <span class="n" style="color: #333;">colSymbolProbs</span><span class="p">);</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">scoreFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">rowProbSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">colProbSum</span><span class="p">));</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"><span class="p">}</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addAmbiguousScores</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">[],</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span><span class="p">,</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rowSymbolProbs</span><span class="p">[],</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">colSymbolProbs</span><span class="p">[])</span> <span class="p">{</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fastMatrix</span><span class="p">[</span><span class="n" style="color: #333;">MAT</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">caseInsensitive</span><span class="p">,</span> <span class="n" style="color: #333;">caseInsensitive</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MAT</span><span class="p">,</span> <span class="n" style="color: #333;">fastMatrix</span><span class="p">);</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">scratch</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">};</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfAmbiguousSymbols</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span> <span class="p">{</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ambiguousSymbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ambiguities</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isIn</span><span class="p">(</span><span class="n" style="color: #333;">colSymbols</span><span class="p">,</span> <span class="n" style="color: #333;">ambiguousSymbol</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">colSymbols</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ambiguousSymbol</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rowSymbols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rSymbols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ambiguityList</span><span class="p">(</span><span class="n" style="color: #333;">rowSymbols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">scratch</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cSymbols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ambiguities</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">jointScore</span><span class="p">(</span><span class="n" style="color: #333;">symbolToIndex</span><span class="p">,</span> <span class="n" style="color: #333;">fastMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">rowSymbolProbs</span><span class="p">,</span> <span class="n" style="color: #333;">colSymbolProbs</span><span class="p">,</span> <span class="n" style="color: #333;">rSymbols</span><span class="p">,</span> <span class="n" style="color: #333;">cSymbols</span><span class="p">);</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">cells</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="p">}</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="p">}</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfAmbiguousSymbols</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ambiguousSymbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ambiguities</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isIn</span><span class="p">(</span><span class="n" style="color: #333;">rowSymbols</span><span class="p">,</span> <span class="n" style="color: #333;">ambiguousSymbol</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">rowSymbols</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ambiguousSymbol</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">cells</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">cells</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">colSymbols</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rSymbols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ambiguities</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cSymbols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ambiguityList</span><span class="p">(</span><span class="n" style="color: #333;">colSymbols</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">scratch</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">jointScore</span><span class="p">(</span><span class="n" style="color: #333;">symbolToIndex</span><span class="p">,</span> <span class="n" style="color: #333;">fastMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">,</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">rowSymbolProbs</span><span class="p">,</span> <span class="n" style="color: #333;">colSymbolProbs</span><span class="p">,</span> <span class="n" style="color: #333;">rSymbols</span><span class="p">,</span> <span class="n" style="color: #333;">cSymbols</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">cells</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="p">}</span></span>
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"><span class="p">}</span></span>
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="cpp"><span class="p">}</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// end namespace cbrc</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#1abcf9a223f6f347de8e1e1bd3495e4900285b34"><strong>src/ScoreMatrix.hh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,23 +15,33 @@</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">uchar</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">uchar</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">INF</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT_MAX</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span> <span class="p">};</span> <span class="c1" style="color: #998; font-style: italic;">// big, but try to avoid overflow</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">MAT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">64</span> <span class="p">};</span> <span class="c1" style="color: #998; font-style: italic;">// matrix size = MAT x MAT</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">OUTPAD</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span> <span class="p">};</span> <span class="c1" style="color: #998; font-style: italic;">// cell-padding for output</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">canonicalName</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">name</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">stringFromName</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">name</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">matchMismatch</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">letters</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setMatchMismatch</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">matchScore</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// usually > 0</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mismatchCost</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// usually > 0</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">symbols</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// case is preserved</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">fromString</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">init</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">encode</span><span class="p">[]</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// unspecified letters get minScore</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">init</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">[]);</span> <span class="c1" style="color: #998; font-style: italic;">// unspecified letters get minScore</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// add scores for e.g. "W" meaning A or T</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">addAmbiguousScores</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">symbolToIndex</span><span class="p">[],</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// "lambda" for getting probabilities</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rowSymbolProbs</span><span class="p">[],</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">colSymbolProbs</span><span class="p">[]);</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeCommented</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// write preceded by "#"</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">row<span class="idiff left">s</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span> <span class="c1" style="color: #998; font-style: italic;">// row headings (letters)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">col<span class="idiff left">s</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span> <span class="c1" style="color: #998; font-style: italic;">// column headings (letters)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">row<span class="idiff left">Symbols</span></span><span class="p"><span class="idiff right">;</span></span> <span class="c1" style="color: #998; font-style: italic;">// row headings (letters)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">col<span class="idiff left">Symbols</span></span><span class="p"><span class="idiff right">;</span></span> <span class="c1" style="color: #998; font-style: italic;">// column headings (letters)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cells</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// scores</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">caseSensitive</span><span class="p">[</span><span class="n" style="color: #333;">MAT</span><span class="p">][</span><span class="n" style="color: #333;">MAT</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">caseInsensitive</span><span class="p">[</span><span class="n" style="color: #333;">MAT</span><span class="p">][</span><span class="n" style="color: #333;">MAT</span><span class="p">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,5 +52,6 @@ struct ScoreMatrix{</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">>></span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mat</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;"><<</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mat</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// end namespace cbrc</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif // SCOREMATRIX_HH</span></span></pre>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<li id="bb715be022c826aae5cd901677082c4701d4254f">
<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#bb715be022c826aae5cd901677082c4701d4254f"><strong>src/SubsetSuffixArray.hh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,6 +32,8 @@ class SubsetSuffixArray{</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="k" style="font-weight: 600;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">LAST_INT_TYPE</span> <span class="n" style="color: #333;">indexT</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Range</span> <span class="p">{</span><span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span><span class="p">;};</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">getSeed</span><span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seed</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">getSeed</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seed</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,8 +46,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">step</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">minimizerWindow</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Sort the suffix array (but don't make the buckets).</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">sortIndex</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxUnsortedInterval</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">childTableType</span></span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">sortIndex</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span><span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxUnsortedInterval</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">childTableType</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">numOfThreads</span></span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Make the buckets. If bucketDepth+1 == 0, then a default</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bucketDepth is used. The default is: the maximum possible</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -121,17 +123,26 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">sort2</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">radixSort1</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">radixSort1</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rangeStack</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">radixSort2</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">radixSort2</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rangeStack</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">radixSort3</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">radixSort3</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rangeStack</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">radixSort4</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">radixSort4</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rangeStack</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">radixSortN</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">radixSortN</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rangeStack</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">subsetCount</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">subsetCount</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bucketSize</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">sortRanges</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333;">stacks</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bucketSizes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">maxUnsortedInterval</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfThreads</span> <span class="p">);</span></span>
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Same as the 1st equalRange, but uses more info and may be faster:</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">equalRange</span><span class="p">(</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#2a1679fed6b9ef7f99d78c180fd4a4c60fc9f422"><strong>src/SubsetSuffixArraySort.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,17 +7,24 @@</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm> // iter_swap, min</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#include <iostream> // for debugging</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAS_CXX_THREADS</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <thread></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">indexT</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Stack</span><span class="p">{</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span><span class="p">;</span> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"> <span class="n" style="color: #333;">Stack</span> <span class="n" style="color: #333;">stack</span><span class="p">[</span><span class="mi" style="color: #099;">1048576</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// big enough???</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"> <span class="n" style="color: #333;">Stack</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stack</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Range</span> <span class="n" style="color: #333;">Range</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PUSH(b, e, d) if( e-b > 1 ) sp->beg = b, sp->end = e, (sp++)->depth = d</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define POP(b, e, d) b = (--sp)->beg, e = sp->end, d = sp->depth</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">pushRange</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">v</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">Range</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">insertionSort</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seed</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span> <span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,7 +67,8 @@ void SubsetSuffixArray::sort2( const uchar* text, indexT* beg,</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Specialized sort for 1 symbol + 1 delimiter.</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// E.g. wildcard positions in spaced seeds.</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">radixSort1</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">radixSort1</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rangeStack</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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64
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// end of '0's</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">begN</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// beginning of delimiters</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,7 +86,7 @@ void SubsetSuffixArray::radixSort1( const uchar* text, const uchar* subsetMap,</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="p">}</span></span>
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="p">}</span></span>
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80
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">PUSH</span></span><span class="p"><span class="idiff right">(</span></span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '0's</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pushRange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeStack</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '0's</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isChildDirectionForward</span><span class="p">(</span> <span class="n" style="color: #333;">beg</span> <span class="p">)</span> <span class="p">){</span></span>
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84
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,7 +99,8 @@ void SubsetSuffixArray::radixSort1( const uchar* text, const uchar* subsetMap,</td>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Specialized sort for 2 symbols + 1 delimiter.</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// E.g. transition-constrained positions in subset seeds.</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">radixSort2</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">radixSort2</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rangeStack</span><span class="p">,</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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95
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span> <span class="p">){</span></span>
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96
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// end of '0's</span></span>
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97
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// end of '1's</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,8 +123,8 @@ void SubsetSuffixArray::radixSort2( const uchar* text, const uchar* subsetMap,</td>
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114
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="p">}</span></span>
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115
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="p">}</span></span>
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116
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">PUSH</span></span><span class="p"><span class="idiff right">(</span></span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '0's</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">PUSH</span></span><span class="p"><span class="idiff right">(</span></span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">end1</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '1's</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pushRange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeStack</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '0's</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pushRange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeStack</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">end1</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '1's</span></span>
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119
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"></span>
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120
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isChildDirectionForward</span><span class="p">(</span> <span class="n" style="color: #333;">beg</span> <span class="p">)</span> <span class="p">){</span></span>
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121
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -132,7 +141,8 @@ void SubsetSuffixArray::radixSort2( const uchar* text, const uchar* subsetMap,</td>
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132
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Specialized sort for 3 symbols + 1 delimiter.</span></span>
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134
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// E.g. subset seeds for bisulfite-converted DNA.</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">radixSort3</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">radixSort3</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rangeStack</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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136
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span> <span class="p">){</span></span>
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137
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// end of '0's</span></span>
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138
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// end of '1's</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -161,9 +171,9 @@ void SubsetSuffixArray::radixSort3( const uchar* text, const uchar* subsetMap,</td>
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161
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="p">}</span></span>
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162
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="p">}</span></span>
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163
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">PUSH</span></span><span class="p"><span class="idiff right">(</span></span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '0's</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">PUSH</span></span><span class="p"><span class="idiff right">(</span></span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">end1</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '1's</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">PUSH</span></span><span class="p"><span class="idiff right">(</span></span> <span class="n" style="color: #333;">beg2</span><span class="p">,</span> <span class="n" style="color: #333;">begN</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '2's</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pushRange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeStack</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '0's</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pushRange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeStack</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">end1</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '1's</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pushRange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeStack</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">beg2</span><span class="p">,</span> <span class="n" style="color: #333;">begN</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '2's</span></span>
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167
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"></span>
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168
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isChildDirectionForward</span><span class="p">(</span> <span class="n" style="color: #333;">beg</span> <span class="p">)</span> <span class="p">){</span></span>
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169
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -183,7 +193,8 @@ void SubsetSuffixArray::radixSort3( const uchar* text, const uchar* subsetMap,</td>
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183
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"><span class="p">}</span></span>
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184
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"></span>
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185
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Specialized sort for 4 symbols + 1 delimiter. E.g. DNA.</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">radixSort4</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">radixSort4</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rangeStack</span><span class="p">,</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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187
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span> <span class="p">){</span></span>
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188
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// end of '0's</span></span>
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189
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// end of '1's</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -218,10 +229,10 @@ void SubsetSuffixArray::radixSort4( const uchar* text, const uchar* subsetMap,</td>
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218
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"> <span class="p">}</span></span>
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219
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"> <span class="p">}</span></span>
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220
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">PUSH</span></span><span class="p"><span class="idiff right">(</span></span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '0's</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">PUSH</span></span><span class="p"><span class="idiff right">(</span></span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">end1</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '1's</span></span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">PUSH</span></span><span class="p"><span class="idiff right">(</span></span> <span class="n" style="color: #333;">end1</span><span class="p">,</span> <span class="n" style="color: #333;">end2</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '2's</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">PUSH</span></span><span class="p"><span class="idiff right">(</span></span> <span class="n" style="color: #333;">beg3</span><span class="p">,</span> <span class="n" style="color: #333;">begN</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '3's</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pushRange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeStack</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '0's</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pushRange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeStack</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">end1</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '1's</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pushRange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeStack</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">end1</span><span class="p">,</span> <span class="n" style="color: #333;">end2</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '2's</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pushRange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeStack</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">beg3</span><span class="p">,</span> <span class="n" style="color: #333;">begN</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// the '3's</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isChildDirectionForward</span><span class="p">(</span> <span class="n" style="color: #333;">beg</span> <span class="p">)</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -244,11 +255,13 @@ void SubsetSuffixArray::radixSort4( const uchar* text, const uchar* subsetMap,</td>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">radixSortN</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">numOfBuckets</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">256</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">radixSortN</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rangeStack</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">subsetCount</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">bucketSize</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// initialized to zero at startup</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* */</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bucketEnd</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// "static" makes little difference to speed</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">subsetCount</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bucketSize</span> <span class="p">){</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bucketEnd</span><span class="p">[</span><span class="n" style="color: #333;">numOfBuckets</span><span class="p">];</span></span>
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"></span>
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253
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// get bucket sizes (i.e. letter counts):</span></span>
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254
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// The intermediate oracle array makes it faster (see "Engineering</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -268,7 +281,7 @@ void SubsetSuffixArray::radixSortN( const uchar* text, const uchar* subsetMap,</td>
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268
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span></span>
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269
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">subsetCount</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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270
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nextPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bucketSize</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">PUSH</span></span><span class="p"><span class="idiff right">(</span></span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">nextPos</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pushRange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeStack</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">nextPos</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextPos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">bucketEnd</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -306,31 +319,91 @@ void SubsetSuffixArray::radixSortN( const uchar* text, const uchar* subsetMap,</td>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sortIndex</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">maxUnsortedInterval</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">childTableType</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">minLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">rangeSize</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Range</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">childTableType</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chibiTable</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">assign</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">suffixArray</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">childTableType</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kiddyTable</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">assign</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">suffixArray</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">childTableType</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">childTable</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">assign</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">suffixArray</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nextRangeSize</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">Range</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">ranges</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rangeSize</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ranges</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">back</span></span><span class="p"><span class="idiff right">()</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"><span class="p"><span class="idiff left right">}</span></span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">PUSH</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">suffixArray</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">suffixArray</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">setChildReverse</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">suffixArray</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">suffixArray</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">()</span> <span class="p">);</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">rangeSizeSum</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ranges</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ranges</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rangeSize</span><span class="p">(</span><span class="n" style="color: #333;">ranges</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfThreadsForOneRange</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfThreads</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">sizeOfThisRange</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">sizeOfAllRanges</span><span class="p">)</span> <span class="p">{</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We want:</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// min(t | sizeOfThisRange / t < sizeOfOtherRanges / (numOfThreads - (t+1)))</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Or equivalently:</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// max(t | sizeOfThisRange / (t-1) >= sizeOfOtherRanges / (numOfThreads - t))</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfThreads</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// use double to avoid overflow</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sizeOfThisRange</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sizeOfAllRanges</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sizeOfAllRanges</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="n" style="color: #333;">sp</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">stack</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span><span class="p">;</span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">POP</span><span class="p">(</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sortRanges</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stacks</span><span class="p">,</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bucketSizes</span><span class="p">,</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">text</span><span class="p">,</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">maxUnsortedInterval</span><span class="p">,</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfThreads</span><span class="p">)</span> <span class="p">{</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">myStack</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stacks</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">myStack</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">){</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAS_CXX_THREADS</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfChunks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">numOfThreads</span><span class="p">,</span> <span class="n" style="color: #333;">myStack</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numOfChunks</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">totalSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rangeSizeSum</span><span class="p">(</span><span class="n" style="color: #333;">myStack</span><span class="p">);</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfNewThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfChunks</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">threads</span><span class="p">(</span><span class="n" style="color: #333;">numOfNewThreads</span><span class="p">);</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfNewThreads</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextRangeSize</span><span class="p">(</span><span class="n" style="color: #333;">myStack</span><span class="p">);</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfThreadsForOneRange</span><span class="p">(</span><span class="n" style="color: #333;">numOfThreads</span><span class="p">,</span> <span class="n" style="color: #333;">thisSize</span><span class="p">,</span> <span class="n" style="color: #333;">totalSize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">maxThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfThreads</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">numOfNewThreads</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">maxThreads</span><span class="p">);</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="n" style="color: #333;">numOfThreads</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">thisThreads</span><span class="p">;</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">totalSize</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">nextRangeSize</span><span class="p">(</span><span class="n" style="color: #333;">myStack</span><span class="p">);</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <span class="n" style="color: #333;">stacks</span><span class="p">[</span><span class="n" style="color: #333;">numOfThreads</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">myStack</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">());</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;">myStack</span><span class="p">.</span><span class="n" style="color: #333;">pop_back</span><span class="p">();</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">thisSize</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">nextRangeSize</span><span class="p">(</span><span class="n" style="color: #333;">myStack</span><span class="p">);</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">myStack</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">numOfThreads</span> <span class="o" style="font-weight: 600;">&&</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">thisSize</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">totalSize</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">numOfThreads</span><span class="p">);</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We want:</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// max(r | sizeSum(r) <= (totalSize - sizeSum(r-1)) / newNumOfThreads)</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sortRanges</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="p">,</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="n" style="color: #333;">stacks</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numOfThreads</span><span class="p">,</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;">bucketSizes</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numOfThreads</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">numOfBuckets</span><span class="p">,</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">maxUnsortedInterval</span><span class="p">,</span> <span class="n" style="color: #333;">thisThreads</span><span class="p">);</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"> <span class="n" style="color: #333;">sortRanges</span><span class="p">(</span><span class="n" style="color: #333;">stacks</span><span class="p">,</span> <span class="n" style="color: #333;">bucketSizes</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">maxUnsortedInterval</span><span class="p">,</span> <span class="n" style="color: #333;">numOfThreads</span><span class="p">);</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfNewThreads</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="p">}</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="p">}</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myStack</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">beg</span><span class="p">;</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myStack</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myStack</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">depth</span><span class="p">;</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="n" style="color: #333;">myStack</span><span class="p">.</span><span class="n" style="color: #333;">pop_back</span><span class="p">();</span></span>
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326
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"></span>
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327
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">interval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">minLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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328
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">interval</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxUnsortedInterval</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minLength</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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329
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"></span>
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330
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">textBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">depth</span><span class="p">;</span></span>
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331
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subsetMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">subsetMap</span><span class="p">(</span><span class="n" style="color: #333;">depth</span><span class="p">);</span></span>
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332
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"></span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">childTable<span class="idiff left">Type</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span> <span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">childTable</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kiddyTable</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chibiTable</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff right">()</span></span> <span class="p">){</span></span>
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334
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">interval</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">10</span> <span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">// ???</span></span>
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335
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">insertionSort</span><span class="p">(</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">subsetMap</span> <span class="p">);</span></span>
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336
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -347,11 +420,30 @@ void SubsetSuffixArray::sortIndex( const uchar* text,</td>
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347
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">depth</span><span class="p">;</span></span>
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348
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp"></span>
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349
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span> <span class="n" style="color: #333;">subsetCount</span> <span class="p">){</span></span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span> <span class="n" style="color: #333;">radixSort1</span><span class="p">(</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
351
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="n" style="color: #333;">radixSort2</span><span class="p">(</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span> <span class="n" style="color: #333;">radixSort3</span><span class="p">(</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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353
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span> <span class="n" style="color: #333;">radixSort4</span><span class="p">(</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span> <span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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354
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">radixSortN</span><span class="p">(</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="n" style="color: #333;">subsetCount</span> <span class="p">);</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span> <span class="n" style="color: #333;">radixSort1</span><span class="p">(</span><span class="n" style="color: #333;">myStack</span><span class="p">,</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="n" style="color: #333;">radixSort2</span><span class="p">(</span><span class="n" style="color: #333;">myStack</span><span class="p">,</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span> <span class="n" style="color: #333;">radixSort3</span><span class="p">(</span><span class="n" style="color: #333;">myStack</span><span class="p">,</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span> <span class="n" style="color: #333;">radixSort4</span><span class="p">(</span><span class="n" style="color: #333;">myStack</span><span class="p">,</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">radixSortN</span><span class="p">(</span><span class="n" style="color: #333;">myStack</span><span class="p">,</span> <span class="n" style="color: #333;">textBase</span><span class="p">,</span> <span class="n" style="color: #333;">subsetMap</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">subsetCount</span><span class="p">,</span> <span class="n" style="color: #333;">bucketSizes</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubsetSuffixArray</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sortIndex</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">text</span><span class="p">,</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">maxUnsortedInterval</span><span class="p">,</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">childTableType</span><span class="p">,</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfThreads</span> <span class="p">){</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">childTableType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="n" style="color: #333;">chibiTable</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">suffixArray</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">childTableType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">)</span> <span class="n" style="color: #333;">kiddyTable</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">suffixArray</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">childTableType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span> <span class="p">)</span> <span class="n" style="color: #333;">childTable</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">suffixArray</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Range</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">stacks</span><span class="p">(</span><span class="n" style="color: #333;">numOfThreads</span><span class="p">);</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">indexT</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bucketSizes</span><span class="p">(</span><span class="n" style="color: #333;">numOfThreads</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">numOfBuckets</span><span class="p">);</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"> <span class="n" style="color: #333;">pushRange</span><span class="p">(</span> <span class="n" style="color: #333;">stacks</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">suffixArray</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">suffixArray</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"> <span class="n" style="color: #333;">setChildReverse</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">suffixArray</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">suffixArray</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">()</span> <span class="p">);</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="n" style="color: #333;">sortRanges</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stacks</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bucketSizes</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">maxUnsortedInterval</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="n" style="color: #333;">numOfThreads</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#7b0830ebdd6062603b37b87c1a3b81a77a1b9578"><strong>src/TantanMasker.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +37,7 @@ T -5 -5 -5 2\n\</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">fromString</span><span class="p">(</span><span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringFromName</span><span class="p">(</span><span class="s" style="color: #d14;">"BL62"</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">alphabetSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alphabet</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">m</span>atchMismatch</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">setM</span>atchMismatch</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">letterToIndex</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#606e6941b339f000d86394f6a0e1d0b6790c48b6"><strong>src/alp/sls_alignment_evaluer.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -463,8 +463,12 @@ double temperature_)</td>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">GaplessPreliminaryTime</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CurrentTimeGaplessPreliminary</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">CurrentTime1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//the choice for the importance sampling</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapOpen</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">alp_data</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Tmin</span><span class="p">(</span><span class="n" style="color: #333;">gapOpen1_</span><span class="p">,</span><span class="n" style="color: #333;">gapOpen2_</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapEpen</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">alp_data</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Tmin</span><span class="p">(</span><span class="n" style="color: #333;">gapEpen1_</span><span class="p">,</span><span class="n" style="color: #333;">gapEpen2_</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//long int gapOpen=alp_data::Tmin(gapOpen1_,gapOpen2_);</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//long int gapEpen=alp_data::Tmin(gapEpen1_,gapEpen2_);</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapEpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alp_data</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Tmin</span><span class="p">(</span><span class="n" style="color: #333;">gapEpen1_</span><span class="p">,</span> <span class="n" style="color: #333;">gapEpen2_</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alp_data</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Tmin</span><span class="p">(</span><span class="n" style="color: #333;">gapOpen1_</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gapEpen1_</span><span class="p">,</span> <span class="n" style="color: #333;">gapOpen2_</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gapEpen2_</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">gapEpen</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">max_time_</span><span class="o" style="font-weight: 600;"><=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp"> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a"><strong>src/lastal.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -96,6 +96,43 @@ void complementMatrix(const ScoreMatrixRow *from, ScoreMatrixRow *to) {</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">to</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">[</span><span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">complement</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]][</span><span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">complement</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]];</span></span>
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Meaningless for PSSMs, unless they have the same scale as the score matrix</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">calculateSubstitutionScoreMatrixStatistics</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"calculating matrix probabilities..."</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// the case-sensitivity of the matrix makes no difference here</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">calculate</span><span class="p">(</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">caseSensitive</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">isBad</span><span class="p">()</span> <span class="p">){</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isQuality</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">temperature</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"can't calculate probabilities: "</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="s" style="color: #d14;">"maybe the mismatch costs are too weak"</span> <span class="p">);</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"can't calculate probabilities: "</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="s" style="color: #d14;">"maybe the mismatch costs are too weak"</span> <span class="p">);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="p">}</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs1</span><span class="p">();</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs2</span><span class="p">();</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"matrix lambda="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">()</span> <span class="p">);</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"matrix letter frequencies (upper=reference, lower=query):"</span> <span class="p">);</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbosity</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="p">){</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span><span class="p">;</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">streamsize</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">.</span><span class="n" style="color: #333;">precision</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">.</span><span class="n" style="color: #333;">precision</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">right</span><span class="p">;</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Set up a scoring matrix, based on the user options</span></span>
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">makeScoreMatrix</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">matrixName</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">matrixFile</span> <span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,11 +140,20 @@ void makeScoreMatrix( const std::string& matrixName,</td>
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103
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">fromString</span><span class="p">(</span> <span class="n" style="color: #333;">matrixFile</span> <span class="p">);</span></span>
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="p">}</span></span>
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105
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">m</span>atchMismatch</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</span><span class="p">,</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">setM</span>atchMismatch</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span> <span class="p">);</span></span>
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108
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span> <span class="p">);</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">);</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">calculateSubstitutionScoreMatrixStatistics</span><span class="p">();</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">dna</span><span class="p">)</span> <span class="p">{</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">addAmbiguousScores</span><span class="p">(</span><span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">,</span> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">(),</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs1</span><span class="p">(),</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs2</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If the input is a PSSM, the score matrix is not used, and its</span></span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// maximum score should not be used. Here, we try to set it to a</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -231,43 +277,8 @@ void makeQualityScorers(){</td>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Calculate statistical parameters for the alignment scoring scheme</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Meaningless for PSSMs, unless they have the same scale as the score matrix</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">calculateScoreStatistics</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">matrixName</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp"> <span class="n" style="color: #333;">countT</span> <span class="n" style="color: #333;">refLetters</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"calculating matrix probabilities..."</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// the case-sensitivity of the matrix makes no difference here</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="cpp"> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">calculate</span><span class="p">(</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">caseSensitive</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">isBad</span><span class="p">()</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isQuality</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">temperature</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"can't calculate probabilities: "</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"> <span class="s" style="color: #d14;">"maybe the mismatch costs are too weak"</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"can't calculate probabilities: "</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp"> <span class="s" style="color: #d14;">"maybe the mismatch costs are too weak"</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs1</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs2</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"matrix lambda="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">()</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"matrix letter frequencies (upper=reference, lower=query):"</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbosity</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">streamsize</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">.</span><span class="n" style="color: #333;">precision</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">.</span><span class="n" style="color: #333;">precision</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">right</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">calculateScoreStatistics</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">matrixName</span><span class="p">,</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">countT</span> <span class="n" style="color: #333;">refLetters</span><span class="p">)</span> <span class="p">{</span></span>
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271
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">canonicalMatrixName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">canonicalName</span><span class="p">(</span> <span class="n" style="color: #333;">matrixName</span> <span class="p">);</span></span>
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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273
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isStandardGeneticCode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">geneticCodeFile</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -275,7 +286,8 @@ void calculateScoreStatistics( const std::string& matrixName,</td>
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275
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span><span class="p">{</span></span>
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276
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span> <span class="n" style="color: #333;">canonicalMatrixName</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</span><span class="p">,</span></span>
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277
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">caseSensitive</span><span class="p">,</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">,</span> <span class="n" style="color: #333;">isGapped</span><span class="p">,</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs1</span><span class="p">(),</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">lambdaCalculator</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs2</span><span class="p">(),</span> <span class="n" style="color: #333;">isGapped</span><span class="p">,</span></span>
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279
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delExist</span><span class="p">,</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delExtend</span><span class="p">,</span></span>
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280
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insExist</span><span class="p">,</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insExtend</span><span class="p">,</span></span>
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281
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">frameshiftCost</span><span class="p">,</span> <span class="n" style="color: #333;">geneticCode</span><span class="p">,</span> <span class="n" style="color: #333;">isStandardGeneticCode</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#de4252990d12a909e50ff0b994d1715eae0ea5fd"><strong>src/lastdb.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -215,7 +215,8 @@ void makeVolume( std::vector< CyclicSubsetSeed >& seeds,</td>
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"sorting..."</span> <span class="p">);</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">myIndex</span><span class="p">.</span><span class="n" style="color: #333;">sortIndex</span><span class="p">(</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">minSeedLimit</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">childTableType</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">myIndex</span><span class="p">.</span><span class="n" style="color: #333;">sortIndex</span><span class="p">(</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">minSeedLimit</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">childTableType</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">numOfThreads</span> <span class="p">);</span></span>
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219
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"></span>
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220
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span> <span class="s" style="color: #d14;">"bucketing..."</span> <span class="p">);</span></span>
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221
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">myIndex</span><span class="p">.</span><span class="n" style="color: #333;">makeBuckets</span><span class="p">(</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bucketDepth</span> <span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2"><strong>src/makefile</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -184,8 +184,8 @@ OneQualityScoreMatrix.o OneQualityScoreMatrix.o8: OneQualityScoreMatrix.cc \</td>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> stringify.hh</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="make"><span class="nl">QualityPssmMaker.o QualityPssmMaker.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">QualityPssmMaker.cc QualityPssmMaker.hh </span>\</span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> ScoreMatrixRow.hh qualityScoreUtil.hh stringify.hh</span></span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="make"><span class="nl">ScoreMatrix.o ScoreMatrix.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">ScoreMatrix.cc ScoreMatrix.hh ScoreMatrixData.hh <span class="idiff left right">zio.hh </span></span>\</span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_zstream.hh</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="make"><span class="nl">ScoreMatrix.o ScoreMatrix.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">ScoreMatrix.cc ScoreMatrix.hh ScoreMatrixData.hh </span>\</span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> <span class="idiff left right">qualityScoreUtil.hh stringify.hh zio.hh </span>mcf_zstream.hh</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="make"><span class="nl">SegmentPair.o SegmentPair.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">SegmentPair.cc SegmentPair.hh</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="make"><span class="nl">SegmentPairPot.o SegmentPairPot.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">SegmentPairPot.cc SegmentPairPot.hh SegmentPair.hh</span></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="make"><span class="nl">SubsetMinimizerFinder.o SubsetMinimizerFinder.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">SubsetMinimizerFinder.cc </span>\</span>
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<a href="https://salsa.debian.org/med-team/last-align/compare/b77d677b0334a9c1d55946ec391106c21f9e246b...041dbcfce9f072a318f56c6f30d1b682d512abb5#8db93325f61aa7d617ad4cbce8b11461c573f871"><strong>src/qualityScoreUtil.hh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,6 +18,14 @@ inline int nearestInt(double x) {</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">probFromScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">lambda</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">scoreFromProb</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">prob</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nearestInt</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">prob</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">lambda</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">phredErrorProb</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qualityScore</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qualityScore</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">qualityScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">0.1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qualityScore</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,7 +59,7 @@ inline double qualityCertainty(double errorProb, double letterProb) {</td>
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51
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">qualityPairScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">expScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">certainty1</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">certainty2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">certainty1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">certainty2</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">expScore</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">nearestInt</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">log</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">lambda</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">scoreFromProb</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lambda</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">x</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">checkQualityCodes</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qualityBeg</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"9<span class="idiff left right">21</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"9<span class="idiff left right">32</span>"</span></span></pre>
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