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<h3>
Steffen Möller pushed to branch upstream
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/60c6d42fe266f0fa717ddee8358bfbb1b71731c1">60c6d42f</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-12-20T23:28:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1044</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="#0a6f228c5aa04e4e51759df327427fcf703fa8ae">
examples/multiMito.maf
</a>
</li>
<li class="file-stats">
<a href="#0c0610d12d971107a85160c6a927e94a1062a01a">
makefile
</a>
</li>
<li class="file-stats">
<a href="#5e55dbeefff2057b414960d9467d183920e31b8a">
src/Alignment.cc
</a>
</li>
<li class="file-stats">
<a href="#bd17e03c676d289c9cc5bb117da6d9d2bde74764">
src/Alignment.hh
</a>
</li>
<li class="file-stats">
<a href="#8f014a93cf121af8fe88d03244d4d4b173d32a6d">
src/GappedXdropAligner.cc
</a>
</li>
<li class="file-stats">
<a href="#7dc5c3172a020d4f7642b87bcfe987675bd222a7">
src/GappedXdropAligner.hh
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</li>
<li class="file-stats">
<a href="#30d72e7e81ec011dcda59c2395cb78f718d054e4">
src/GappedXdropAligner2qual.cc
</a>
</li>
<li class="file-stats">
<a href="#e75886b250f69fee392d9c70ddf2853930e49922">
src/GappedXdropAligner3frame.cc
</a>
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<li class="file-stats">
<a href="#6821496f966af651583944bcdf3b822e5123d4a1">
src/GappedXdropAligner3framePssm.cc
</a>
</li>
<li class="file-stats">
<a href="#fe292bc81098de48178ce05c67f141fe55186348">
<span class="new-file">
+
src/GappedXdropAlignerDna.cc
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<li class="file-stats">
<a href="#0dc2fc6ce4e90db3e92c8d5394d9fff8563e7f2a">
src/GappedXdropAlignerInl.hh
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<li class="file-stats">
<a href="#35f9fe39feef01a50cdd57a941b460c37cbaffba">
src/GappedXdropAlignerPssm.cc
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<li class="file-stats">
<a href="#dfce2568fc6cc43ff1901906cedd463b1de40be4">
src/ScoreMatrixRow.hh
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<li class="file-stats">
<a href="#729036dee8937546a072eb76b6399452aa5a4d9f">
src/alp/njn_matrix.hpp
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<li class="file-stats">
<a href="#4c715de0a3b171ab50630e7b084fcb00cf21922d">
src/alp/njn_random.cpp
</a>
</li>
<li class="file-stats">
<a href="#6b6442cb28cf1bf48dae1f18dbaed740b8b5e86e">
src/alp/njn_vector.hpp
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<li class="file-stats">
<a href="#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">
src/lastal.cc
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<li class="file-stats">
<a href="#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">
src/makefile
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<li class="file-stats">
<a href="#41d595f670dd7b4262c1bb10368de0bd8264c46a">
src/mcf_contiguous_queue.hh
</a>
</li>
<li class="file-stats">
<a href="#8266f3ec3e8e19e5efa1a2f239f8ba579e89eb00">
src/mcf_gap_costs.cc
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</li>
<li class="file-stats">
<a href="#f4c2aa5ffe5ddbfe5093d67a91ae22b61c035703">
src/mcf_gap_costs.hh
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</li>
<li class="file-stats">
<a href="#8f7fbcfe09309590155e6ce5e2cf7a91f2e85743">
<span class="new-file">
+
src/mcf_reverse_queue.hh
</span>
</a>
</li>
<li class="file-stats">
<a href="#649c21f7a438af6deba63905bb1e34fc0783b83b">
src/mcf_simd.hh
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<li class="file-stats">
<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">
src/version.hh
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</li>
</ul>
<h4>Changes:</h4>
<li id="57bf262130f956caf76c405086f0815caf4e0a89">
<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2019-12-20 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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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"> * src/GappedXdropAligner.hh, src/GappedXdropAlignerDna.cc,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> src/mcf_simd.hh, test/last-test.out, test/last-test.sh:</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"> Maybe make lastal gapped alignment a bit faster</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [11810fcff80c] [tip]</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">2019-12-19 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAligner.hh,</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> src/GappedXdropAlignerDna.cc, src/makefile,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> src/mcf_reverse_queue.hh, src/mcf_simd.hh:</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> Maybe make lastal gapped alignment a bit faster</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> [2be7c5f313a5]</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">2019-12-16 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> * src/Alignment.cc, src/GappedXdropAligner.hh,</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> src/GappedXdropAlignerDna.cc, src/mcf_simd.hh:</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Make lastal DNA gapped alignment faster</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> [daa684e4956e]</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> * src/Alignment.cc, src/GappedXdropAligner.hh,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> src/GappedXdropAlignerDna.cc, src/ScoreMatrixRow.hh,</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> src/mcf_simd.hh:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> Make lastal DNA gapped alignment faster</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> [7fdb95aea8e3]</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"> * src/Alignment.cc, src/Alignment.hh, src/GappedXdropAlignerDna.cc,</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> src/lastal.cc, src/mcf_simd.hh:</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> [b1fc3a37fe34]</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">2019-12-12 Martin C. Frith <Martin C. Frith></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"> * src/Alignment.cc, src/GappedXdropAligner.cc,</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> src/GappedXdropAligner.hh, src/GappedXdropAlignerDna.cc,</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> src/GappedXdropAlignerPssm.cc, src/makefile, src/mcf_simd.hh, test</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> /last-test.out, test/last-test.sh:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> Make lastal DNA gapped alignment faster</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> [a02f4aab6116]</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAlignerPssm.cc,</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> src/mcf_simd.hh:</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> [d21b748f5540]</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAligner.hh,</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> src/GappedXdropAlignerPssm.cc:</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> [84db4d2edb22]</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAligner2qual.cc,</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> src/GappedXdropAlignerInl.hh, src/GappedXdropAlignerPssm.cc:</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> [759bd401fd1b]</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">2019-12-11 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAligner2qual.cc,</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> src/GappedXdropAlignerPssm.cc, test/last-train-test.out:</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> Change lastal probabilities slightly</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> [1cd65b7f8fdb]</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> * src/GappedXdropAligner2qual.cc:</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> [f888698950e8]</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAligner2qual.cc,</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> src/GappedXdropAligner3frame.cc,</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> src/GappedXdropAligner3framePssm.cc, src/GappedXdropAlignerInl.hh,</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> src/GappedXdropAlignerPssm.cc:</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> Refactor & robustify the code</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> [6ee595437d4c]</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> * src/Alignment.cc, src/GappedXdropAligner.cc,</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> src/GappedXdropAligner.hh, src/GappedXdropAligner2qual.cc,</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> src/GappedXdropAlignerInl.hh, src/GappedXdropAlignerPssm.cc,</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> src/mcf_gap_costs.cc, src/mcf_gap_costs.hh:</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> Refactor</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> [14a1fdd74624]</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">2019-12-10 Martin C. Frith <Martin C. Frith></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAlignerPssm.cc,</span>
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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> src/alp/njn_matrix.hpp, src/alp/njn_random.cpp,</span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> src/alp/njn_vector.hpp, src/makefile, src/mcf_simd.hh:</span>
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<td class="diff-line-num new new_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> Robustify compilation</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> [5b00a436e53c]</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">2019-12-09 Martin C. Frith <Martin C. Frith></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAligner.hh,</span>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> src/GappedXdropAlignerPssm.cc, src/mcf_simd.hh:</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> Refactor</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> [e0434cbfa780]</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAligner.hh,</span>
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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> src/GappedXdropAligner2qual.cc, src/GappedXdropAligner3frame.cc,</span>
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<td class="diff-line-num new new_line" data-linenumber="100" 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">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> src/GappedXdropAligner3framePssm.cc, src/GappedXdropAlignerPssm.cc:</span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> Refactor</span>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> [29b88752b6d6]</span>
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<td class="diff-line-num new new_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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> * makefile, src/makefile:</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="plaintext"> Fix compile error (thanks: V Brendel & D Eccles)</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> [cf7b477fbeaf]</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"></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="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAlignerPssm.cc,</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="plaintext"> src/mcf_contiguous_queue.hh:</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> Refactor</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> [4b2847c49990]</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"></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="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAlignerPssm.cc:</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="plaintext"> Refactor</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> [8410315ff484]</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"></span>
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<td class="diff-line-num new old_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="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAligner2qual.cc,</span>
</pre>
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<td class="diff-line-num new old_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="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> src/GappedXdropAlignerPssm.cc:</span>
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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> Refactor</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> [c614e7fba41c]</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAligner2qual.cc,</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> src/GappedXdropAlignerPssm.cc:</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> [ede8e6df999a]</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> * src/GappedXdropAligner.cc, src/GappedXdropAlignerPssm.cc,</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> src/mcf_contiguous_queue.hh:</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> [aa391569f221]</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"> * examples/multiMito.maf, src/GappedXdropAligner.cc,</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> src/GappedXdropAligner2qual.cc, src/GappedXdropAlignerInl.hh,</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> src/GappedXdropAlignerPssm.cc, test/last-test.out, test/last-train-</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> test.out, test/maf-swap-test.out:</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> Change lastal probabilities slightly</span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> [c24e24e0c606]</span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"></span>
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1
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext">2019-11-28 Martin C. Frith <Martin C. Frith></span>
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2
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext"> * doc/last-train.txt, scripts/last-train, test/last-train-test.out:</span>
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4
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext"> train: double scale if integer-rounding is bad</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> [887c0e6339d1]<span class="idiff left right"> [tip]</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> [887c0e6339d1]</span>
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6
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="plaintext"></span>
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7
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="plaintext">2019-11-27 Martin C. Frith <Martin C. Frith></span>
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8
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#0a6f228c5aa04e4e51759df327427fcf703fa8ae"><strong>examples/multiMito.maf</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">@@ -3,7 +3,7 @@ s humanMito 598 349 + 16571 CAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCAC-CCCATAA</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">s mouseMito 18 346 + 16299 CAAAGCAAAGCACTGAAAATGCTTAGATGGA-TAATTGTAT-CCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACAT-TTACTTAAAATTTAAGGAGAGGGT-ATCAAGCACATTAAAAT--AGCTTAAGACACCTTGCCTA-GCCACACCCCCACGGGACT-CAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCT--CTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTA-TCTTCGGCGTAAAACGTG</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">s chickenMito 1246 353 + 16775 CAAAGCATGGCACTGAAGATGCCAAGATGGTACCTACTATA-CCTGTGGGCAAA-AGACTTAGTCCTAACCTTTCTATTGGTTTTTGCTAGACATATACATGCAAGTATCCGCATCCCAGTGAAAATGCCCCCAAACCTTTCTTCCCAAGCAAAAGGAGCAGGT-ATCAGGCACACTCAGCAGTAGCCCAAGACGCCTTGCTTAAGCCACACCCCCACGGGTACTCAGCAGTAATTAACCTTAAGCAATAAGTGTAAACTTGACTTAGCCATAGCAACCC-AGGGTTGGTAAATCTTGTGCCAGCCACCGCGGTCATACAAGAAACCCAAATCAATAGCTACCCGGCGTAAAGAGTG</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">s fuguMito 16 350 + 16447 CAAAGCAGAGTACTGAAGATGCTAAGATGGGCCCTGAAAAGTCCCGCAGGCACAAAAGCTTGGTCCTGACTTTACTAACAACTCTGATCAAACTTACACATGCAAGTATCCGCATCCCAGTGAAaatgccccccgcc---ccccgtcCGGAAATAGGGAGTTGGTATCAGGCACACAAATTTGTAGCCCATGACACCTAGCTTT-GCCACGCCCCCAAGGGAATTCAGCAGTGATAAACATTAAGCCATAAGTGAAAACTTGACTTAGTTATGAT--CTAAAGAGTCGGTAAAACTCGTGCCAGCCACCGCGGTTATACGAGAGACCCAAGTTGTTAG-CCAACGGCGTAAAGGGTG</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">p '<span class="idiff left right">.37<?ABBCGLPTWXYYYXU</span>MKIC:1'%#"!+-.///045~68;DMRTV\]ZZZ`fghghjjljig_a_^XVSSSUYZYUSSRRQRU]a`_chilmmmmmke\TKJHHFECBBAAA>8542---,,,,,,,*)($"$"~*+-........./12222222357~9:::96/,%##""""""""/9BIKSVVWXWWVWW`fhlm~mkjllkgeeegllhffb^_~ejmmmmmlg_\\\[[\\[_gljjlihillihikgfeaejf^UKB?=<7/%#$"*,/8AHJSX_be`bdgghlmmmkkmmkkljjlljkmlicilmmjifd^[ZTRPOOOOOMM~MNOPT\^fhaXROIGE@></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">p '<span class="idiff left right">,159<>>?@DIMQTUVVVVT</span>MKIC:1'%#"!+-.///045~68;DMRTV\]ZZZ`fghghjjljig_a_^XVSSSUYZYUSSRRQRU]a`_chilmmmmmke\TKJHHFECBBAAA>8542---,,,,,,,*)($"$"~*+-........./12222222357~9:::96/,%##""""""""/9BIKSVVWXWWVWW`fhlm~mkjllkgeeegllhffb^_~ejmmmmmlg_\\\[[\\[_gljjlihillihikgfeaejf^UKB?=<7/%#$"*,/8AHJSX_be`bdgghlmmmkkmmkkljjlljkmlicilmmjifd^[ZTRPOOOOOMM~MNOPT\^fhaXROIGE@></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">p %*/37:;<<=BFIKLLMMMMMMMMMMMLLLKKKKKKKLLNO~TX]bgkosuvwyz~~~~~~~~~~~~~~~{wrmmlllkjggfffffffffeeedb^ZVQLHC>944210.*))))))))))(((((((((((((((((~((((((((((((((((((((((((~)))))))))))))))))))-1355899;<<>>@AFJOTY~]bglquz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}yuqlggeb^YTTSSTTUZ_chmquxz{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{wrmhd_ZUQLKKKJJHH~HHHHHHHHGGFDA=<<;:</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">p (())))))))))))))))))))))))))(((((((''''''~'''''''''&%$#)+,-.015<BEIKLQVZ^afgbZWPPMMLLKJJJJHHHJQWYafilmmjjichhc`^_^^]_`_VQH>;:8887776632,$++#,01246<>DFNQUWWVUTTZZZ[]~ef_ULIB?>=<;;;;;;>>GPUUVRPIIG@744432,*##-47@INKHGFEA8/,+%$""/9BLU]b`cghiihgc`_biljjib_[ZZUUTTTUVXZ__]_^VMJC:0-,+%#""/579@CJLSUZ\]Z[[~~~~~~~~~~~~~~~~~~~`a`\\[Z^`ba`\YWWRJG@7.##()+-47=???><940+'</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">p ''(((((((((((((((((((((((((((((((((((((((~((((((((((((()**+.016:?CFHIMRW[`cefgggggggghhhhhhhhilnosx|~~~~~~zywtplkiiggfda]YTONNNNNNNNNMMMMLLLMMMNOOPQRSX]adfghhhjklmm~oppqppppomlkkjjkkmmqsttvwwwwwvtqqoonlkjglqvz~~~~~~~|xsniedbafkotx{}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{wvvutqninsw|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{vutppnnnmljgc^ZYWTPKGB============<:73/*%</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" 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">@@ -115,7 +115,7 @@ p cb`^aghlmid_abdigf`ZYY`cee_ab`djiiibed`b`]\__cb`</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext">p ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{zxutttuuuvwwyzzzyyyz{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{{yyy{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zxwwwvvvuusponkjjjhhhgggggghhiiiiikkkllmqtuvy{|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}||}~~~~~~~~~~~~|{|{|||~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}}~~}}|{zyyy{|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|{|{{}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~||zxwwwyz~~~~~~~~~}ytssssuvvwwwvvww~wwx{|}~~~~~~~~~~{vrqol~~~h~~~geeeeddddeeeeeeeeffffffffffgggijjlllmmmmnqtuuuuuvvvy{|~~~~~~~~~~~~~~~~~~}|{zxwwx{|}}}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}}~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~zvqlkjfbbaaaaaaabbccccccccccdddddddeeefijkmnoopstux{||}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{vrmhgeb^]\[ZZZ]_`~~~dhklmmnsx}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|yup~~~kgb]\ZZZ\]^^~~~~~^^^^^^^]\ZZZZZZZZZZZZZZZZZ[[[[[[[[[[\\_abbcccccdddfglquz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|yxwvvvvvvw{}~~~~~}{zyvutqmiddbaaaaaaaaaaaaaccefghiijnprsstx|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|{{||~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">p SRNNOOQTTPNMLKJJKKKKQRVWYZaehjjljjiceeaejhfbYXWUU]`^_^``^ca_acggebhhghjjmmmlibejgffdadaded_a^_^][\XXWVVYbhd\SSSSSTTTSRRQQRRTV]ZXQNMLKF>;:99999999::::;;ABELPPPQRSRQQPPRTXYY[adhifc`\]][\[XYYY]`^a\VTSQQRTW_a_`_ca_billged`]^^ailkkmmkebhiig``deb`cjlhffbZZY[cjmmmkklihebhg`bcc`b`ghcihceeaekjjmmkebhgab]Z[YXYWSSSSTTUXXXWTPOOLJE<:94+++*****))&$$$$$$#####$$$$$%%%%%%%%&&&'*./1233336?IQVW[``gkjkmmkdb`dadgciicgc_`~~~~~~~~~~~~~~~~`ab`ZXX[\[^`^_fijlkjmmlib_`_cb_b`]^^]_\\`fhjd`a_chijhgchjhd\\bdjhbdfcgjjg_XVUTTTUW`deglmjd[XUTTRRRRUUUVVTTUXZ_gjeadgbejge``ghijebfhiiib^^bhgcfc_`_^`fd\YXWW_ec_a]]_`_cfadfab_`_gjjjhfbYYWPNLKJHHHHKSYZZ[`_\WTTVY`ciebgeaggcggchg`ZXY_gklihillic`a_dda^`bghljiihgc_abb`cjllhfa^]\[]_dedailmmmjca_bijjlhgb[\\\dhijebilkg`\]ZZZ[[^`ggfa[\dhijdb_bdkmmmlhgb_[[[bdkljc`cjjjmmkecbb^_][[[Z[adgbYYXVVVVY__giifedefijlkdb[[cbZWVVWW]eecc^_`abdahijjd\\\[aeaeigfebggd^]ZZ[ZZ\]_a_edahkmjjje]VVVVX[[bcagdaekmmmjihcfcZZ]\``dd^[XVWZ^cfhb_^]__][Z[__^`a`gkkg`XUUWY^^ejhga]]__bc[[[YY_ehica`^_\XWW[^fkljjh`ZYYahjhbXOLJJJIHHHHHJLSV\\\[\\Z[]]ejhbegcjlmmmkklia^__]^]\]]]ehchebhkjecafgjjmmkkmkebfgchgaccagiihgcihaYWUUUUVZZ\]YY\\`e`]]]\][[[VVUUTVUUU\^^]ahjdb`daYPPOPPPRXY\dhdb`ddaba`gijkebgebhijmmmmmmkebgf_``_gkkic^^`^^`_djlkg``_]_a`b`]]__beijgbeeaekmmmkecahkih~~ciljeb`dkmkhc[WV~~VZZ]_]YXXZY[[WUOLEA9211100000//////-,!!"#$&&((/1566~6655320,"$$"~~~$$$%%%%%%%%%%%%%%%%%%%&&&&')+2566788888:CJMNONNOPQRRQQQQXZ\^glljcZZY[[YVTNNNNMMNPVZZZ]`\ZYXWRRRSUUWXZ`hlkebillhfaba`gica^ZZ]\YXXXZ[bdddb[[cdcc`bdjic_bc]\]`fhkigc`cjmmmjc]]WRQQRVZYWXX]`fdbahhbekmlhggebhhggg`a`^ZZZ^^_aa`eglmmlh_\ZZVUSRQPQQSQQRQPOOPQRRUUUTTUXYXUUVUUSQOKKKIHHHJKNUXWXYZ_``^XXXWWYYZ^ehd\[\`efbfb_a\SPPPVXWWXY]``fgfc]TQJA>=74~~~.+)#&&#()+--.7>AABJMNNNPPPVWTTV^`_defkkf^VSQNLKIC@=8/"#$"#%()~~~*+-.~~~~~../012458~?BCCCCCCCCCBBBA;:5421110000001:CJLLMNMMMMNKJJJKNR\dggebgd[[`^`^_dadg`aimmmkkmmjgaa[YY^`bjmmmmmmkklhc[UUWY\ehilmmmlha[[_[\[ZVMGEDCCBBCDDDFFFGIIJJKLLLNNOOPQQPQQQQPPPPQPPQPPQSX]cdbghfaXSRRSXafklkg_`^\YY]]ccailmligd]URPPPQSUX_ailkec`deea[RI?>=9777777789;>??ADLQROOQY^a`fdbikkhcghjjlihhiheaffaehimmlia^]YY^]`ca_a^`bcddb^[XWQI@?<;:5321000000111</span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext">p iiiiiiiiiiihhhhhhhhhijkkmnsx|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}yupkjihgea`_^][WWUUSQQQPOMIEDDDCCCCCCCCCCCCCCCCBBBAAA@@@@@@???????@@@@CDEGGHHHJKKKKKLMMOOPQUZ_cgikknoprstvvwxxxxxxxwvvvwz|}}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|yuusrqonmkjifeda]YTPKFEC@@>;;9664211111111000/.....--,,,,+++++++*****************************+./036779:?CGJLLOQRW\`ejnqsttvvyzz}~~~~~~~~~~~~~~~~~~~~~~~~~~~}}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{wrqqppppqqqrrrrrtuy}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|wsrpmllkkkkkkklmmmmnnnnnnotx|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|{zyyyy{{~~~~~~~~~~~~~~}||{|}}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|{{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~yxxyyxxyyz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}}~}~~}}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|}||~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|yu~~pomjfb]\ZWSOJEA@~~?????>=<<<<<<<;962-)$##############################~############~~~#######################################$(+-.///114566778<AEILMMNNNNNNNNNNNNNNNNNOSVXY]`bccccccddffiklquy|~~~~~~~~~~~~~~~}yxxwuuuvwx}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}yyyz}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|wsnihffeb_^^^^^^^^^]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]^^^^^^_______________________________^]]]]]]]\\]]\\\\\[ZZYVSOJJ~~~HEA<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;:9888752.)$$$$$$$$~~~$$$$~~~~~$$$$$$$$$~$$$$$$$$$$$$$$$$$$$$$$$$$$$$%%&'''''''''''''''()-13555666666677788:;;<AEJOTX\`bcceffglpuz~~~~~~~~~~~~~~~~~~~~~yupkgb]\\[[ZYVSNNMMMMMMMMMMMMMMMMMMMMNNNNNNNNNNNNNNNNOOOOOOOOPTX[\]_abbbbbbchmquy{}}~~~~~~~~~~~~~~~~~{vvtsssty~~~~~~~~~~}zuqlhcbbaaaaaaaaabfikkorsttttux{}}~~~~~~~~~~~~~~~~~~~~~~~~~~~yupkfb]\\[[ZYVVTTSQNIE@;7641-,***)))((''''''''</span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext">p $$$%%%%%%%%%%%%%%%%%%&&&&''((()*+.016:?DHKMNNPPPQTVV[_``^a_\\\\_efhd`cdagd`ca^^cdcb__eijdb`c`ba]\]XYXXX[dhbYONNNNOQZ`ggaccaggbcb]\^]`^VTSSTSRPPOOOPPPRZ_acc\SPPONHFFFFFFMPWY_bffb]VRQPONLLLNORVW[aa`_^efaeiebghljjmmmlhffb__fkmlhfbZZ]ekjjibded__bijd_a`YYY[ab`ghbekjjjjmmmihd`baghcjmmjjjjljie_^``fdafc`cifd_[[YXXVVXWVUUSSSPNHE><52222222222000000000000111679<===========>>>?ABFGJKLT\bb_ZZ\\`hlkecahlkebikjf^\]afhkjjjjlkkljcigffgf``ehiiic__fijlkjlmlibdfacb_a`]^^^[[[_ehjeaeefhbegfchhgbZXXY^`^cfcgjkjcZWUTTUUW`deglmmlhffhljjlkdb_ba^^ccacahgeda^`b^^`_edbhijjjjjmmmkjkeaejjca_biic`]]_\YSJIHHHHHHHHHHHHHIQVVWVUUTQIG@?????@ADKPRSXYY[[YVUV[beiebgdaddacc_\\ZYZ`fkljca_billkebghijjjjjljijigc_abb~~~~~~~~~~~~~~~~~~~~~~~~~~cfkihc`cjlihiljkljjkebiijib]]]\_bgfd^XXZ^_^`_]acjlmmjc`a`^djjjkga`_bijjmmkdb``^c_\\[[\ab`dihgcZWUUW^dc`baaab`djlkklia^^XXXWVWZ`acfa_]\^_fhhe\YYZYahijlihillkhbbafe__cikibekmmmmjjiaXUUVVX^^cgilmmmmmmmjihcgc[Z]]`fgf_\YXXY[\_ca_^]_`_]]bca_adc_^[[YSQRRTWX`ffe`ZXYYac_abb`dijg`abdga^^afgiciiih`ZYYahjlmlg_XWYWUUWW\]_egkg`]^][\^]egbdb^]_^cjlkkmmlihc__^\]]]ehchebgdaghljjjjmlhgbeiimmmmmmkebgdaeecikhfa]^^ZXXUUWUUVVVVPPQQQUVY]\]^][][Z[```^bijec`edaggf`bdihbeklihijjlkkmmjjkebhijljkmmmmmmkfbhg`abdkmmmmlic`bc`djg_`_XUSSUW]_]]cggc`cjllibekjd[SIF?<5,+!"!""#$$%)0222210,#)$-5:DLQQRUW[dghhhca[SQJGFD@7.--*)('''~'&&%%%%$$$####,1234443~~~/"#%"#%))*+-/56899999::;;<<<===>@BIMNOOOOOOPPPQRRRRRRRRTSTX`eefgkg^VLKKHHHHHHFEDCCCDDFFFFFHKLMMNONNNPQUWY^bafdaeebfilkkmlh`][ZZ\]YXXXZ[cdddb[[_^]\[]`fd[WW]\[[\cejjjljjmljchg`a_]WWX[\YWWVUUUXXY_^XX\ejhggebhgeda^__\[]\^__ab]]\WWTQJA?====<<<;;;;;;<<<<<<==>>>>>>>>>>>>>>=============>>>>>>>>>>>>???????@@@@AJT\cgcgebilmkh`a_^[\^_^ZXYY`a`hlmmkkl~~~ihe~~~affc\WW\djhfgdb`fedcc`WWX[djihijebge^URPOMGDDA:~~~60/-,~~~'%$$'&%$$'))*,1246~=FMPVXZ]YQHCA@???==<<<<<<<;;;<<<<<<<==>>ABCENS<span class="idiff left right">UTTVV[\YWWUUUZ</span>Z\\ad``[SPPQY^``\YY`daYVVXX[\XX\dig`bb`c`^\]]`hiikhbdf`a_bc\\[XQNKJIHEEECCA@????AAAA@=5332222222222211111111111246:;<======>>@AHJT]d`WVWWVWZZab`hlmmjif^VVUUVWW]__bjlia]]`cahklhb\ZWVTSTTTSSTUUUUWX\\XVV_daZZabahkjd`bdhilihhiihbdgbehilljf`\XTONMLLLLLLKKIEA=<::863..,++++*******))('</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">p $$$%%%%%%%%%%%%%%%%%%&&&&''((()*+.016:?DHKMNNPPPQTVV[_``^a_\\\\_efhd`cdagd`ca^^cdcb__eijdb`c`ba]\]XYXXX[dhbYONNNNOQZ`ggaccaggbcb]\^]`^VTSSTSRPPOOOPPPRZ_acc\SPPONHFFFFFFMPWY_bffb]VRQPONLLLNORVW[aa`_^efaeiebghljjmmmlhffb__fkmlhfbZZ]ekjjibded__bijd_a`YYY[ab`ghbekjjjjmmmihd`baghcjmmjjjjljie_^``fdafc`cifd_[[YXXVVXWVUUSSSPNHE><52222222222000000000000111679<===========>>>?ABFGJKLT\bb_ZZ\\`hlkecahlkebikjf^\]afhkjjjjlkkljcigffgf``ehiiic__fijlkjlmlibdfacb_a`]^^^[[[_ehjeaeefhbegfchhgbZXXY^`^cfcgjkjcZWUTTUUW`deglmmlhffhljjlkdb_ba^^ccacahgeda^`b^^`_edbhijjjjjmmmkjkeaejjca_biic`]]_\YSJIHHHHHHHHHHHHHIQVVWVUUTQIG@?????@ADKPRSXYY[[YVUV[beiebgdaddacc_\\ZYZ`fkljca_billkebghijjjjjljijigc_abb~~~~~~~~~~~~~~~~~~~~~~~~~~cfkihc`cjlihiljkljjkebiijib]]]\_bgfd^XXZ^_^`_]acjlmmjc`a`^djjjkga`_bijjmmkdb``^c_\\[[\ab`dihgcZWUUW^dc`baaab`djlkklia^^XXXWVWZ`acfa_]\^_fhhe\YYZYahijlihillkhbbafe__cikibekmmmmjjiaXUUVVX^^cgilmmmmmmmjihcgc[Z]]`fgf_\YXXY[\_ca_^]_`_]]bca_adc_^[[YSQRRTWX`ffe`ZXYYac_abb`dijg`abdga^^afgiciiih`ZYYahjlmlg_XWYWUUWW\]_egkg`]^][\^]egbdb^]_^cjlkkmmlihc__^\]]]ehchebgdaghljjjjmlhgbeiimmmmmmkebgdaeecikhfa]^^ZXXUUWUUVVVVPPQQQUVY]\]^][][Z[```^bijec`edaggf`bdihbeklihijjlkkmmjjkebhijljkmmmmmmkfbhg`abdkmmmmlic`bc`djg_`_XUSSUW]_]]cggc`cjllibekjd[SIF?<5,+!"!""#$$%)0222210,#)$-5:DLQQRUW[dghhhca[SQJGFD@7.--*)('''~'&&%%%%$$$####,1234443~~~/"#%"#%))*+-/56899999::;;<<<===>@BIMNOOOOOOPPPQRRRRRRRRTSTX`eefgkg^VLKKHHHHHHFEDCCCDDFFFFFHKLMMNONNNPQUWY^bafdaeebfilkkmlh`][ZZ\]YXXXZ[cdddb[[_^]\[]`fd[WW]\[[\cejjjljjmljchg`a_]WWX[\YWWVUUUXXY_^XX\ejhggebhgeda^__\[]\^__ab]]\WWTQJA?====<<<;;;;;;<<<<<<==>>>>>>>>>>>>>>=============>>>>>>>>>>>>???????@@@@AJT\cgcgebilmkh`a_^[\^_^ZXYY`a`hlmmkkl~~~ihe~~~affc\WW\djhfgdb`fedcc`WWX[djihijebge^URPOMGDDA:~~~60/-,~~~'%$$'&%$$'))*,1246~=FMPVXZ]YQHCA@???==<<<<<<<;;;<<<<<<<==>>ABCENS<span class="idiff left right">TTTUVZ[XVVUTTY</span>Z\\ad``[SPPQY^``\YY`daYVVXX[\XX\dig`bb`c`^\]]`hiikhbdf`a_bc\\[XQNKJIHEEECCA@????AAAA@=5332222222222211111111111246:;<======>>@AHJT]d`WVWWVWZZab`hlmmjif^VVUUVWW]__bjlia]]`cahklhb\ZWVTSTTTSSTUUUUWX\\XVV_daZZabahkjd`bdhilihhiihbdgbehilljf`\XTONMLLLLLLKKIEA=<::863..,++++*******))('</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">p """##################$$$$%%&&&'(),./48=BFIKLLNNNORTUY]`abefgjlmqvz|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|ytpooonnnoooonnnmlkiiheeedddcbbbbbbbbbbbcccdimrvz}~~~~~~~~~~~~~~~~~~~~~~~~~~|{zzz{|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|wsnid`[ZZYYXWWVTSROLHCB@@@?????>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>???????@@ACDDFFIKLPTVWWWXZ[_dimprrw{}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~zyyxvtpommmlllllllllllllllkiiheba`_______`dfghjkkmmnnnosx{~~~~~~~~~~~~~~}}}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|}||~~~~~~~~~~~~~~~~~~~~~~~~~~~~}yxxxz{~~~~~~~~~~~~~~~~~|xwvutrqqqrttx|~~~}}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}zvusssrrssssrrssstuwxxyzzyyyyy}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|{zvrnie`[ZXUTSSSSSSUUUVVVVVVVVVVVW[^`abbbbbbcccccccb`]\ZZYYXVSRQNJIIII~IIIHHHGFFFEEEDDDDDDDDD~~~DDDDDDDDDEEILNORTUVVVVVVVVVVVVVVVWWWXXXXXXXXXYZZZZZZZ[[[[\^```aaa```^^][[[[[ZZZZZZZZZZZZ[[\`cefffffghikmmprruwwz|}~~~~~~~~~~}yxxwuuuvwx}~~~~~~~~~~~~~~~~~~~~}|}~~~~~~~~~~~~~~~~~~}|}~~~}}||~~~~~~~~~~~~~~~~~~~~~|wvuqqqpponlhdca^^\YVQPPPPPPPPPPPPPPPPPPPPPQQQQQQQQQQQQQQQQQQQQQQQQQQQQRRRSSSSTUUUUUUUUUVVXX[]^cgknopsuvz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{wrmihhgggeb_ZVQPNKGBBAA?<<:7~~~4/.-,~~~++****************~**********************************************************+++++,,,,,,,,-.///////0000000000000000000000000000000///////...-,))'''''&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&''''''''''())++.001112223458:;@DIMQSTUUUVVY[[^`aehjkkklmnnooooonmmlllllllllllllmmmmmnnqrsssvxy~~~~~~~~~~~~~~~~~~~{{yvrnie`[VRMLJJIIIIIHGEB>:97653/+*(((''''&&&&&&&%#</span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">a</span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#0c0610d12d971107a85160c6a927e94a1062a01a"><strong>makefile</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-msse4</span><span class="idiff left right">.1</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-DHAS_CXX_THREADS</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-msse4</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-DHAS_CXX_THREADS</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">cd </span>src <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="nv" style="color: #008080;">CXXFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(CXXFLAGS)</span><span class="s2" style="color: #d14;">"</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#5e55dbeefff2057b414960d9467d183920e31b8a"><strong>src/Alignment.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">@@ -60,7 +60,8 @@ static bool isNext( const SegmentPair& x, const SegmentPair& y ){</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">centroid</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">GreedyXdropAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGreedy</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;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</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;">seq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMin</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mcf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">frameshiftCost</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="88" 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">@@ -87,7 +88,7 @@ void Alignment::makeXdrop( Centroid& centroid,</td>
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87
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<pre style="margin: 0;"> <span id="LC88" 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="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">columnAmbiguityCodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">columnAmbiguityCodes</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;">extend</span><span class="p">(</span> <span class="n" style="color: #333;">blocks</span><span class="p">,</span> <span class="n" style="color: #333;">columnAmbiguityCodes</span><span class="p">,</span> <span class="n" style="color: #333;">centroid</span><span class="p">,</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">,</span> <span class="n" style="color: #333;">isGreedy</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;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">beg1</span><span class="p">(),</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">beg2</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">globality</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;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">frameshiftCost</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;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">smMin</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">frameshiftCost</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="cpp"> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span> <span class="n" style="color: #333;">qual1</span><span class="p">,</span> <span class="n" style="color: #333;">qual2</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span></span>
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92
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">extras</span><span class="p">,</span> <span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">outputType</span> <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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" 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">@@ -107,7 +108,7 @@ void Alignment::makeXdrop( Centroid& centroid,</td>
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107
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<pre style="margin: 0;"> <span id="LC108" 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="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">forwardAmbiguities</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">extend</span><span class="p">(</span> <span class="n" style="color: #333;">forwardBlocks</span><span class="p">,</span> <span class="n" style="color: #333;">forwardAmbiguities</span><span class="p">,</span> <span class="n" style="color: #333;">centroid</span><span class="p">,</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">,</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">end1</span><span class="p">(),</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">end2</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></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;">smMax</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">frameshiftCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">smMin</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">frameshiftCost</span><span class="p">,</span></span>
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span> <span class="n" style="color: #333;">qual1</span><span class="p">,</span> <span class="n" style="color: #333;">qual2</span><span class="p">,</span> <span class="n" style="color: #333;">alph</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="n" style="color: #333;">extras</span><span class="p">,</span> <span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">outputType</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="279" 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">@@ -279,8 +280,8 @@ void Alignment::extend( std::vector< SegmentPair >& chunks,</td>
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279
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280
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<pre style="margin: 0;"> <span id="LC280" 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;">seq1</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;">seq2</span><span class="p">,</span></span>
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280
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>
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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="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left right">maxDrop</span></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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mcf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span></span>
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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="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left right">smMin</span></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="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">maxDrop</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mcf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span></span>
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284
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">frameshiftCost</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TwoQualityScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="325" 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">@@ -324,25 +325,38 @@ void Alignment::extend( std::vector< SegmentPair >& chunks,</td>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">start2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isSimdMatrix</span> <span class="o" style="font-weight: 600;">=</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="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">isAffine</span> <span class="o" style="font-weight: 600;">&&</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">smMin</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">SCHAR_MIN</span> <span class="o" style="font-weight: 600;">&&</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">maxDrop</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">smMax</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">smMin</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">UCHAR_MAX</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC331" 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="mi" style="color: #099;">4</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="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;">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="mi" style="color: #099;">4</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="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sm</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;">sm</span><span class="p">[</span><span class="n" style="color: #333;">alph</span><span class="p">.</span><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="n" style="color: #333;">j</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">isSimdMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extensionScore</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">isGreedy</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">.</span><span class="n" style="color: #333;">align</span><span class="p">(</span> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">sm</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</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="LC330" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sm2qual</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">align2qual</span><span class="p">(</span> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">qual1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="n" style="color: #333;">qual2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span> <span class="n" style="color: #333;">sm2qual</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;">del</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">pairCost</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">pssm2</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">alignPssm</span><span class="p">(</span> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">pssm2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">isGreedy</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">.</span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">sm</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</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="LC339" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sm2qual</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">align2qual</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">qual1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="n" style="color: #333;">qual2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">pairCost</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">align</span><span class="p">(</span> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span> <span class="n" style="color: #333;">sm</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">pairCost</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">pairCost</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">isAffine</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">pssm2</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">alignPssm</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">pssm2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">pairCost</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">isAffine</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">isSimdMatrix</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">alignDna</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">sm</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">growCost</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;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">numbersToUppercase</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span> <span class="n" style="color: #333;">sm</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="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">growCost</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="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">pairCost</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">isAffine</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">extensionScore</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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348
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">score</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 class="c1" style="color: #998; font-style: italic;">// avoid score overflow</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="356" 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">@@ -356,6 +370,11 @@ void Alignment::extend( std::vector< SegmentPair >& chunks,</td>
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356
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isGreedy</span> <span class="p">){</span></span>
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357
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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;">while</span><span class="p">(</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">.</span><span class="n" style="color: #333;">getNextChunk</span><span class="p">(</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;">size</span> <span class="p">)</span> <span class="p">)</span></span>
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358
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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;">chunks</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span> <span class="n" style="color: #333;">SegmentPair</span><span class="p">(</span> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">end2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">size</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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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isSimdMatrix</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">pssm2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">sm2qual</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">getNextChunkDna</span><span class="p">(</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;">size</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">ins</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">))</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;">chunks</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">SegmentPair</span><span class="p">(</span><span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">end2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">size</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="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">getNextChunk</span><span class="p">(</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;">size</span><span class="p">,</span></span>
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">del</span><span class="p">.</span><span class="n" style="color: #333;">growCost</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#bd17e03c676d289c9cc5bb117da6d9d2bde74764"><strong>src/Alignment.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">@@ -80,7 +80,7 @@ struct Alignment{</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">centroid</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">GreedyXdropAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC82" 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;">seq1</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;">seq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span><span class="idiff left"> </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">smMin</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mcf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">frameshiftCost</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</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;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm2</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">@@ -133,7 +133,7 @@ struct Alignment{</td>
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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;">seq1</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;">seq2</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;">size_t</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</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;">bool</span> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</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;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDrop</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;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">smMin</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 right"> </span><span class="n" style="color: #333;">maxDrop</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mcf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span></span>
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138
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">frameshiftCost</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>
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139
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139
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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;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#8f014a93cf121af8fe88d03244d4d4b173d32a6d"><strong>src/GappedXdropAligner.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">@@ -54,25 +54,6 @@</td>
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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="LC55" 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="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Puts 2 "dummy" antidiagonals at the start, so that we can safely</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// look-back from subsequent antidiagonals.</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GappedXdropAligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">init</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreOrigins</span><span class="p">.</span><span class="n" style="color: #333;">resize</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="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreEnds</span><span class="p">.</span><span class="n" style="color: #333;">resize</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="LC62" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">xdropPadLen</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="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">xdropPadLen</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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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mNegInf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdSet1</span><span class="p">(</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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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">xdropPadLen</span><span class="p">],</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">xdropPadLen</span><span class="p">],</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">xdropPadLen</span><span class="p">],</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">bestAntidiagonal</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="LC74" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GappedXdropAligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">align</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;">seq1</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="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;">seq2</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isForward</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">@@ -83,103 +64,95 @@ int GappedXdropAligner::align(const uchar *seq1,</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffine</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMatchScore</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mNegInf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Set1</span></span><span class="p">(</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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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mDelOpenCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Set1</span></span><span class="p">(</span><span class="n" style="color: #333;">delExistenceCost</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;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mDelGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Set1</span></span><span class="p">(</span><span class="n" style="color: #333;">delExtensionCost</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsOpenCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Set1</span></span><span class="p">(</span><span class="n" style="color: #333;">insExistenceCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Set1</span></span><span class="p">(</span><span class="n" style="color: #333;">insExtensionCost</span><span class="p">);</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mNegInf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Fill</span></span><span class="p">(</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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71
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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;">SimdInt</span> <span class="n" style="color: #333;">mDelOpenCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Fill</span></span><span class="p">(</span><span class="n" style="color: #333;">delExistenceCost</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mDelGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Fill</span></span><span class="p">(</span><span class="n" style="color: #333;">delExtensionCost</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsOpenCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Fill</span></span><span class="p">(</span><span class="n" style="color: #333;">insExistenceCost</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Fill</span></span><span class="p">(</span><span class="n" style="color: #333;">insExtensionCost</span><span class="p">);</span></span>
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93
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isAffineGaps</span><span class="p">(</span><span class="n" style="color: #333;">delExistenceCost</span><span class="p">,</span> <span class="n" style="color: #333;">delExtensionCost</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="cpp"> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span> <span class="n" style="color: #333;">insExtensionCost</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;">gapUnalignedCost</span><span class="p">);</span></span>
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97
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">maxSeq1begs</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 class="mi" style="color: #099;">9</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">minSeq1ends</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</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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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</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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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</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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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</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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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</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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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</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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100
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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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101
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</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="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mBestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left">Set1</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mBestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left">Zero</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestEdgeScore</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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104
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</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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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"></span>
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106
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">init</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="n" style="color: #333;"><span class="idiff left right">seq1q</span>ueue</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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89
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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 right">pssmQ</span>ueue</span><span class="p">.</span><span class="n" style="color: #333;">clear</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;">seq2queue</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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109
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC110" 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;">simdLen</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;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">scores</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="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">scores</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2queue</span><span class="p">.</span><span class="n" style="color: #333;">push</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="LC115" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDelimiter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDelimiter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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116
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">-<span id="LC117" 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;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* noop */</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</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;">maxSeq1begs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">maxSeq1begs</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</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;">minSeq1ends</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">minSeq1ends</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="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;">simdLen</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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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</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="n" style="color: #333;">pssmQueue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">i</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="cpp"> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">x</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="cpp"> <span class="n" style="color: #333;">seq2queue</span><span class="p">.</span><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;">seq2</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="LC100" class="line" lang="cpp"> <span class="p">}</span></span>
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120
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seq1beg</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">seq1end</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">break</span></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;"><span class="idiff left">seq2</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">seqIncrement</span></span><span class="p">;</span></span>
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122
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"> <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">scoreEnd</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">scoreEnds</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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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </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">antidiagonal</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="cm" style="color: #998; font-style: italic;"><span class="idiff">/* noop */</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">antidiagonal</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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124
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</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>
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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;">initAntidiagonal</span><span class="p">(</span><span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numCells</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>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">simdLen</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;">seq1queue</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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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">scores</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</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;">seq1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">scores</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="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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_int_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq1queue</span><span class="p">[</span><span class="n" style="color: #333;">seq1beg</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="cpp"></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;">size_t</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">simdLen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seq2queue</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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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2queue</span><span class="p">.</span><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;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">numCells</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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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</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;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</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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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_int_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pssmQueue</span><span class="p">.</span><span class="n" style="color: #333;">fromEnd</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;">simdLen</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="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;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2queue</span><span class="p">.</span><span class="n" style="color: #333;">begin</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>
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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;">initAntidiagonal</span><span class="p">(</span><span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">thisPos</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">;</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;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC115" 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;">z0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">horiPos</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="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">horiPos</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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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</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="cpp"></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;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">isDelimiter1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">isDelimiter2</span><span class="p">))</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="n" style="color: #333;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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139
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <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 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;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq2queue</span><span class="p">[</span><span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">simdLen</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="LC141" class="line" lang="cpp"></span>
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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;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scorer</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;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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144
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123
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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;">int</span> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">maxScoreDrop</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mMinScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdSet1</span><span class="p">(</span><span class="n" style="color: #333;">minScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC148" 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;">x0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">scoreEnd</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;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">scoreEnd</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC150" 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;">z0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">scoreEnd</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">hori</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">vert</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)];</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp"></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="p">,</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span> <span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">;</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">y0</span><span class="p">,</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span> <span class="n" style="color: #333;">y0</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">;</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">z0</span><span class="p">,</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span> <span class="n" style="color: #333;">z0</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</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="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mMinScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill</span><span class="p">(</span><span class="n" style="color: #333;">minScore</span><span class="p">);</span></span>
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158
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"></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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<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;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">s2</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">scorer</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">antidiagonal</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="p"><span class="idiff right">)</span>];</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter<span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diag<span class="idiff left right">Pos</span></span><span class="p">];</span></span>
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161
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">z1</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;">insExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">z2</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;">gapUnalignedCost</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="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;">minScore</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="cpp"> <span class="n" style="color: #333;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</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;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</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;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</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;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</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="p">}</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter1</span><span class="p">)</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">],</span> <span class="n" style="color: #333;">y1</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">delExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">y2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapUnalignedCost</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="cpp"> <span class="n" style="color: #333;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</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="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1end</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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165
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="p">}</span></span>
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166
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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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167
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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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isAffine</span><span class="p">)</span> <span class="p">{</span></span>
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168
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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;">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;">numCells</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;">simdLen</span><span class="p">)</span> <span class="p">{</span></span>
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169
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdSet</span><span class="p">(</span></span>
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170
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __SSE4_1__</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#ifdef __AVX2__</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef WANT_AVX2</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">7</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="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">]],</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;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</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="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __AVX2__</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]],</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">][</span><span class="n" style="color: #333;">s2</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="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]],</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]],</span></span>
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<pre style="margin: 0;"> <span id="LC150" 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="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-</span></span><span class="mi" style="color: #099;">3</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-</span></span><span class="mi" style="color: #099;">2</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-</span></span><span class="mi" style="color: #099;">1</span><span class="p">]],</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]],</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="n" style="color: #333;">s2</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="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">s2</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="LC154" 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="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-</span></span><span class="mi" style="color: #099;">0</span><span class="p">]]);</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">s2</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="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="n" style="color: #333;">x2</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="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdSub</span><span class="p">(</span><span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="n" style="color: #333;">y1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">mDelGrowCost</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="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdSub</span><span class="p">(</span><span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="n" style="color: #333;">z1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">mInsGrowCost</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" 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="163" 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">@@ -190,7 +163,7 @@ int GappedXdropAligner::align(const uchar *seq1,</td>
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190
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">y0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">simdMax</span><span class="p">(</span><span class="n" style="color: #333;">simdSub</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">mDelOpenCost</span><span class="p">),</span> <span class="n" style="color: #333;">y</span><span class="p">));</span></span>
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191
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">z0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">simdMax</span><span class="p">(</span><span class="n" style="color: #333;">simdSub</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">mInsOpenCost</span><span class="p">),</span> <span class="n" style="color: #333;">z</span><span class="p">));</span></span>
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192
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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;">s1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">simdLen</span><span class="p">;</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="cpp"> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">-</span>=</span> <span class="n" style="color: #333;">simdLen</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;">s2</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">+</span>=</span> <span class="n" style="color: #333;">simdLen</span><span class="p">;</span></span>
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194
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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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195
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"></span>
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196
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newBestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdHorizontalMax</span><span class="p">(</span><span class="n" style="color: #333;">mBestScore</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">@@ -199,8 +172,8 @@ int GappedXdropAligner::align(const uchar *seq1,</td>
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199
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">bestAntidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>
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200
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="p">}</span></span>
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201
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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 class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">antidiagonal</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="p"><span class="idiff right">)</span>];</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">antidiagonal</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="p"><span class="idiff right">)</span>];</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diag<span class="idiff left right">Pos</span></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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diag<span class="idiff left right">Pos</span></span><span class="p">];</span></span>
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204
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177
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<pre style="margin: 0;"> <span id="LC177" 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;">numCells</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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205
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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206
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">y1</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;">delExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">y2</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;">gapUnalignedCost</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="217" 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">@@ -217,26 +190,33 @@ int GappedXdropAligner::align(const uchar *seq1,</td>
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217
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">x0</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;">y0</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;">z0</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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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><span class="idiff left right">--</span></span><span class="n" style="color: #333;">s2</span><span class="p">;</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><span class="idiff left right">++</span></span><span class="n" style="color: #333;">s2</span><span class="p">;</span></span>
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <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="p">}</span></span>
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">seq1back</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1queue</span><span class="p">[</span><span class="n" style="color: #333;">seq1end</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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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos</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="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</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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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>
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225
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">seq1back</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)];</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</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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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">],</span> <span class="n" style="color: #333;">y1</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">delExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">y2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC230" 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;">minScore</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1end</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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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="p">[</span><span class="n" style="color: #333;">n</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="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1end</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="cpp"> <span class="k" style="font-weight: 600;">const</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;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</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="cpp"> <span class="n" style="color: #333;">pssmQueue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">simdLen</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 class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">x</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="cpp"> <span class="n" style="color: #333;">isDelimiter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pssmQueue</span><span class="p">.</span><span class="n" style="color: #333;">fromEnd</span><span class="p">(</span><span class="n" style="color: #333;">simdLen</span><span class="p">));</span></span>
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233
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="p">}</span></span>
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234
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"></span>
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235
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<pre style="margin: 0;">-<span id="LC235" 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;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">seq1back</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 class="n" style="color: #333;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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237
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp"></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;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="239" 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">
239
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="cpp"> <span class="n" style="color: #333;">updateFiniteEdges</span><span class="p">(</span><span class="n" style="color: #333;">maxSeq1begs</span><span class="p">,</span> <span class="n" style="color: #333;">minSeq1ends</span><span class="p">,</span> <span class="n" style="color: #333;">x0base</span><span class="p">,</span> <span class="n" style="color: #333;">x0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">numCells</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><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 class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</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="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INF</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</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="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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</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="n" style="color: #333;">seq2queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">y</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;">simdLen</span><span class="p">);</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</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="cpp"> <span class="n" style="color: #333;">isDelimiter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">scorer</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="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="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1beg</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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq1end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <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>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#7dc5c3172a020d4f7642b87bcfe987675bd222a7"><strong>src/GappedXdropAligner.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">@@ -46,6 +46,7 @@</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define GAPPED_XDROP_ALIGNER_HH</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="cp" style="color: #999; font-weight: 600;">#include "mcf_contiguous_queue.hh"</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "mcf_reverse_queue.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "mcf_simd.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ScoreMatrixRow.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC52" 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">@@ -61,10 +62,13 @@ typedef unsigned char uchar;</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">const</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;">const_int_ptr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC63" 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;">typedef</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>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">TinyScore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TwoQualityScoreMatrix</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdLen</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdBytes</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"></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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">droppedTinyScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UCHAR_MAX</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"></span>
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69
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GappedXdropAligner</span> <span class="p">{</span></span>
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70
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="nl">public:</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="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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,6 +82,7 @@ class GappedXdropAligner {</td>
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78
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span></span>
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79
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span></span>
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80
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapUnalignedCost</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffine</span><span class="p">,</span></span>
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81
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span></span>
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82
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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83
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88
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<pre style="margin: 0;"> <span id="LC88" 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">@@ -91,6 +96,7 @@ class GappedXdropAligner {</td>
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91
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExistenceCost</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span></span>
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93
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffine</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span></span>
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95
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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96
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" 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">@@ -107,9 +113,26 @@ class GappedXdropAligner {</td>
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107
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span></span>
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108
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span></span>
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109
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffine</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span></span>
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111
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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112
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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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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;">// Like "align", but maybe faster for DNA. Assumes that</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// scorer[i<4][j<4] fits in signed char. Each sequence element is</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// first mapped through "toUnmasked". If an unmasked sequence</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// element >= 4 appears, alignDna falls back to a slower algorithm.</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;">int</span> <span class="n" style="color: #333;">alignDna</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;">seq1</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;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isForward</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;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scorer</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delExistenceCost</span><span class="p">,</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delExtensionCost</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExistenceCost</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExtensionCost</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxScoreDrop</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;">maxMatchScore</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="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;">toUnmasked</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>
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113
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Call this repeatedly to get each gapless chunk of the alignment.</span></span>
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114
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// The chunks are returned in far-to-near order. The chunk's end</span></span>
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115
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// coordinates in each sequence (relative to the start of extension)</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">@@ -125,6 +148,15 @@ class GappedXdropAligner {</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// After "alignDna", must use this instead of "getNextChunk"</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">getNextChunkDna</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">end1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">end2</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">length</span><span class="p">,</span></span>
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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;">delExistenceCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delExtensionCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExtensionCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Like "align", but it aligns a protein sequence to a DNA sequence.</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// The DNA should be provided as 3 protein sequences, one for each</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// reading frame. seq2frame0 is the in-frame start point.</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">@@ -225,8 +257,9 @@ class GappedXdropAligner {</td>
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<pre style="margin: 0;"> <span id="LC257" 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="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">scoreOrigins</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// score origin for each antidiagonal</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">scoreEnds</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// score end pos for each antidiagonal</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="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">ContiguousQueue</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</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;">seq1queue</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"> <span class="n" style="color: #333;">ContiguousQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seq2queue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="n" style="color: #333;">ContiguousQueue</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</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;">pssmQueue</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="cpp"> <span class="n" style="color: #333;">ContiguousQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seq1queue</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 class="n" style="color: #333;">ReverseQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seq2queue</span><span class="p">;</span></span>
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"></span>
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Our position during the trace-back:</span></span>
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232
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bestAntidiagonal</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">@@ -240,9 +273,31 @@ class GappedXdropAligner {</td>
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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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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC243" 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>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisEnd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span><span class="p">)</span> <span class="p">{</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mNegInf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill</span><span class="p">(</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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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nextEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numCells</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="cpp"> <span class="n" style="color: #333;">scoreEnds</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">nextEnd</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="cpp"> <span class="n" style="color: #333;">scoreOrigins</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">nextEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1end</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;">resizeScoresIfSmaller</span><span class="p">(</span><span class="n" style="color: #333;">nextEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">simdLen</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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282
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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;">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;">xdropPadLen</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;">simdLen</span><span class="p">)</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="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">thisEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">mNegInf</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;">simdStore</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">thisEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">mNegInf</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;">simdStore</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">thisEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <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>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">scoreEnd</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Puts 2 "dummy" antidiagonals at the start, so that we can safely</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// look-back from subsequent antidiagonals</span></span>
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<pre style="margin: 0;">+<span id="LC291" 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="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreOrigins</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">0</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="cpp"> <span class="n" style="color: #333;">scoreEnds</span><span class="p">.</span><span class="n" style="color: #333;">resize</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="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</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 class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">,</span> <span class="mi" 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="cpp"> <span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">xdropPadLen</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;">0</span><span class="p">;</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">bestAntidiagonal</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="LC298" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initAntidiagonal3</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">scoreEnd</span><span class="p">)</span> <span class="p">{</span></span>
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246
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreOrigins</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1end</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">resizeScoresIfSmaller</span><span class="p">(</span><span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">simdLen</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="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreEnds</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scoreEnd</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">@@ -260,6 +315,53 @@ class GappedXdropAligner {</td>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">init3</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Everything below here is for alignDna & getNextChunkDna</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC321" 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;">TinyScore</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">xTinyScores</span><span class="p">;</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" 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;">TinyScore</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">yTinyScores</span><span class="p">;</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" 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;">TinyScore</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">zTinyScores</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC325" 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="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">scoreRises</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// increase of best score, per antidiagonal</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">resizeTinyScoresIfSmaller</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xTinyScores</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;">size</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">xTinyScores</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="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">yTinyScores</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="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">zTinyScores</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="LC332" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="p">}</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initAntidiagonalTiny</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisEnd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span><span class="p">)</span> <span class="p">{</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mNegInf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdOnes</span><span class="p">();</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nextEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreEnds</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">nextEnd</span><span class="p">);</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreOrigins</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">nextEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1end</span><span class="p">);</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">resizeTinyScoresIfSmaller</span><span class="p">(</span><span class="n" style="color: #333;">nextEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">simdBytes</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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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">thisEnd</span><span class="p">],</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">thisEnd</span><span class="p">],</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">thisEnd</span><span class="p">],</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initTiny</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">scoreOffset</span><span class="p">)</span> <span class="p">{</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreOrigins</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreEnds</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonalTiny</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 class="mi" style="color: #099;">0</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;">initAntidiagonalTiny</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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="n" style="color: #333;">xTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">xdropPadLen</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;">scoreOffset</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">bestAntidiagonal</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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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreRises</span><span class="p">.</span><span class="n" style="color: #333;">resize</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="LC354" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">calcBestSeq1positionTiny</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">scoreOffset</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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1start</span><span class="p">(</span><span class="n" style="color: #333;">bestAntidiagonal</span><span class="p">);</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TinyScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">bestAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)];</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TinyScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x2</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;">int</span> <span class="n" style="color: #333;">target</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreOffset</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">scoreRises</span><span class="p">[</span><span class="n" style="color: #333;">bestAntidiagonal</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreRises</span><span class="p">[</span><span class="n" style="color: #333;">bestAntidiagonal</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;">scoreRises</span><span class="p">[</span><span class="n" style="color: #333;">bestAntidiagonal</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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362
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<pre style="margin: 0;">+<span id="LC362" 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;">x2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">target</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">x2</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 class="n" style="color: #333;">bestSeq1position</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">x2beg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="cpp"><span class="p">}</span></span>
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<li id="30d72e7e81ec011dcda59c2395cb78f718d054e4">
<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#30d72e7e81ec011dcda59c2395cb78f718d054e4"><strong>src/GappedXdropAligner2qual.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">@@ -22,15 +22,16 @@ int GappedXdropAligner::align2qual(const uchar *seq1,</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffine</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxScoreDrop</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;">int</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mNegInf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdSet1</span><span class="p">(</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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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isAffineGaps</span><span class="p">(</span><span class="n" style="color: #333;">delExistenceCost</span><span class="p">,</span> <span class="n" style="color: #333;">delExtensionCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span> <span class="n" style="color: #333;">insExtensionCost</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;">gapUnalignedCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</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="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="LC29" 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;">size_t</span> <span class="n" style="color: #333;">maxSeq1begs</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 class="mi" style="color: #099;">9</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;">size_t</span> <span class="n" style="color: #333;">minSeq1ends</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</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="LC30" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</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="LC32" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</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="LC33" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</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="LC34" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</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="LC35" class="line" lang="cpp"></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;">int</span> <span class="n" style="color: #333;">bestScore</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="LC37" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestEdgeScore</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,15 +40,8 @@ int GappedXdropAligner::align2qual(const uchar *seq1,</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">init</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC42" 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;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* noop */</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</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;">maxSeq1begs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">maxSeq1begs</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="LC43" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</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;">minSeq1ends</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">minSeq1ends</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="LC44" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">seq1end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"></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;">size_t</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreEnds</span><span class="p">.</span><span class="n" style="color: #333;">back</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;">size_t</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numCells</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</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="LC45" class="line" lang="cpp"></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;">size_t</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,33 +50,40 @@ int GappedXdropAligner::align2qual(const uchar *seq1,</td>
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<pre style="margin: 0;"> <span id="LC50" 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;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq2pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC51" 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;">q2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">qual2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">qual2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq2pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC59" 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;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter2qual</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</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;">initAntidiagonal</span><span class="p">(</span><span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">thisPos</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</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;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC57" 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;">z0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">horiPos</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">horiPos</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="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</span><span class="p">];</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDelimiter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter2qual</span><span class="p">(</span><span class="n" style="color: #333;">s1</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;">seqIncrement</span><span class="p">]);</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDelimiter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter2qual</span><span class="p">(</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="cpp"></span>
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<pre style="margin: 0;">+<span id="LC65" 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;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">isDelimiter1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">isDelimiter2</span><span class="p">))</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="cpp"> <span class="n" style="color: #333;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">maxScoreDrop</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC64" 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;">x0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">scoreEnd</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC65" 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;">y0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">scoreEnd</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC66" 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;">z0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">scoreEnd</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;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">hori</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)];</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">vert</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)];</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)];</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="p">,</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span> <span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</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="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">y0</span><span class="p">,</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span> <span class="n" style="color: #333;">y0</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</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="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">z0</span><span class="p">,</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span> <span class="n" style="color: #333;">z0</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</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="cpp"></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numCells</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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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter2qual</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</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;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC81" 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;">minScore</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 class="n" style="color: #333;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">,</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</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="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter2</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">z1</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;">insExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">z2</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;">gapUnalignedCost</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;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</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="cpp"> <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">);</span></span>
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84
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</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;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">],</span> <span class="n" style="color: #333;">y1</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">delExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">y2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1end</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="LC83" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC84" 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;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isAffine</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isForward</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;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_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>
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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">@@ -123,8 +124,8 @@ int GappedXdropAligner::align2qual(const uchar *seq1,</td>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">s1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">q1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">q2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">x0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">y0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">z0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">y1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">z1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">x2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC126" 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="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">antidiagonal</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="p"><span class="idiff right">)</span>];</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;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">antidiagonal</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="p"><span class="idiff right">)</span>];</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;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diag<span class="idiff left right">Pos</span></span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diag<span class="idiff left right">Pos</span></span><span class="p">];</span></span>
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128
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2</span><span class="p">;</span></span>
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130
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delExtensionCost</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">gapUnalignedCost</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">@@ -142,23 +143,25 @@ int GappedXdropAligner::align2qual(const uchar *seq1,</td>
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142
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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;">else</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z0</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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143
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x0last</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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144
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">x0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">y0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">z0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">y1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">z1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">x2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">y2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">z2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">isForward</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </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">s1</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">q1</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">s2</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">q2</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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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </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">s1</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">q1</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">s2</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">q2</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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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">s1</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">seqIncrement</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">q1</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">seqIncrement</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">s2</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">seqIncrement</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">q2</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">seqIncrement</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"></span>
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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;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter2qual</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1end</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="LC152" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delExtensionCost</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC153" 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;">minScore</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;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1end</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="LC156" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</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="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC158" 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;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter2qual</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</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="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INF</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1end</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">updateFiniteEdges</span><span class="p">(</span><span class="n" style="color: #333;">maxSeq1begs</span><span class="p">,</span> <span class="n" style="color: #333;">minSeq1ends</span><span class="p">,</span> <span class="n" style="color: #333;">x0base</span><span class="p">,</span> <span class="n" style="color: #333;">x0</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;">numCells</span><span class="p">);</span></span>
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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;">x0</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">n</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="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos</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="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">seq1end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</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="p">}</span></span>
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162
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <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>
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164
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#e75886b250f69fee392d9c70ddf2853930e49922"><strong>src/GappedXdropAligner3frame.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">@@ -62,13 +62,13 @@ void GappedXdropAligner::init3() {</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreOrigins</span><span class="p">.</span><span class="n" style="color: #333;">resize</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="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreEnds</span><span class="p">.</span><span class="n" style="color: #333;">resize</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="LC64" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="mi" style="color: #099;">0</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="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="mi" style="color: #099;">0</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="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal<span class="idiff left right">3</span></span><span class="p">(</span><span class="mi" style="color: #099;">0</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="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal<span class="idiff left right">3</span></span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal<span class="idiff left right">3</span></span><span class="p">(</span><span class="mi" style="color: #099;">0</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="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal<span class="idiff left right">3</span></span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal<span class="idiff left right">3</span></span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal<span class="idiff left right">3</span></span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal<span class="idiff left right">3</span></span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC73" 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;">fill_n</span><span class="p">(</span><span class="n" style="color: #333;">xScores</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="mi" style="color: #099;">14</span><span class="p">,</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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<pre style="margin: 0;"> <span id="LC74" 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;">fill_n</span><span class="p">(</span><span class="n" style="color: #333;">yScores</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="mi" style="color: #099;">14</span><span class="p">,</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="122" 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="122" 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">@@ -122,7 +122,7 @@ int GappedXdropAligner::align3(const uchar *seq1,</td>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreEnds</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numCells</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;">// + 2 pad cells</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal<span class="idiff left right">3</span></span><span class="p">(</span><span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numCells</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;">// + 2 pad cells</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"></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;">seq2</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">whichFrame</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq2frame0</span><span class="p">,</span> <span class="n" style="color: #333;">seq2frame1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2frame2</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="220" 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">@@ -220,7 +220,7 @@ int GappedXdropAligner::align3(const uchar *seq1,</td>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scorer</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">updateFiniteEdges3</span><span class="p">(</span><span class="n" style="color: #333;">maxSeq1begs</span><span class="p">,</span> <span class="n" style="color: #333;">minSeq1ends</span><span class="p">,</span> <span class="n" style="color: #333;">x0base</span><span class="p">,</span> <span class="n" style="color: #333;">x0</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;">numCells</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#6821496f966af651583944bcdf3b822e5123d4a1"><strong>src/GappedXdropAligner3framePssm.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">@@ -34,7 +34,7 @@ int GappedXdropAligner::align3pssm(const uchar *seq,</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreEnds</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</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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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numCells</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;">// + 2 pad cells</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal<span class="idiff left right">3</span></span><span class="p">(</span><span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numCells</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;">// + 2 pad cells</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="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">whichFrame</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">pssmFrame0</span><span class="p">,</span> <span class="n" style="color: #333;">pssmFrame1</span><span class="p">,</span> <span class="n" style="color: #333;">pssmFrame2</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>
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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">@@ -132,7 +132,7 @@ int GappedXdropAligner::align3pssm(const uchar *seq,</td>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssmFrame2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssmFrame0</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">updateFiniteEdges3</span><span class="p">(</span><span class="n" style="color: #333;">maxSeq1begs</span><span class="p">,</span> <span class="n" style="color: #333;">minSeq1ends</span><span class="p">,</span> <span class="n" style="color: #333;">x0base</span><span class="p">,</span> <span class="n" style="color: #333;">x0</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;">numCells</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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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#fe292bc81098de48178ce05c67f141fe55186348"><strong>src/GappedXdropAlignerDna.cc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Author: Martin C. Frith 2019</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// SPDX-License-Identifier: GPL-3.0-or-later</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></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 "GappedXdropAligner.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 "GappedXdropAlignerInl.hh"</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC7" 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="LC8" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC9" 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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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqLoadLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdBytes</span><span class="p">;</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delimiter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GappedXdropAligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">alignDna</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;">seq1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC16" 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;">seq2</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isForward</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;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scorer</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delOpenCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delGrowCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insOpenCost</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;">int</span> <span class="n" style="color: #333;">insGrowCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMatchScore</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;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">toUnmasked</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">badScoreDrop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxScoreDrop</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="LC27" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">delGrowCost</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;">delGrowCost</span><span class="p">,</span> <span class="n" style="color: #333;">badScoreDrop</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">delOpenCost</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;">delOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">badScoreDrop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delGrowCost</span><span class="p">);</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="n" style="color: #333;">insGrowCost</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;">insGrowCost</span><span class="p">,</span> <span class="n" style="color: #333;">badScoreDrop</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">insOpenCost</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;">insOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">badScoreDrop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insGrowCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mNegInf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdOnes</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mDelOpenCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill1</span><span class="p">(</span><span class="n" style="color: #333;">delOpenCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mDelGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill1</span><span class="p">(</span><span class="n" style="color: #333;">delGrowCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsOpenCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill1</span><span class="p">(</span><span class="n" style="color: #333;">insOpenCost</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;">SimdInt</span> <span class="n" style="color: #333;">mInsGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill1</span><span class="p">(</span><span class="n" style="color: #333;">insGrowCost</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;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</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="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="LC40" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">scoreOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxMatchScore</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="LC41" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">scorer4x4</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">simdSet1</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __AVX2__</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">3</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="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</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;">scorer</span><span class="p">[</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="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</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="LC49" 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="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</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;">scorer</span><span class="p">[</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="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</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="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</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="LC56" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</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="LC57" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</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="LC58" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</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="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</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="LC60" class="line" lang="cpp"></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;">int</span> <span class="n" style="color: #333;">bestScore</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="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mBestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mBadScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill1</span><span class="p">(</span><span class="n" style="color: #333;">scoreOffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">badScoreDrop</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mScoreRise1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdZero</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mScoreRise2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdZero</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="cpp"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">initTiny</span><span class="p">(</span><span class="n" style="color: #333;">scoreOffset</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="cpp"> <span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">clear</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="cpp"> <span class="n" style="color: #333;">seq2queue</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDna</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">toUnmasked</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</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;">toUnmasked</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" 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;">seqLoadLen</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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74
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<pre style="margin: 0;">+<span id="LC74" 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;">toUnmasked</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</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="cpp"> <span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">x</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="cpp"> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">*</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;">delimiter</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="cpp"> <span class="n" style="color: #333;">seq2queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">toUnmasked</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</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="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="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC82" 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;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* noop */</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">)</span> <span class="p">{</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</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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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" 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;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">fromEnd</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;">seqLoadLen</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="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;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2queue</span><span class="p">.</span><span class="n" style="color: #333;">begin</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="cpp"></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonalTiny</span><span class="p">(</span><span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">thisPos</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</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="cpp"> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</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="cpp"> <span class="n" style="color: #333;">TinyScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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="cpp"> <span class="n" style="color: #333;">TinyScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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="cpp"> <span class="n" style="color: #333;">TinyScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TinyScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">horiPos</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TinyScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">horiPos</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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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TinyScore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</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>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mScoreRise12</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdAdd1</span><span class="p">(</span><span class="n" style="color: #333;">mScoreRise1</span><span class="p">,</span> <span class="n" style="color: #333;">mScoreRise2</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mDelGrowCost1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdAdd1</span><span class="p">(</span><span class="n" style="color: #333;">mDelGrowCost</span><span class="p">,</span> <span class="n" style="color: #333;">mScoreRise1</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsGrowCost1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdAdd1</span><span class="p">(</span><span class="n" style="color: #333;">mInsGrowCost</span><span class="p">,</span> <span class="n" style="color: #333;">mScoreRise1</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>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isDna</span><span class="p">)</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;">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;">numCells</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;">simdBytes</span><span class="p">)</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="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">fwd1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="n" style="color: #333;">s1</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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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">rev2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="n" style="color: #333;">s2</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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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdOr</span><span class="p">(</span><span class="n" style="color: #333;">simdLeft</span><span class="p">(</span><span class="n" style="color: #333;">fwd1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span> <span class="n" style="color: #333;">rev2</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="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdChoose1</span><span class="p">(</span><span class="n" style="color: #333;">scorer4x4</span><span class="p">,</span> <span class="n" style="color: #333;">j</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;">SimdInt</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">mScoreRise12</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="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="n" style="color: #333;">y1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">mDelGrowCost1</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;">SimdInt</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="n" style="color: #333;">z1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">mInsGrowCost1</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;">SimdInt</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">simdMin1</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="n" style="color: #333;">z</span><span class="p">);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">isDrop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdEq1</span><span class="p">(</span><span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">mBadScore</span><span class="p">),</span> <span class="n" style="color: #333;">mBadScore</span><span class="p">);</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;">mBestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">mBestScore</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;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">simdOr</span><span class="p">(</span><span class="n" style="color: #333;">simdSub1</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">),</span> <span class="n" style="color: #333;">isDrop</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;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">y0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">mDelOpenCost</span><span class="p">),</span> <span class="n" style="color: #333;">y</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;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">z0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">mInsOpenCost</span><span class="p">),</span> <span class="n" style="color: #333;">z</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="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" 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="LC119" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDelimiter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">delimiter</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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDelimiter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">s2</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;">delimiter</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;">isDelimiter1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">isDelimiter2</span><span class="p">)</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;">badScoreDrop</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;">badScoreDrop</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;">maxMatchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">mBadScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill1</span><span class="p">(</span><span class="n" style="color: #333;">scoreOffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">badScoreDrop</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <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>
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126
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<pre style="margin: 0;">+<span id="LC126" 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;">numCells</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;">simdBytes</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdSet1</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __SSE4_1__</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __AVX2__</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">31</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">31</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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">30</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">30</span><span class="p">]],</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">29</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">29</span><span class="p">]],</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">28</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">28</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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">27</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">27</span><span class="p">]],</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">26</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">26</span><span class="p">]],</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">25</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">25</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="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">24</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">24</span><span class="p">]],</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">23</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">23</span><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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">22</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">22</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 class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">21</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">21</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="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">20</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">20</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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">19</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">19</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="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">18</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">18</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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">17</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">17</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="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">16</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">16</span><span class="p">]],</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">15</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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">14</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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">13</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="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">12</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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">11</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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">10</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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]],</span></span>
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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;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">8</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="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]],</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]][</span><span class="n" style="color: #333;">s2</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="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">5</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="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]],</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]],</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]][</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="mi" style="color: #099;">0</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>
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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;">SimdInt</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">mScoreRise12</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;">SimdInt</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="n" style="color: #333;">y1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">mDelGrowCost1</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="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="n" style="color: #333;">z1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">mInsGrowCost1</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="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">simdMin1</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="n" style="color: #333;">z</span><span class="p">);</span></span>
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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;">SimdInt</span> <span class="n" style="color: #333;">isDrop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdEq1</span><span class="p">(</span><span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">mBadScore</span><span class="p">),</span> <span class="n" style="color: #333;">mBadScore</span><span class="p">);</span></span>
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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;">mBestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">mBestScore</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="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">simdOr</span><span class="p">(</span><span class="n" style="color: #333;">simdSub1</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">),</span> <span class="n" style="color: #333;">isDrop</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="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">y0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">mDelOpenCost</span><span class="p">),</span> <span class="n" style="color: #333;">y</span><span class="p">));</span></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="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">z0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">mInsOpenCost</span><span class="p">),</span> <span class="n" style="color: #333;">z</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="cpp"> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">simdBytes</span><span class="p">;</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;">s2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">simdBytes</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="cpp"> <span class="p">}</span></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="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isDelimiter2</span><span class="p">)</span> <span class="n" style="color: #333;">x0</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;">droppedTinyScore</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="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isDelimiter1</span><span class="p">)</span> <span class="n" style="color: #333;">x0</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">droppedTinyScore</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// maybe n=0</span></span>
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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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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="n" style="color: #333;">mScoreRise2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mScoreRise1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">mScoreRise1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdZero</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newBestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdHorizontalMin1</span><span class="p">(</span><span class="n" style="color: #333;">mBestScore</span><span class="p">);</span></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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rise</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 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="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">newBestScore</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoreOffset</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">rise</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreOffset</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">newBestScore</span><span class="p">;</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rise</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="cpp"> <span class="n" style="color: #333;">bestAntidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</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="cpp"> <span class="n" style="color: #333;">mBestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">;</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">mScoreRise1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill1</span><span class="p">(</span><span class="n" style="color: #333;">rise</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="p">}</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreRises</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">rise</span><span class="p">);</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos</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="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</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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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</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>
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<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">droppedTinyScore</span><span class="p">)</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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1end</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="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;">toUnmasked</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</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="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">seqLoadLen</span><span class="p">);</span></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="cpp"> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">*</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;">delimiter</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;">+<span id="LC203" 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;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">fromEnd</span><span class="p">(</span><span class="n" style="color: #333;">seqLoadLen</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="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">4</span><span class="p">)</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 class="n" style="color: #333;">isDna</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</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="cpp"> <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="p">}</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</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;">droppedTinyScore</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="210" 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">
210
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<pre style="margin: 0;">+<span id="LC210" 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;">toUnmasked</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="211" 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">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">y</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;">seqLoadLen</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="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</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="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">4</span><span class="p">)</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="cpp"> <span class="n" style="color: #333;">isDna</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</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="p">}</span></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="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1beg</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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos</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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos</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;">seq1beg</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq1end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</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="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="p">}</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"></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;">calcBestSeq1positionTiny</span><span class="p">(</span><span class="n" style="color: #333;">scoreOffset</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestScore</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="cpp"><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>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">GappedXdropAligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getNextChunkDna</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">end1</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">end2</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;">size_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">length</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delOpenCost</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delGrowCost</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insOpenCost</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;">int</span> <span class="n" style="color: #333;">insGrowCost</span><span class="p">)</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bestAntidiagonal</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="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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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="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestSeq1position</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="n" style="color: #333;">end2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestAntidiagonal</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bestSeq1position</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>
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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;">int</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="n" style="color: #333;">z</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="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hori</span><span class="p">(</span><span class="n" style="color: #333;">bestAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</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;">size_t</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vert</span><span class="p">(</span><span class="n" style="color: #333;">bestAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">bestAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="245" 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">
245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">d</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoreRises</span><span class="p">[</span><span class="n" style="color: #333;">bestAntidiagonal</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="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">yTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">h</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delGrowCost</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insGrowCost</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="248" 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">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">y</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">bestAntidiagonal</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;">break</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="n" style="color: #333;">bestAntidiagonal</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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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">bestSeq1position</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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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <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>
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<td class="diff-line-num new new_line" data-linenumber="253" 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">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">length</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;">bestSeq1position</span><span class="p">;</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bestAntidiagonal</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="nb" style="color: #0086b3;">true</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>
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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;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDel</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">bestAntidiagonal</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="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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isDel</span><span class="p">)</span> <span class="n" style="color: #333;">bestSeq1position</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="260" 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">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hori</span><span class="p">(</span><span class="n" style="color: #333;">bestAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vert</span><span class="p">(</span><span class="n" style="color: #333;">bestAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</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 class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">bestAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">d</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoreRises</span><span class="p">[</span><span class="n" style="color: #333;">bestAntidiagonal</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;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">yTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">h</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delGrowCost</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 class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zTinyScores</span><span class="p">[</span><span class="n" style="color: #333;">v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insGrowCost</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isDel</span><span class="p">)</span> <span class="p">{</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">delOpenCost</span><span class="p">;</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" 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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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">insOpenCost</span><span class="p">;</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <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="k" style="font-weight: 600;">if</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;">y</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">z</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</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="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>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#0dc2fc6ce4e90db3e92c8d5394d9fff8563e7f2a"><strong>src/GappedXdropAlignerInl.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">@@ -59,13 +59,6 @@ T whichFrame(size_t antidiagonal, T frame0, T frame1, T frame2) {</td>
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59
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="p">}</span></span>
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60
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"><span class="p">}</span></span>
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61
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffineGaps</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delExistenceCost</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delExtensionCost</span><span class="p">,</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExtensionCost</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gapUnalignedCost</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">delExtensionCost</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insExtensionCost</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC66" 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;">max</span><span class="p">(</span><span class="n" style="color: #333;">delExistenceCost</span><span class="p">,</span> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// The next two functions will stop the alignment at delimiters. But</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// this is not guaranteed if bestScore > INF / 2. We could avoid this</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// restriction by replacing -INF / 2 with bestScore - INF.</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">@@ -97,10 +90,11 @@ inline void checkGappedXdropScore(int bestScore) {</td>
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<pre style="margin: 0;"> <span id="LC90" 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="n" style="color: #333;">updateBest1</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;">bestScore</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bestAntidiagonal</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bestSeq1position</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minScore</span><span class="p">,</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;">int</span> <span class="n" style="color: #333;">score</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1position</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestScore</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">><span class="idiff left">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">minScore</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">score</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;">bestScore</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">bestScore</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="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">bestAntidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">bestSeq1position</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1position</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" 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">@@ -119,26 +113,13 @@ inline void GappedXdropAligner::updateBest(int &bestScore, int score,</td>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC115" 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="n" style="color: #333;">updateMaxScoreDrop</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;">maxScoreDrop</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC122" 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 right">numCell</span>s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC116" 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 right">maxMatche</span>s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If the current antidiagonal touches a sentinel/delimiter, then</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// maxMatches is the maximum possible number of matches starting</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// from the next antidiagonal.</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;">int</span> <span class="n" style="color: #333;">maxMatches</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="n" style="color: #333;">numCells</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="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">maxScoreDrop</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;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatches</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">maxMatchScore</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="LC121" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC130" 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="n" style="color: #333;">updateFiniteEdges</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">maxSeq1begs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">minSeq1ends</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0base</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0end</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;">size_t</span> <span class="n" style="color: #333;">numCells</span><span class="p">)</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;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x0end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">numCells</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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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">maxSeq1begs</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;">maxSeq1begs</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;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">maxSeq1begs</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;">finiteBeg</span><span class="p">(</span><span class="n" style="color: #333;">x0beg</span><span class="p">,</span> <span class="n" style="color: #333;">x0end</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">x0base</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">minSeq1ends</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;">minSeq1ends</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="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">minSeq1ends</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;">finiteEnd</span><span class="p">(</span><span class="n" style="color: #333;">x0beg</span><span class="p">,</span> <span class="n" style="color: #333;">x0end</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">x0base</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="LC140" class="line" lang="cpp"><span class="p">}</span></span>
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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="LC123" 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="n" style="color: #333;">updateFiniteEdges3</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">maxSeq1begs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">minSeq1ends</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0base</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0end</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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numCells</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#35f9fe39feef01a50cdd57a941b460c37cbaffba"><strong>src/GappedXdropAlignerPssm.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">@@ -14,96 +14,86 @@ int GappedXdropAligner::alignPssm(const uchar *seq,</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffine</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">vectorOfMatchScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssm</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mNegInf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Set1</span></span><span class="p">(</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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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mDelOpenCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Set1</span></span><span class="p">(</span><span class="n" style="color: #333;">delExistenceCost</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;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mDelGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Set1</span></span><span class="p">(</span><span class="n" style="color: #333;">delExtensionCost</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;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsOpenCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Set1</span></span><span class="p">(</span><span class="n" style="color: #333;">insExistenceCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Set1</span></span><span class="p">(</span><span class="n" style="color: #333;">insExtensionCost</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;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mNegInf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Fill</span></span><span class="p">(</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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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mDelOpenCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Fill</span></span><span class="p">(</span><span class="n" style="color: #333;">delExistenceCost</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;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mDelGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Fill</span></span><span class="p">(</span><span class="n" style="color: #333;">delExtensionCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsOpenCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Fill</span></span><span class="p">(</span><span class="n" style="color: #333;">insExistenceCost</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;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Fill</span></span><span class="p">(</span><span class="n" style="color: #333;">insExtensionCost</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</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="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="LC26" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isAffineGaps</span><span class="p">(</span><span class="n" style="color: #333;">delExistenceCost</span><span class="p">,</span> <span class="n" style="color: #333;">delExtensionCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span> <span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></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;">size_t</span> <span class="n" style="color: #333;">maxSeq1begs</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 class="mi" style="color: #099;">9</span> <span class="p">};</span></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;">size_t</span> <span class="n" style="color: #333;">minSeq1ends</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</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="LC28" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</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="LC29" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</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="LC30" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</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="LC31" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</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="LC32" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</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="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</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="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mBestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left">Set1</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mBestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simd<span class="idiff left">Zero</span></span><span class="p"><span class="idiff right">(</span>);</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;">int</span> <span class="n" style="color: #333;">bestEdgeScore</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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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</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="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">init</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;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">clear</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;"><span class="idiff left right">seq2q</span>ueue</span><span class="p">.</span><span class="n" style="color: #333;">clear</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;"><span class="idiff left right">pssmQ</span>ueue</span><span class="p">.</span><span class="n" style="color: #333;">clear</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="LC42" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// xxx the queue names are flipped: seq1queue <=> seq2queue</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDelimiter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">vectorOfMatchScores</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDelimiter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">vectorOfMatchScores</span><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="LC44" 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;">simdLen</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></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="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;"><span class="idiff left right">c</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">seq<span class="idiff left">2queue</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">push</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">c</span></span><span class="p"><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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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">c</span></span><span class="p">,</span> <span class="n" style="color: #333;">vectorOfMatchScores</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;"><span class="idiff left">seq1queue</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">push</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vectorOfMatchScores</span></span><span class="p"><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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<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;">simdLen</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="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;"><span class="idiff left right">x</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</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;">seq<span class="idiff left">1queue</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">push</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="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="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="p">,</span> <span class="n" style="color: #333;">vectorOfMatchScores</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pssmQueue</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">push</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vectorOfMatchScores</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </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="LC51" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC51" 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;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* noop */</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</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;">maxSeq1begs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">maxSeq1begs</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="LC53" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</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;">minSeq1ends</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">minSeq1ends</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="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">seq1end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</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;">pssm</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</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="LC57" class="line" lang="cpp"> <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">scoreEnd</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">scoreEnds</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="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </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">antidiagonal</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="cm" style="color: #998; font-style: italic;"><span class="idiff">/* noop */</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">antidiagonal</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="LC56" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><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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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numCells</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">simdLen</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;">seq2queue</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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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</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="cpp"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">vectorOfMatchScores</span><span class="p">);</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</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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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"></span>
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59
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<pre style="margin: 0;">+<span id="LC59" 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;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">fromEnd</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;">simdLen</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_int_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pssmQueue</span><span class="p">.</span><span class="n" style="color: #333;">fromEnd</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">thisPos</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">);</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</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="cpp"> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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="cpp"> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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="cpp"> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">horiPos</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">horiPos</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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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</span><span class="p">];</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" 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;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">isDelimiter1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">isDelimiter2</span><span class="p">))</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="cpp"> <span class="n" style="color: #333;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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66
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="p">}</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" 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;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq2queue</span><span class="p">[</span><span class="n" style="color: #333;">seq1beg</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">simdLen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seq1queue</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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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><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;">pssm</span><span class="p">,</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">numCells</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="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</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="cpp"> <span class="p">}</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_int_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq1queue</span><span class="p">[</span><span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">simdLen</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="LC75" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC76" 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;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter</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;">s2</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">maxScoreDrop</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mMinScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdSet1</span><span class="p">(</span><span class="n" style="color: #333;">minScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"></span>
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82
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<pre style="margin: 0;">-<span id="LC82" 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;">x0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">scoreEnd</span><span class="p">];</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" 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;">y0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">scoreEnd</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="cpp"> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">scoreEnd</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">hori</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)];</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">vert</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)];</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</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;">SimdInt</span> <span class="n" style="color: #333;">mMinScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill</span><span class="p">(</span><span class="n" style="color: #333;">minScore</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="p">,</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span> <span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</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;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">y0</span><span class="p">,</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span> <span class="n" style="color: #333;">y0</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</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;">simdStore</span><span class="p">(</span><span class="n" style="color: #333;">z0</span><span class="p">,</span> <span class="n" style="color: #333;">mNegInf</span><span class="p">);</span> <span class="n" style="color: #333;">z0</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"></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;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter</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;">s2</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)];</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</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;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">z1</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;">insExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">z2</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;">gapUnalignedCost</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC96" 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;">minScore</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC84" 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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter1</span><span class="p">)</span> <span class="p">{</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">],</span> <span class="n" style="color: #333;">y1</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">delExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">y2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapUnalignedCost</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="cpp"> <span class="n" style="color: #333;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">,</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1end</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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99
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="p">}</span></span>
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100
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>
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101
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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;">isAffine</span><span class="p">)</span> <span class="p">{</span></span>
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102
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93
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<pre style="margin: 0;"> <span id="LC93" 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;">numCells</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;">simdLen</span><span class="p">)</span> <span class="p">{</span></span>
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103
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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;">SimdInt</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdSet</span><span class="p">(</span></span>
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104
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __SSE4_1__</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#ifdef __AVX2__</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef WANT_AVX2</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __AVX2__</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">7</span><span class="p">][</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]],</span></span>
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108
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">][</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]],</span></span>
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109
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">][</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]],</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" 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">@@ -133,8 +123,8 @@ int GappedXdropAligner::alignPssm(const uchar *seq,</td>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">bestAntidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</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="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC125" 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="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">antidiagonal</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="p"><span class="idiff right">)</span>];</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">antidiagonal</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="p"><span class="idiff right">)</span>];</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diag<span class="idiff left right">Pos</span></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;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diag<span class="idiff left right">Pos</span></span><span class="p">];</span></span>
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138
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128
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<pre style="margin: 0;"> <span id="LC128" 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;">numCells</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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139
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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140
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">y1</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;">delExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">y2</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;">gapUnalignedCost</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="155" 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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -155,22 +145,30 @@ int GappedXdropAligner::alignPssm(const uchar *seq,</td>
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155
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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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156
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="p">}</span></span>
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157
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">seq1back</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2queue</span><span class="p">[</span><span class="n" style="color: #333;">seq1end</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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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="n" style="color: #333;">seq1back</span><span class="p">,</span> <span class="n" style="color: #333;">vectorOfMatchScores</span><span class="p">))</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yScores</span><span class="p">[</span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</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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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">],</span> <span class="n" style="color: #333;">y1</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">delExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">y2</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapUnalignedCost</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="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;">minScore</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;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</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;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1end</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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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos</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;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</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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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</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>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="p">[</span><span class="n" style="color: #333;">n</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="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1end</span><span class="p">;</span></span>
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<td class="diff-line-num new new_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">
154
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<pre style="margin: 0;">+<span id="LC154" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</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="cpp"> <span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">simdLen</span><span class="p">);</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">vectorOfMatchScores</span><span class="p">);</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">isDelimiter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">fromEnd</span><span class="p">(</span><span class="n" style="color: #333;">simdLen</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="cpp"> <span class="n" style="color: #333;">vectorOfMatchScores</span><span class="p">);</span></span>
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167
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="p">}</span></span>
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168
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"></span>
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169
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<pre style="margin: 0;">-<span id="LC169" 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;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="n" style="color: #333;">seq1back</span><span class="p">,</span> <span class="n" style="color: #333;">vectorOfMatchScores</span><span class="p">))</span></span>
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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;">updateMaxScoreDrop</span><span class="p">(</span><span class="n" style="color: #333;">maxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">,</span> <span class="n" style="color: #333;">maxMatchScore</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="cpp"></span>
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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;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x0base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">updateFiniteEdges</span><span class="p">(</span><span class="n" style="color: #333;">maxSeq1begs</span><span class="p">,</span> <span class="n" style="color: #333;">minSeq1ends</span><span class="p">,</span> <span class="n" style="color: #333;">x0base</span><span class="p">,</span> <span class="n" style="color: #333;">x0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">numCells</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</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="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</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="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INF</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</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="cpp"> <span class="k" style="font-weight: 600;">const</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;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssm</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="cpp"> <span class="n" style="color: #333;">pssmQueue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">y</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;">simdLen</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;">pssm</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</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;">isDelimiter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">y</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="p">}</span> <span class="k" style="font-weight: 600;">else</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="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1beg</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="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos</span><span class="p">;</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq1end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</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="cpp"> <span class="p">}</span></span>
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174
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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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175
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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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176
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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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#dfce2568fc6cc43ff1901906cedd463b1de40be4"><strong>src/ScoreMatrixRow.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">@@ -15,10 +15,17 @@ enum { scoreMatrixRowSize = ALPHABET_CAPACITY };</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;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// An "infinite" score. Delimiters at the ends of sequences get a</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// score of -INF. We want it high enough to terminate alignments</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// immediately, but not so high that it causes overflow errors.</span></span>
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21
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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>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Substitution score for delimiter symbols at the ends of sequences.</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// It should be highly negative, to terminate alignments immediately,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// but not so negative that it causes overflow errors.</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// The delimiter score when using short ints:</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">shortDelimiterScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SHRT_MIN</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">SCHAR_MIN</span><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="c1" style="color: #998; font-style: italic;">// We want: short(delimiterScore) = shortDelimiterScore</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delimiterScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT_MIN</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span><span class="n" style="color: #333;">shortDelimiterScore</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC28" 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="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">delimiterScore</span> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><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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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#729036dee8937546a072eb76b6399452aa5a4d9f"><strong>src/alp/njn_matrix.hpp</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">@@ -597,7 +597,7 @@ namespace Njn {</td>
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<pre style="margin: 0;"> <span id="LC597" 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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getM</span> <span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p">[]</span> <span class="n" style="color: #333;">d_matrix_p</span> <span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span> <span class="n" style="color: #333;">d_matrix_p</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;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getM</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;"><span class="idiff left">delete</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">d_matrix_p</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d_matrix_p</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 right">;</span></span></span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getM</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="p"><span class="idiff left">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">delete</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">d_matrix_p</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d_matrix_p</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="p"><span class="idiff right">}</span></span></span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="cpp"></span>
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602
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="cpp"> <span class="n" style="color: #333;">d_m</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="LC603" class="line" lang="cpp"> <span class="n" style="color: #333;">d_n</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,7 +85,7 @@ void Random::seed (long x)</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">Random</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">number</span> <span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;">// uniform random x : 0 <= x <= exp2 (31) - 1</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="idiff left right"> </span><span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="idiff left right"> </span><span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rK</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;">r</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rJ</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#6b6442cb28cf1bf48dae1f18dbaed740b8b5e86e"><strong>src/alp/njn_vector.hpp</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">@@ -330,7 +330,7 @@ namespace Njn {</td>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></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;">void</span> <span class="n" style="color: #333;">Vector</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">free2</span> <span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"> <span class="p">{</span></span>
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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;">getM</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;"><span class="idiff left">delete</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">d_vector_p</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d_vector_p</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 right">;</span></span></span>
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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;">getM</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="p"><span class="idiff left">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">delete</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">d_vector_p</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d_vector_p</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="p"><span class="idiff right">}</span></span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">d_m</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="LC336" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#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">@@ -673,7 +673,8 @@ void alignGapped( LastAligner& aligner,</td>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// do gapped extension from each end of the seed:</span></span>
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="cpp"> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">centroid</span><span class="p">,</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">greedyAligner</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">globality</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">globality</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <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;">frameSize</span><span class="p">,</span></span>
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679
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gappedExtensionCount</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">@@ -742,8 +743,8 @@ void alignFinish( LastAligner& aligner, const AlignmentPot& gappedAlns,</td>
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="cpp"> <span class="n" style="color: #333;">probAln</span><span class="p">.</span><span class="n" style="color: #333;">seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">seed</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="cpp"> <span class="n" style="color: #333;">probAln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span> <span class="n" style="color: #333;">centroid</span><span class="p">,</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">greedyAligner</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">globality</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">d</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="cpp"><span class="idiff left right"> </span> <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;">frameSize</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">scoreMatrix</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">minScore</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">gapCosts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff right">,</span></span> <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;">frameSize</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gamma</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="p">);</span></span>
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750
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">score</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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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2"><strong>src/makefile</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-msse4</span>.1 <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wextra</span> <span class="nt" style="color: #000080;">-Wcast-qual</span> <span class="nt" style="color: #000080;">-Wswitch-enum</span> <span class="se" style="color: #d14;">\</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="make"><span class="nt" style="color: #000080;">-Wundef</span> <span class="nt" style="color: #000080;">-Wcast-align</span> <span class="nt" style="color: #000080;">-pedantic</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: #000080;">-pthread</span> <span class="se" style="color: #d14;">\</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="make"><span class="nt" style="color: #000080;">-DHAS_CXX_THREADS</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-msse4</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wextra</span> <span class="nt" style="color: #000080;">-Wcast-qual</span> <span class="nt" style="color: #000080;">-Wswitch-enum</span> <span class="nt" style="color: #000080;">-Wundef</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="nt" style="color: #000080;">-Wcast-align</span> <span class="nt" style="color: #000080;">-pedantic</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-DHAS_CXX_THREADS</span></span>
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4
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># -Wconversion</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># -fomit-frame-pointer ?</span></span>
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<pre style="margin: 0;"> <span id="LC5" 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">@@ -32,12 +31,12 @@ SubsetSuffixArraySort.o lastdb.o</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"><span class="nv" style="color: #008080;">alignObj0</span> <span class="o" style="font-weight: 600;">=</span> Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make">ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make">tantan.o LastalArguments.o GappedXdropAligner.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="make">GappedXdropAligner<span class="idiff left right">Pssm.o GappedXdropAligner2qual</span>.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="make">GappedXdropAligner<span class="idiff left right">3frame.o mcf_gap_costs.o GeneticCode</span>.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="make">G<span class="idiff left right">reedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="make"><span class="idiff left right">QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o </span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="make">gapless<span class="idiff left right">PssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg</span>.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="make">mcf_substitution_matrix_stats.o <span class="nv" style="color: #008080;">$(alpObj)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="make">GappedXdropAligner<span class="idiff left right">Dna.o GappedXdropAlignerPssm</span>.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="make">GappedXdropAligner<span class="idiff left right">2qual.o GappedXdropAligner3frame.o mcf_gap_costs</span>.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make">G<span class="idiff left right">eneticCode.o GreedyXdropAligner.o LastEvaluer.o </span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="make"><span class="idiff left right">OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="make">gapless<span class="idiff left right">Xdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop</span>.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="make"><span class="idiff left right">cbrc_linalg.o </span>mcf_substitution_matrix_stats.o <span class="nv" style="color: #008080;">$(alpObj)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="make"><span class="nv" style="color: #008080;">alignObj4</span> <span class="o" style="font-weight: 600;">=</span> Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="make">DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="146" 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">@@ -146,9 +145,9 @@ depend:</td>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mv </span>m makefile</span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="make"><span class="nl">Alignment.o Alignment.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Alignment.cc Alignment.hh ScoreMatrixRow.hh SegmentPair.hh </span>\</span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_gap_costs.hh Alphabet.hh Centroid.hh GappedXdropAligner.hh </span>\</span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_<span class="idiff left right">simd.hh OneQualityScoreMatrix</span>.hh </span>\</span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> <span class="idiff left right">mcf_substitution_matrix_stats.hh GeneticCode.hh GreedyXdropAligner</span>.hh </span>\</span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> TwoQualityScoreMatrix.hh</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_<span class="idiff left right">reverse_queue.hh mcf_simd</span>.hh </span>\</span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> <span class="idiff left right">OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh GeneticCode</span>.hh </span>\</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> <span class="idiff left right">GreedyXdropAligner.hh </span>TwoQualityScoreMatrix.hh</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="make"><span class="nl">AlignmentPot.o AlignmentPot.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">AlignmentPot.cc AlignmentPot.hh Alignment.hh </span>\</span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> ScoreMatrixRow.hh SegmentPair.hh mcf_gap_costs.hh</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="make"><span class="nl">AlignmentWrite.o AlignmentWrite.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">AlignmentWrite.cc Alignment.hh ScoreMatrixRow.hh </span>\</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" 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="158" 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">@@ -159,28 +158,32 @@ AlignmentWrite.o AlignmentWrite.o8: AlignmentWrite.cc Alignment.hh ScoreMatrixRo</td>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> Alphabet.hh</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="make"><span class="nl">Alphabet.o Alphabet.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Alphabet.cc Alphabet.hh</span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="make"><span class="nl">Centroid.o Centroid.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Centroid.cc Centroid.hh GappedXdropAligner.hh </span>\</span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_simd.hh ScoreMatrixRow.hh mcf_gap_costs.hh </span>\</span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> SegmentPair.hh OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh </span>\</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_reverse_queue.hh mcf_simd.hh </span>\</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> ScoreMatrixRow.hh mcf_gap_costs.hh SegmentPair.hh </span>\</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh </span>\</span>
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164
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAlignerInl.hh</span></span>
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165
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="make"><span class="nl">CyclicSubsetSeed.o CyclicSubsetSeed.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">CyclicSubsetSeed.cc CyclicSubsetSeed.hh </span>\</span>
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166
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> CyclicSubsetSeedData.hh zio.hh mcf_zstream.hh stringify.hh</span></span>
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167
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="make"><span class="nl">DiagonalTable.o DiagonalTable.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">DiagonalTable.cc DiagonalTable.hh</span></span>
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168
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="make"><span class="nl">GappedXdropAligner.o GappedXdropAligner.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">GappedXdropAligner.cc GappedXdropAligner.hh </span>\</span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_<span class="idiff left right">simd.hh ScoreMatrixRow</span>.hh </span>\</span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAlignerInl.hh</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_<span class="idiff left right">reverse_queue.hh mcf_simd</span>.hh </span>\</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> <span class="idiff left right">ScoreMatrixRow.hh </span>GappedXdropAlignerInl.hh</span></span>
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171
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="make"><span class="nl">GappedXdropAligner2qual.o GappedXdropAligner2qual.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">GappedXdropAligner2qual.cc </span>\</span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_<span class="idiff left right">simd</span>.hh </span>\</span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> <span class="idiff left right">ScoreMatrixRow.hh GappedXdropAlignerInl.hh TwoQualityScoreMatrix</span>.hh </span>\</span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_substitution_matrix_stats.hh</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_<span class="idiff left right">reverse_queue</span>.hh </span>\</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> <span class="idiff left right">mcf_simd.hh ScoreMatrixRow.hh GappedXdropAlignerInl</span>.hh </span>\</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> <span class="idiff left right">TwoQualityScoreMatrix.hh </span>mcf_substitution_matrix_stats.hh</span></span>
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175
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="make"><span class="nl">GappedXdropAligner3frame.o GappedXdropAligner3frame.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">GappedXdropAligner3frame.cc </span>\</span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_<span class="idiff left right">simd</span>.hh </span>\</span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> ScoreMatrixRow.hh GappedXdropAlignerInl.hh</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_<span class="idiff left right">reverse_queue</span>.hh </span>\</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> <span class="idiff left right">mcf_simd.hh </span>ScoreMatrixRow.hh GappedXdropAlignerInl.hh</span></span>
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178
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="make"><span class="nl">GappedXdropAligner3framePssm.o GappedXdropAligner3framePssm.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">GappedXdropAligner3framePssm.cc </span>\</span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_simd.hh </span>\</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_reverse_queue.hh </span>\</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_simd.hh ScoreMatrixRow.hh GappedXdropAlignerInl.hh</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="make"><span class="nl">GappedXdropAlignerDna.o GappedXdropAlignerDna.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">GappedXdropAlignerDna.cc GappedXdropAligner.hh </span>\</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_reverse_queue.hh mcf_simd.hh </span>\</span>
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180
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> ScoreMatrixRow.hh GappedXdropAlignerInl.hh</span></span>
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181
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="make"><span class="nl">GappedXdropAlignerPssm.o GappedXdropAlignerPssm.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">GappedXdropAlignerPssm.cc GappedXdropAligner.hh </span>\</span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_<span class="idiff left right">simd.hh ScoreMatrixRow</span>.hh </span>\</span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAlignerInl.hh</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_<span class="idiff left right">reverse_queue.hh mcf_simd</span>.hh </span>\</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> <span class="idiff left right">ScoreMatrixRow.hh </span>GappedXdropAlignerInl.hh</span></span>
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184
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="make"><span class="nl">GeneticCode.o GeneticCode.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">GeneticCode.cc GeneticCode.hh GeneticCodeData.hh </span>\</span>
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185
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> Alphabet.hh zio.hh mcf_zstream.hh</span></span>
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186
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="make"><span class="nl">GreedyXdropAligner.o GreedyXdropAligner.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">GreedyXdropAligner.cc GreedyXdropAligner.hh </span>\</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="204" 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="207" 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">@@ -204,8 +207,9 @@ OneQualityScoreMatrix.o OneQualityScoreMatrix.o8: OneQualityScoreMatrix.cc \</td>
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204
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207
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<pre style="margin: 0;"> <span id="LC207" 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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205
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<pre style="margin: 0;"> <span id="LC208" 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="LC209" 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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207
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<pre style="margin: 0;">-<span id="LC207" 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="LC208" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> qualityScoreUtil.hh stringify.hh zio.hh mcf_zstream.hh</span></span>
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<pre style="margin: 0;">+<span id="LC210" 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 ScoreMatrixRow.hh </span>\</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> ScoreMatrixData.hh qualityScoreUtil.hh stringify.hh zio.hh </span>\</span>
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212
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<pre style="margin: 0;">+<span id="LC212" 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="LC213" 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="LC214" 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="LC215" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="244" 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="248" 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">@@ -244,11 +248,12 @@ lastal.o lastal.o8: lastal.cc last.hh Alphabet.hh MultiSequence.hh \</td>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> alp/sls_falp_alignment_evaluer.hpp alp/sls_fsa1_pvalues.hpp </span>\</span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GeneticCode.hh SubsetMinimizerFinder.hh SubsetSuffixArray.hh </span>\</span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> CyclicSubsetSeed.hh Centroid.hh GappedXdropAligner.hh </span>\</span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_simd.hh mcf_gap_costs.hh SegmentPair.hh </span>\</span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> AlignmentPot.hh Alignment.hh SegmentPairPot.hh ScoreMatrix.hh </span>\</span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> TantanMasker.hh tantan.hh DiagonalTable.hh GreedyXdropAligner.hh </span>\</span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> gaplessXdrop.hh gaplessPssmXdrop.hh gaplessTwoQualityXdrop.hh zio.hh </span>\</span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_zstream.hh threadUtil.hh version.hh</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_reverse_queue.hh mcf_simd.hh </span>\</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_gap_costs.hh SegmentPair.hh AlignmentPot.hh Alignment.hh </span>\</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> SegmentPairPot.hh ScoreMatrix.hh TantanMasker.hh tantan.hh </span>\</span>
</pre>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> DiagonalTable.hh GreedyXdropAligner.hh gaplessXdrop.hh </span>\</span>
</pre>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> gaplessPssmXdrop.hh gaplessTwoQualityXdrop.hh zio.hh mcf_zstream.hh </span>\</span>
</pre>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> threadUtil.hh version.hh</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="make"><span class="nl">lastdb.o lastdb.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">lastdb.cc last.hh Alphabet.hh MultiSequence.hh </span>\</span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> ScoreMatrixRow.hh VectorOrMmap.hh Mmap.hh fileMap.hh stringify.hh </span>\</span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> SequenceFormat.hh qualityScoreUtil.hh LastdbArguments.hh </span>\</span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#41d595f670dd7b4262c1bb10368de0bd8264c46a"><strong>src/mcf_contiguous_queue.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">@@ -13,25 +13,19 @@ template <typename T> class ContiguousQueue {</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">clear</span><span class="p">()</span> <span class="p">{</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"> <span class="n" style="color: #333;">start</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="LC16" class="line" lang="cpp"> <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="LC19" 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="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;">start</span> <span class="o" style="font-weight: 600;">+</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="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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">push</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">item</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">newStart</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;">size_t</span> <span class="n" style="color: #333;">oldSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newStart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</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;">oldSize</span> <span class="o" style="font-weight: 600;">></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;">2</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;">v</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">oldSize</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;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newStart</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">push</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">item</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfOldItemsToKeep</span><span class="p">)</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numOfOldItemsToKeep</span> <span class="o" style="font-weight: 600;"><=</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;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">numOfOldItemsToKeep</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <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;">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;">item</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="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">&</span><span class="k" style="font-weight: 600;"><span class="idiff left">operator</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[]</span></span><span class="idiff"> </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">n</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </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">n</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">start</span></span><span class="p">];</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;">const</span> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;"><span class="idiff left">fromEnd</span></span><span class="p"><span class="idiff">(</span></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">n</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </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">end</span></span><span class="p"><span class="idiff">()[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff right">n</span></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>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="nl">private:</span></span>
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<pre style="margin: 0;"> <span id="LC28" 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;">T</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="LC34" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="p">};</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="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#8266f3ec3e8e19e5efa1a2f239f8ba579e89eb00"><strong>src/mcf_gap_costs.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">@@ -39,6 +39,9 @@ void GapCosts::assign(const std::vector<int> &delOpenCosts,</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">pairCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openCost</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growCost</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">insPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openCost</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growCost</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 class="n" style="color: #333;">isAffine</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">delPieces</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;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">insPieces</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;">2</span> <span class="o" style="font-weight: 600;">&&</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">pairCost</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">delPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growCost</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growCost</span> <span class="o" style="font-weight: 600;">+</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;">max</span><span class="p">(</span><span class="n" style="color: #333;">delPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">insPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openCost</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"></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;">GapCosts</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cost</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">refInsertLen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qryInsertLen</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</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">@@ -31,6 +31,8 @@ struct GapCosts {</td>
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<pre style="margin: 0;"> <span id="LC31" 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;">Piece</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">insPieces</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;">int</span> <span class="n" style="color: #333;">pairCost</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffine</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Assign piecewise linear open and grow costs, and one pairCost.</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If unalignedPairCost <= 0, assign non-generalized costs.</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Throw a runtime_error if any growCost is <= 0.</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Author: Martin C. Frith 2019</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// SPDX-License-Identifier: GPL-3.0-or-later</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;">#ifndef MCF_REVERSE_QUEUE</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;">#define MCF_REVERSE_QUEUE</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 <new></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 <stdlib.h></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">mcf</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ReverseQueue</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"> <span class="n" style="color: #333;">ReverseQueue</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">buf</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</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 class="n" style="color: #333;">end</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">clear</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="n" style="color: #333;">beg</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="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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">push</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">item</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">numOfOldItemsToKeep</span><span class="p">)</span> <span class="p">{</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">buf</span><span class="p">)</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">len</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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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numOfOldItemsToKeep</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</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;">beg</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;">numOfOldItemsToKeep</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="n" style="color: #333;">numOfOldItemsToKeep</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">T</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 class="k" style="font-weight: 600;">else</span> <span class="p">{</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;">size_t</span> <span class="n" style="color: #333;">newLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">128</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">newBytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">T</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;">newBytes</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">))</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bad_alloc</span><span class="p">();</span></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="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;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">newBytes</span><span class="p">);</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" 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;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bad_alloc</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">end</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="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">newLen</span><span class="p">;</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">beg</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;">numOfOldItemsToKeep</span><span class="p">;</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="n" style="color: #333;">numOfOldItemsToKeep</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">));</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">buf</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="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="p">}</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="p">}</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <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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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <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;">item</span><span class="p">;</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="p">}</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">ReverseQueue</span><span class="p">()</span> <span class="p">{</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="p">}</span></span>
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51
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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="nl">private:</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="p">;</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">T</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="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">T</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="LC56" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"></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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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#649c21f7a438af6deba63905bb1e34fc0783b83b"><strong>src/mcf_simd.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">@@ -8,11 +8,20 @@</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">mcf</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#if defined __AVX2__</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;">#if defined WANT_AVX2</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;">#if defined __AVX2__</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">__m256i</span> <span class="n" style="color: #333;">SimdInt</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdBytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdZero</span><span class="p">()</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;">return</span> <span class="n" style="color: #333;">_mm256_setzero_si256</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="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdOnes</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;">_mm256_set1_epi32</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="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="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</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;">_mm256_loadu_si256</span><span class="p">((</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="o" style="font-weight: 600;">*</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="LC27" 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">@@ -21,37 +30,112 @@ static inline void simdStore(void *p, SimdInt x) {</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm256_storeu_si256</span><span class="p">((</span><span class="n" style="color: #333;">SimdInt</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="p">}</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="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdOr</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_or_si256</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="LC35" class="line" lang="cpp"><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="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdBlend</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mask</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;">return</span> <span class="n" style="color: #333;">_mm256_blendv_epi8</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="n" style="color: #333;">mask</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdLen2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSet</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i7</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i6</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i5</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i4</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_set_epi32</span><span class="p">(</span><span class="n" style="color: #333;">i7</span><span class="p">,</span> <span class="n" style="color: #333;">i6</span><span class="p">,</span> <span class="n" style="color: #333;">i5</span><span class="p">,</span> <span class="n" style="color: #333;">i4</span><span class="p">,</span> <span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="n" style="color: #333;">i0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC48" 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;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSet1</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSet2</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">iF</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">iE</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">iD</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">iC</span><span class="p">,</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;">short</span> <span class="n" style="color: #333;">iB</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">iA</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i9</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i8</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i7</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i6</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i5</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i4</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="52" 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="LC52" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_set_epi16</span><span class="p">(</span><span class="n" style="color: #333;">iF</span><span class="p">,</span> <span class="n" style="color: #333;">iE</span><span class="p">,</span> <span class="n" style="color: #333;">iD</span><span class="p">,</span> <span class="n" style="color: #333;">iC</span><span class="p">,</span> <span class="n" style="color: #333;">iB</span><span class="p">,</span> <span class="n" style="color: #333;">iA</span><span class="p">,</span> <span class="n" style="color: #333;">i9</span><span class="p">,</span> <span class="n" style="color: #333;">i8</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="54" 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="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">i7</span><span class="p">,</span> <span class="n" style="color: #333;">i6</span><span class="p">,</span> <span class="n" style="color: #333;">i5</span><span class="p">,</span> <span class="n" style="color: #333;">i4</span><span class="p">,</span> <span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="n" style="color: #333;">i0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"><span class="p">}</span></span>
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56
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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="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSet1</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">jF</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">jE</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">jD</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">jC</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">jB</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">jA</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">j9</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">j8</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">j7</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">j6</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">j5</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">j4</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">j3</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">j2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">j1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">j0</span><span class="p">,</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iF</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iE</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iD</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iC</span><span class="p">,</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iB</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iA</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i9</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i8</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i7</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i6</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i5</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i4</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="64" 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">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_set_epi8</span><span class="p">(</span><span class="n" style="color: #333;">jF</span><span class="p">,</span> <span class="n" style="color: #333;">jE</span><span class="p">,</span> <span class="n" style="color: #333;">jD</span><span class="p">,</span> <span class="n" style="color: #333;">jC</span><span class="p">,</span> <span class="n" style="color: #333;">jB</span><span class="p">,</span> <span class="n" style="color: #333;">jA</span><span class="p">,</span> <span class="n" style="color: #333;">j9</span><span class="p">,</span> <span class="n" style="color: #333;">j8</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">j7</span><span class="p">,</span> <span class="n" style="color: #333;">j6</span><span class="p">,</span> <span class="n" style="color: #333;">j5</span><span class="p">,</span> <span class="n" style="color: #333;">j4</span><span class="p">,</span> <span class="n" style="color: #333;">j3</span><span class="p">,</span> <span class="n" style="color: #333;">j2</span><span class="p">,</span> <span class="n" style="color: #333;">j1</span><span class="p">,</span> <span class="n" style="color: #333;">j0</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="67" 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">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">iF</span><span class="p">,</span> <span class="n" style="color: #333;">iE</span><span class="p">,</span> <span class="n" style="color: #333;">iD</span><span class="p">,</span> <span class="n" style="color: #333;">iC</span><span class="p">,</span> <span class="n" style="color: #333;">iB</span><span class="p">,</span> <span class="n" style="color: #333;">iA</span><span class="p">,</span> <span class="n" style="color: #333;">i9</span><span class="p">,</span> <span class="n" style="color: #333;">i8</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">i7</span><span class="p">,</span> <span class="n" style="color: #333;">i6</span><span class="p">,</span> <span class="n" style="color: #333;">i5</span><span class="p">,</span> <span class="n" style="color: #333;">i4</span><span class="p">,</span> <span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="n" style="color: #333;">i0</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="cpp"><span class="p">}</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdFill</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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36
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_set1_epi32</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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37
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"><span class="p">}</span></span>
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38
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdFill2</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_set1_epi16</span><span class="p">(</span><span class="n" style="color: #333;">x</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="cpp"><span class="p">}</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdFill1</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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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_set1_epi8</span><span class="p">(</span><span class="n" style="color: #333;">x</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="cpp"><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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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdEq1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_cmpeq_epi8</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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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"><span class="p">}</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"></span>
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39
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<td class="diff-line-num new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdGt</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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40
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<td class="diff-line-num new_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_cmpgt_epi32</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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41
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"><span class="p">}</span></span>
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42
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdGt2</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_cmpgt_epi16</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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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"><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>
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43
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<td class="diff-line-num new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdAdd</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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44
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<td class="diff-line-num new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_add_epi32</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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45
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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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46
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdAdd2</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_add_epi16</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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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"><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>
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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;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdAdd1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_add_epi8</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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<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="p">}</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"></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="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_adds_epu8</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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<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="p">}</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"></span>
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47
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<td class="diff-line-num new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSub</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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48
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<td class="diff-line-num new_line" data-linenumber="112" 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">
112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_sub_epi32</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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49
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"><span class="p">}</span></span>
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50
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<td class="diff-line-num new_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">
114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSub2</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_sub_epi16</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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<td class="diff-line-num new new_line" data-linenumber="117" 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">
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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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSub1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="120" 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">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_sub_epi8</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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<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="cpp"><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="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="123" 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">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdLeft</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bits</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="124" 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">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_slli_epi32</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">bits</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"><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>
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51
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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;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdMax</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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52
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<td class="diff-line-num new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_max_epi32</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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53
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<td class="diff-line-num new_line" data-linenumber="129" 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">
129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"><span class="p">}</span></span>
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54
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<td class="diff-line-num 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">
130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="131" 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">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdMax2</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_max_epi16</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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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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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_min_epu8</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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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"><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>
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55
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdHorizontalMax</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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56
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<td class="diff-line-num new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">__m128i</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_castsi256_si128</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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57
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<td class="diff-line-num 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">
141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_max_epi32</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_extracti128_si256</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="144" 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">@@ -60,10 +144,40 @@ static inline int simdHorizontalMax(SimdInt x) {</td>
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60
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_cvtsi128_si32</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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61
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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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62
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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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<td class="diff-line-num new new_line" data-linenumber="147" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdHorizontalMax2</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">__m128i</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_castsi256_si128</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_max_epi16</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_extracti128_si256</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</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="150" 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">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_epi16</span><span class="p">(</span><span class="n" style="color: #333;">_mm_set1_epi16</span><span class="p">(</span><span class="mi" style="color: #099;">32767</span><span class="p">),</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_minpos_epu16</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">32767</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">_mm_extract_epi16</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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="p">}</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdHorizontalMin1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">__m128i</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_castsi256_si128</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_min_epu8</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_extracti128_si256</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</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="158" 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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_min_epu8</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_srli_epi16</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_minpos_epu16</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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<td class="diff-line-num new new_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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_extract_epi16</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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="cpp"><span class="p">}</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" 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;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdChoose1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">items</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">choices</span><span class="p">)</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm256_shuffle_epi8</span><span class="p">(</span><span class="n" style="color: #333;">items</span><span class="p">,</span> <span class="n" style="color: #333;">choices</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="p">}</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"></span>
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63
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#elif defined __SSE4_1__</span></span>
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64
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"></span>
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65
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">__m128i</span> <span class="n" style="color: #333;">SimdInt</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdBytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</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="cpp"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdZero</span><span class="p">()</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;">return</span> <span class="n" style="color: #333;">_mm_setzero_si128</span><span class="p">();</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"><span class="p">}</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdOnes</span><span class="p">()</span> <span class="p">{</span></span>
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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;">return</span> <span class="n" style="color: #333;">_mm_set1_epi32</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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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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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"></span>
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67
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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;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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68
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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69
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183
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<pre style="margin: 0;"> <span id="LC183" 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="72" 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="186" 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">@@ -72,48 +186,130 @@ static inline void simdStore(void *p, SimdInt x) {</td>
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72
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm_storeu_si128</span><span class="p">((</span><span class="n" style="color: #333;">SimdInt</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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73
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"><span class="p">}</span></span>
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74
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdOr</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></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="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_or_si128</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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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"><span class="p">}</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"></span>
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75
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<td class="diff-line-num 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">
193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdBlend</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="p">{</span></span>
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76
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<td class="diff-line-num new_line" data-linenumber="194" 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">
194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_blendv_epi8</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="n" style="color: #333;">mask</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// SSE4.1</span></span>
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77
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"><span class="p">}</span></span>
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78
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"></span>
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79
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdLen2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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80
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"></span>
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81
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSet</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i0</span><span class="p">)</span> <span class="p">{</span></span>
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82
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<td class="diff-line-num new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_set_epi32</span><span class="p">(</span><span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="n" style="color: #333;">i0</span><span class="p">);</span></span>
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83
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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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84
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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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<td class="diff-line-num old old_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSet1</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="204" 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">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSet2</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i7</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i6</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i5</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i4</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="205" 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">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">i0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="206" 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">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_set_epi16</span><span class="p">(</span><span class="n" style="color: #333;">i7</span><span class="p">,</span> <span class="n" style="color: #333;">i6</span><span class="p">,</span> <span class="n" style="color: #333;">i5</span><span class="p">,</span> <span class="n" style="color: #333;">i4</span><span class="p">,</span> <span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="n" style="color: #333;">i0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" 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">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" 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">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="209" 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">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSet1</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iF</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iE</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iD</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iC</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="210" 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">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iB</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iA</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i9</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i8</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="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i7</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i6</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i5</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i4</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="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">i0</span><span class="p">)</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="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_set_epi8</span><span class="p">(</span><span class="n" style="color: #333;">iF</span><span class="p">,</span> <span class="n" style="color: #333;">iE</span><span class="p">,</span> <span class="n" style="color: #333;">iD</span><span class="p">,</span> <span class="n" style="color: #333;">iC</span><span class="p">,</span> <span class="n" style="color: #333;">iB</span><span class="p">,</span> <span class="n" style="color: #333;">iA</span><span class="p">,</span> <span class="n" style="color: #333;">i9</span><span class="p">,</span> <span class="n" style="color: #333;">i8</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="cpp"> <span class="n" style="color: #333;">i7</span><span class="p">,</span> <span class="n" style="color: #333;">i6</span><span class="p">,</span> <span class="n" style="color: #333;">i5</span><span class="p">,</span> <span class="n" style="color: #333;">i4</span><span class="p">,</span> <span class="n" style="color: #333;">i3</span><span class="p">,</span> <span class="n" style="color: #333;">i2</span><span class="p">,</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="n" style="color: #333;">i0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="215" 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">
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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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="217" 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">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdFill</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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86
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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;">return</span> <span class="n" style="color: #333;">_mm_set1_epi32</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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87
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"><span class="p">}</span></span>
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88
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220
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<pre style="margin: 0;"> <span id="LC220" 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="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdFill2</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">x</span><span class="p">)</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;">return</span> <span class="n" style="color: #333;">_mm_set1_epi16</span><span class="p">(</span><span class="n" style="color: #333;">x</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="p">}</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdFill1</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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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;">_mm_set1_epi8</span><span class="p">(</span><span class="n" style="color: #333;">x</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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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="229" 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">
229
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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="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdEq1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_cmpeq_epi8</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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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"><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>
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89
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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;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdGt</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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90
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<td class="diff-line-num new_line" data-linenumber="234" 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">
234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</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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91
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"><span class="p">}</span></span>
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92
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<td class="diff-line-num new_line" data-linenumber="236" 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">
236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="237" 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">
237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdGt2</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="238" 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">
238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_cmpgt_epi16</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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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"><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>
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93
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<td class="diff-line-num new_line" data-linenumber="241" 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">
241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdAdd</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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94
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_add_epi32</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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95
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"><span class="p">}</span></span>
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96
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdAdd2</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="246" 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">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_add_epi16</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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<td class="diff-line-num new new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"><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>
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<td class="diff-line-num new new_line" data-linenumber="249" 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">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdAdd1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="250" 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">
250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_add_epi8</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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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"><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>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdAdds1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="254" 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">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_adds_epu8</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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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"></span>
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97
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<td class="diff-line-num new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSub</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="98" 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">
98
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<td class="diff-line-num new_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_sub_epi32</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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99
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<td class="diff-line-num new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"><span class="p">}</span></span>
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100
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<td class="diff-line-num new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="101" 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="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSub2</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="101" 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="262" 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">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_sub_epi16</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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<td class="diff-line-num new new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"><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>
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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;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdSub1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_sub_epi8</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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<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="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>
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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;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdLeft</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bits</span><span class="p">)</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_slli_epi32</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">bits</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="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" 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">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="101" 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">
101
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<td class="diff-line-num new_line" data-linenumber="273" 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">
273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdMax</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="102" 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">
102
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<td class="diff-line-num new_line" data-linenumber="274" 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">
274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_max_epi32</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="c1" style="color: #998; font-style: italic;">// SSE4.1</span></span>
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103
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"><span class="p">}</span></span>
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104
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"></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="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdMax2</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</span><span class="p">)</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;">return</span> <span class="n" style="color: #333;">_mm_max_epi16</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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<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="p">}</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"></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;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdMin1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">y</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;">return</span> <span class="n" style="color: #333;">_mm_min_epu8</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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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"><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>
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105
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<td class="diff-line-num new_line" data-linenumber="285" 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">
285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdHorizontalMax</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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106
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<td class="diff-line-num new_line" data-linenumber="286" 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">
286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdMax</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_shuffle_epi32</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="mh" style="color: #099;">0x4E</span><span class="p">));</span></span>
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107
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<td class="diff-line-num new_line" data-linenumber="287" 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">
287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdMax</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_shuffle_epi32</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="mh" style="color: #099;">0xB1</span><span class="p">));</span></span>
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108
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<td class="diff-line-num new_line" data-linenumber="288" 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">
288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_cvtsi128_si32</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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109
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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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110
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<td class="diff-line-num new_line" data-linenumber="290" 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">
290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"></span>
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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="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdHorizontalMax2</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="292" 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">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdSub2</span><span class="p">(</span><span class="n" style="color: #333;">simdFill2</span><span class="p">(</span><span class="mi" style="color: #099;">32767</span><span class="p">),</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="293" 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">
293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_minpos_epu16</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// SSE4.1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="294" 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">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">32767</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">_mm_extract_epi16</span><span class="p">(</span><span class="n" style="color: #333;">x</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="295" 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">
295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"><span class="p">}</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdHorizontalMin1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</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="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_min_epu8</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_srli_epi16</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="299" 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">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_minpos_epu16</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// SSE4.1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="300" 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">
300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_extract_epi16</span><span class="p">(</span><span class="n" style="color: #333;">x</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="301" 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">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="302" 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">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="303" 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">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">simdChoose1</span><span class="p">(</span><span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">items</span><span class="p">,</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">choices</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="304" 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">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_shuffle_epi8</span><span class="p">(</span><span class="n" style="color: #333;">items</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="p">);</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"><span class="p">}</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"></span>
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111
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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112
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"></span>
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113
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">SimdInt</span><span class="p">;</span></span>
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114
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<td class="diff-line-num new_line" data-linenumber="310" 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">
310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdLen</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 old_line" data-linenumber="115" 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">
115
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<td class="diff-line-num new_line" data-linenumber="311" 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">
311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdSet</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="116" 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">
116
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<td class="diff-line-num new_line old" data-linenumber="312" 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="LC116" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Set1</span></span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="312" 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">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simd<span class="idiff left right">Fill</span></span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">;</span> <span class="p">}</span></span>
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117
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<td class="diff-line-num new_line" data-linenumber="313" 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">
313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdLoad</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">p</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="118" 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">
118
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<td class="diff-line-num new_line" data-linenumber="314" 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">
314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">simdStore</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;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</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;">x</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">simdGt</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">y</span><span class="p">;</span> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/60c6d42fe266f0fa717ddee8358bfbb1b71731c1#69737f84c540417aafef4e696f66adcc9f92fa66"><strong>src/version.hh</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"10<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;">"10<span class="idiff left right">44</span>"</span></span></pre>
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