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<h3>
Nilesh Patra 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/4dc09e39224756822117fb8a9fed8dbdf3619956">4dc09e39</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-14T23:13:59+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1167</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#57bf262130f956caf76c405086f0815caf4e0a89">
ChangeLog.txt
</a>
</li>
<li class="file-stats">
<a href="#bf068196d49b041029d9a269a6e3d52acda15f9f">
doc/last-train.html
</a>
</li>
<li class="file-stats">
<a href="#03dd50d6a64beb7787e3bcc9eb6da79c482759d5">
doc/last-train.txt
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<li class="file-stats">
<a href="#0bf0c2b9afb77a75953faf3468b6707da7098872">
doc/lastdb.html
</a>
</li>
<li class="file-stats">
<a href="#485665224376f8470c80c62ef464a2a01e61c7e7">
doc/lastdb.txt
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<li class="file-stats">
<a href="#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0">
scripts/last-train
</a>
</li>
<li class="file-stats">
<a href="#5e55dbeefff2057b414960d9467d183920e31b8a">
src/Alignment.cc
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</li>
<li class="file-stats">
<a href="#bd17e03c676d289c9cc5bb117da6d9d2bde74764">
src/Alignment.hh
</a>
</li>
<li class="file-stats">
<a href="#8758dc959aa5524be83960d0bfd56945bc432a26">
src/AlignmentWrite.cc
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<li class="file-stats">
<a href="#ab919b3eb596acbd0affb15613fb99fee03165d8">
src/Alphabet.cc
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<li class="file-stats">
<a href="#50bbab11fc8cfa2a0b2a909b040fb5e75e3bf421">
src/Alphabet.hh
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<li class="file-stats">
<a href="#76a46dca9f85ee73b2a8d67a89f4b9bf80c34b4b">
src/Centroid.cc
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<li class="file-stats">
<a href="#7dc5c3172a020d4f7642b87bcfe987675bd222a7">
src/GappedXdropAligner.hh
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<li class="file-stats">
<a href="#aa38e532f19f245fda3e2e3b5a4ac462598ab91f">
src/GappedXdropAlignerFrame.cc
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</li>
<li class="file-stats">
<a href="#651801b243983c0404fde32d39e03c30a9dd0adc">
src/GeneticCode.cc
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<li class="file-stats">
<a href="#3c0366b16bdb441bbd5135e07608d67f42e74a37">
src/GeneticCode.hh
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<li class="file-stats">
<a href="#5f9dbaf068df9da9d036ea6546a588a0c71778be">
src/LastEvaluer.cc
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<li class="file-stats">
<a href="#8ad69f8f5b121bdf5620a1b9db78266650ef63ed">
src/LastEvaluer.hh
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<li class="file-stats">
<a href="#4b7be8c3b80efc62977b307791d1a304c23e1fa4">
src/LastalArguments.cc
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<li class="file-stats">
<a href="#c41d15f61c8e13ecbdb96a800b59fc069d2c6695">
src/LastalArguments.hh
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<li class="file-stats">
<a href="#54925a3b3158a751c06af7acce6d06070e5ac813">
src/LastdbArguments.cc
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<li class="file-stats">
<a href="#175041df6bc020fee30bcd9a8a104c617f1d9feb">
src/LastdbArguments.hh
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<li class="file-stats">
<a href="#166cfea9495f22785b4b042c1f067c32d00762cb">
src/MultiSequence.cc
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<li class="file-stats">
<a href="#de5a928be30a99dcb150a5f687171caed2e9c00c">
src/MultiSequence.hh
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<li class="file-stats">
<a href="#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">
src/lastal.cc
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</li>
<li class="file-stats">
<a href="#de4252990d12a909e50ff0b994d1715eae0ea5fd">
src/lastdb.cc
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<li class="file-stats">
<a href="#b8658dba55bc28b741dfef5e4ea001b2623bdb9e">
src/mcf_frameshift_xdrop_aligner.cc
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<li class="file-stats">
<a href="#7b7b86f617ae717ef44a71c27b54fe7b613973d1">
src/mcf_frameshift_xdrop_aligner.hh
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</li>
<li class="file-stats">
<a href="#f9ba055bb143316361a1f420366c034ad9589728">
src/mcf_substitution_matrix_stats.cc
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</li>
<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/4dc09e39224756822117fb8a9fed8dbdf3619956#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2020-12-11 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/GeneticCode.cc, src/GeneticCode.hh, src/lastal.cc, test/last-</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> 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"> Better rep-masking for codons & new frameshifts</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> [c1fbf7da4f68] [tip]</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> * src/GappedXdropAlignerFrame.cc, src/GeneticCode.cc,</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> src/GeneticCode.hh, src/lastal.cc:</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> Refactor</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"> [f0ef1bb760a6]</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></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">2020-12-04 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * doc/last-train.txt, scripts/last-train:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Add last-train --scale option</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> [f8298e7154b0]</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">2020-12-03 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> * scripts/last-train:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> [8d973000becc]</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> * src/GappedXdropAligner.hh, src/GappedXdropAlignerFrame.cc:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> [f85ac4b37611]</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/mcf_frameshift_xdrop_aligner.cc:</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> Change expected-count output for new frameshifts</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> [6295d6a32b28]</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> * src/Centroid.cc:</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> [ee8f8ed3fd4e]</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> * scripts/last-train:</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> [e35d9df1d54c]</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> * doc/lastdb.txt, src/Alphabet.cc, src/Alphabet.hh,</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> src/LastdbArguments.cc, src/LastdbArguments.hh,</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> src/MultiSequence.cc, src/MultiSequence.hh, src/lastdb.cc,</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> src/mcf_substitution_matrix_stats.cc, test/last-test.out, test/last-</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> test.sh:</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> Add lastdb -q option</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> [74ad9d8977ec]</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">2020-12-02 Martin C. Frith <Martin C. Frith></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> * src/lastal.cc, test/last-test.out, test/last-test.sh:</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> Protein-codon alignment: use tantan on the DNA</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> [8ac7c496f9be]</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> * src/Alignment.cc, src/Alignment.hh, src/AlignmentWrite.cc,</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> src/LastEvaluer.cc, src/LastEvaluer.hh, src/lastal.cc, test/last-</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> test.out, test/last-test.sh:</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> E-values for new-style frameshifts!</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> [fffb08324c7d]</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">2020-12-01 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> * src/mcf_frameshift_xdrop_aligner.cc,</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> src/mcf_frameshift_xdrop_aligner.hh:</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> Start implementing frameshift E-value simulation</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> [d73a654fdabb]</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> * src/LastalArguments.cc, src/LastalArguments.hh, src/lastal.cc:</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> Allow for non-integer alignment scores</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> [4bc305f33933]</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">2020-11-30 Martin C. Frith <Martin C. Frith></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> * src/LastEvaluer.cc, src/LastEvaluer.hh, src/lastal.cc:</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> Refactor</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> [f5a5aed6d38e]</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> * src/AlignmentWrite.cc, src/LastEvaluer.cc, src/LastalArguments.cc:</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> Refactor</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> [49942e88c59e]</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">2020-11-27 Martin C. Frith <Martin C. Frith></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> * src/AlignmentWrite.cc:</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> Protein-codon alignment: fix writing X and *</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> [922917aa2dd8]</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">2020-11-26 Martin C. Frith <Martin C. Frith></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> * src/lastal.cc:</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> Reduce lastal memory use, sometimes</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> [bc682cb4f508]</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> * src/LastEvaluer.cc, test/last-test.out:</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> Fix minor bugs in E-value finite-size correction</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> [8d49928d5e10]</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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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> * src/LastEvaluer.cc, src/LastEvaluer.hh:</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> Refactor</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> [814e3863ab23]</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> * scripts/last-train:</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> Refactor</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> [a1e4ab7fd745]</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> * scripts/last-train:</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> Refactor</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> [70149e6fb67a]</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">2020-11-25 Martin C. Frith <Martin C. Frith></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> * scripts/last-train, src/lastal.cc:</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> Refactor</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> [249167a86543]</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"></span>
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1
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">2020-11-06 Martin C. Frith <Martin C. Frith></span>
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2
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"></span>
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3
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"> * src/mcf_frameshift_xdrop_aligner.hh:</span>
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4
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"> Try to appease C++ compilers</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> [62a147543f2b]<span class="idiff left right"> [tip]</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> [62a147543f2b]</span>
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<td class="diff-line-num old_line" data-linenumber="6" 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">
6
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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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7
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"> * doc/last-split.txt:</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext"> Add awk mismap trick to doc</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">@@ -392,6 +392,13 @@ shorter, it is never picked. 0 means use everything.</td></tr></td>
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>--sample-length=<span class="nt" style="color: #000080;"><var></span>L<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Use randomly-chosen chunks of length L.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>--scale=<span class="nt" style="color: #000080;"><var></span>S<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Output scores in units of 1/S bits. Traditional values</span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="html">include 2 for half-bit scores and 3 for 1/3-bit scores.</span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="html">(Note that 1/3-bit scores essentially equal Phred scores</span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="html">a.k.a. decibans, because log10(2) ≈ 3/10.) The default is to</span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="html">infer a scale from the initial score parameters.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="html"><span class="nt" style="color: #000080;"></tbody></span></span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="html"><span class="nt" style="color: #000080;"></table></span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="html"><span class="nt" style="color: #000080;"></blockquote></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">@@ -524,11 +531,6 @@ output, so it will override lastal's default.</p></td>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>last-train (and lastal) converts between path and alignment</span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="html">parameters as in Supplementary Section 3.1 of <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://doi.org/10.1093/bioinformatics/btz576"</span><span class="nt" style="color: #000080;">></span>btz576<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>last-train converts probabilities to scores using an arbitrary scale</span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="html">factor. (If all the scores are multiplied by any positive constant,</span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="html">it makes no difference to alignment.) This scale is determined by</span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="html">the initial score parameters.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>last-train uses parameters with <span class="ni" style="color: #800080;">"</span>homogeneous letter probabilities<span class="ni" style="color: #800080;">"</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="html">and <span class="ni" style="color: #800080;">"</span>balanced length probability<span class="ni" style="color: #800080;">"</span> (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://doi.org/10.1093/bioinformatics/btz576"</span><span class="nt" style="color: #000080;">></span>btz576<span class="nt" style="color: #000080;"></a></span>).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="html"><span class="nt" style="color: #000080;"></li></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">@@ -536,8 +538,8 @@ and "balanced length probability" (<a class="reference external" href=</td>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="html">inaccurate. It then finds an adjusted scale factor (without</span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="html">changing the scores), which makes the integer-rounded scores</span>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="html">correspond to homogeneous letter probabilities and balanced length</span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="html">probability. It writes this adjusted scale <span class="idiff left">as a </span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">-t</span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff right"> option for</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="html">lastal, e.g. <span class="ni" style="color: #800080;">"</span>-t4.4363<span class="ni" style="color: #800080;">"</span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="html">probability. It writes this adjusted scale <span class="idiff left right">(in nats, not bits) as a</span></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="html"><span class="ni" style="color: #800080;"><span class="idiff left">"</span></span><span class="idiff">-t</span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff right"> option for </span>lastal, e.g. <span class="ni" style="color: #800080;">"</span>-t4.4363<span class="ni" style="color: #800080;">"</span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>In rare cases, it may be impossible to find such an adjusted scale</span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="html">factor. If that happens, last-train doubles the original scale (to</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#03dd50d6a64beb7787e3bcc9eb6da79c482759d5"><strong>doc/last-train.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,6 +59,12 @@ Training options</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> shorter, it is never picked. 0 means use everything.</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> --sample-length=L</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> Use randomly-chosen chunks of length L.</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> --scale=S</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> Output scores in units of 1/S bits. Traditional values</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> include 2 for half-bit scores and 3 for 1/3-bit scores.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> (Note that 1/3-bit scores essentially equal Phred scores</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> a.k.a. decibans, because log10(2) ≈ 3/10.) The default is to</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> infer a scale from the initial score parameters.</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">All options below this point are passed to lastal to do the</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">alignments: they are described in more detail at `<lastal.html>`_.</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">@@ -142,11 +148,6 @@ Details</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext">* last-train (and lastal) converts between path and alignment</span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"> parameters as in Supplementary Section 3.1 of btz576_.</span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext">* last-train converts probabilities to scores using an arbitrary scale</span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"> factor. (If all the scores are multiplied by any positive constant,</span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext"> it makes no difference to alignment.) This scale is determined by</span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext"> the initial score parameters.</span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext">* last-train uses parameters with "homogeneous letter probabilities"</span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"> and "balanced length probability" (btz576_).</span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"></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">@@ -154,8 +155,8 @@ Details</td>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext"> inaccurate. It then finds an adjusted scale factor (without</span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext"> changing the scores), which makes the integer-rounded scores</span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext"> correspond to homogeneous letter probabilities and balanced length</span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="plaintext"> probability. It writes this adjusted scale <span class="idiff left right">as a "-t" option for</span></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext"> lastal, e.g. "-t4.4363".</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> probability. It writes this adjusted scale <span class="idiff left right">(in nats, not bits) as a</span></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"> <span class="idiff left right">"-t" option for </span>lastal, e.g. "-t4.4363".</span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext">* In rare cases, it may be impossible to find such an adjusted scale</span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext"> factor. If that happens, last-train doubles the original scale (to</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">@@ -469,6 +469,10 @@ Default fasta</td>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: #000080;">></span>The fastq formats are described in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal.html<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="html"><span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-q<span class="nt" style="color: #000080;"></span></kbd></td></span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Interpret the sequences as proteins, use a 21-letter alphabet</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="html">with <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>*<span class="nt" style="color: #000080;"></tt></span> meaning STOP, and append <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>*<span class="nt" style="color: #000080;"></tt></span> to each sequence.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-P <span class="nt" style="color: #000080;"><var></span>THREADS<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Divide the work between this number of threads running in</span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="html">parallel. 0 means use as many threads as your computer claims</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">@@ -594,9 +598,12 @@ bytes.</p></td>
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>lastdb8: makes the index twice as big.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>-u, -m: Multiple patterns multiply the index size. For example,</span>
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>-u, -m<span class="idiff left right">, -d</span>: Multiple patterns multiply the index size. For example,</span>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-seeds.html"</span><span class="nt" style="color: #000080;">></span>MAM8<span class="nt" style="color: #000080;"></a></span> makes it 8 times bigger.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>-u, -d: may reduce the index, e.g. <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-seeds.html"</span><span class="nt" style="color: #000080;">></span>RY32<span class="nt" style="color: #000080;"></a></span> makes</span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="html">it 32 times smaller.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>-s: does not change the total size, but splits it into volumes.<span class="nt" style="color: #000080;"></p></span></span>
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601
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608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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602
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>-S2: doubles the size of everything.<span class="nt" style="color: #000080;"></p></span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#485665224376f8470c80c62ef464a2a01e61c7e7"><strong>doc/lastdb.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -136,6 +136,9 @@ Advanced Options</td>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"> The fastq formats are described in `<lastal.html>`_.</span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> -q Interpret the sequences as proteins, use a 21-letter alphabet</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> with ``*`` meaning STOP, and append ``*`` to each sequence.</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext"> -P THREADS</span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext"> Divide the work between this number of threads running in</span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="plaintext"> parallel. 0 means use as many threads as your computer claims</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">@@ -258,9 +261,12 @@ This is modified by several options.</td>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="plaintext">* lastdb8: makes the index twice as big.</span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="plaintext"></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="plaintext">* -u, -m: Multiple patterns multiply the index size. For example,</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">* -u, -m<span class="idiff left right">, -d</span>: Multiple patterns multiply the index size. For example,</span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="plaintext"> `MAM8 <last-seeds.html>`_ makes it 8 times bigger.</span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">* -u, -d: may reduce the index, e.g. `RY32 <last-seeds.html>`_ makes</span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> it 32 times smaller.</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"></span>
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="plaintext">* -s: does not change the total size, but splits it into volumes.</span>
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265
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="plaintext"></span>
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266
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="plaintext">* -S2: doubles the size of everything.</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0"><strong>scripts/last-train</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">@@ -6,7 +6,7 @@</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># [Fri19] How sequence alignment scores correspond to probability models,</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># MC Frith, Bioinformatics, 2019.</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;"><span class="idiff left">division</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">print_function</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">math</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">@@ -18,6 +18,8 @@ import subprocess</td>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="n" style="color: #333;">proteinAlphabet20</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACDEFGHIKLMNPQRSTVWY"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># faster than fileinput</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdin</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">@@ -25,7 +27,7 @@ def myOpen(fileName): # faster than fileinput</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="s" style="color: #d14;">"rt"</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># xxx dubious for Python2</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rootOfIncreasingFunction</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">,</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">,</span> <span class="n" style="color: #333;">upperBound</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rootOfIncreasingFunction</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">,</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">,</span> <span class="n" style="color: #333;">upperBound</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Find x such that func(x, *args) == 0</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">upperBound</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">@@ -36,6 +38,17 @@ def rootOfIncreasingFunction(func, lowerBound, upperBound, *args):</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rootOfDecreasingFunction</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">,</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">,</span> <span class="n" style="color: #333;">upperBound</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Find x such that func(x, *args) == 0</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">upperBound</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">lowerBound</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">upperBound</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mid</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">func</span><span class="p">(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">homogeneousLetterFreqs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Solve the simultaneous equations in Section 2.1 of [Fri19]</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">expMat</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matScores</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">@@ -162,13 +175,6 @@ def getSeqSample(opts, queryFiles, outfile):</td>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <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>
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">writeSegment</span><span class="p">(</span><span class="n" style="color: #333;">outfile</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="LC177" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">versionFromHeader</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">words</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"version"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">words</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">words</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="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"couldn't read the version"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">scaleFromHeader</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</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">@@ -177,41 +183,38 @@ def scaleFromHeader(lines):</td>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"couldn't read the scale"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">countsFromLastOutput</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">numTransitionCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># use +1 pseudocounts as a kludge to mitigate numerical problems:</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">deletes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0</span> <span class="c1" style="color: #998; font-style: italic;"># 1 open + 1 extension</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">inserts</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0</span> <span class="c1" style="color: #998; font-style: italic;"># 1 open + 1 extension</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">delOpens</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">insOpens</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">nTransitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">tranCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nTransitions</span> <span class="c1" style="color: #998; font-style: italic;"># +1 pseudocounts</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">tranCounts</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="mf" style="color: #099;">2.0</span> <span class="c1" style="color: #998; font-style: italic;"># deletes: opens + extensions, so 2 pseudocounts</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">tranCounts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0</span> <span class="c1" style="color: #998; font-style: italic;"># inserts: opens + extensions, so 2 pseudocounts</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">countMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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188
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># no pseudocount here</span></span>
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189
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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190
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"s"</span><span class="p">:</span></span>
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191
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># slow?</span></span>
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192
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"c"</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="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">1</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="python"> <span class="n" style="color: #333;">transCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">numTransitionCounts</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="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">matrix</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">numTransitionCounts</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="mf" style="color: #099;">1.0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrixSize</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</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="python"> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">c</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;">matrixSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</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="python"> <span class="n" style="color: #333;">alignmentLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transCounts</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;">transCounts</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;">transCounts</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="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">pid</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignmentLength</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</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="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</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="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">S</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"0"</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="python"> <span class="n" style="color: #333;">matrix</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;">c</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;">matrixSize</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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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</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="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">countMatrix</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="python"> <span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nTransitions</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">nCols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</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="python"> <span class="n" style="color: #333;">nRows</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">//</span> <span class="n" style="color: #333;">nCols</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">countMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="mf" style="color: #099;">1.0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nCols</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nRows</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="python"> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">counts</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;">nCols</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nRows</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="python"> <span class="n" style="color: #333;">alignmentLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">3</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="python"> <span class="k" style="font-weight: 600;">if</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">pid</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignmentLength</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="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nRows</span><span class="p">):</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nCols</span><span class="p">):</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">S</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"1"</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="python"> <span class="n" style="color: #333;">countMatrix</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;">counts</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;">nCols</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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205
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</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="python"> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">c</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;">matrixSize</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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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">transCounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">deletes</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">transCounts</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="python"> <span class="n" style="color: #333;">inserts</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">transCounts</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="python"> <span class="n" style="color: #333;">delOpens</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">transCounts</span><span class="p">[</span><span class="mi" style="color: #099;">3</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="python"> <span class="n" style="color: #333;">insOpens</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">transCounts</span><span class="p">[</span><span class="mi" style="color: #099;">4</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="python"> <span class="n" style="color: #333;">countMatrix</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">counts</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;">nCols</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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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nTransitions</span><span class="p">):</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">tranCounts</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;">counts</span><span class="p">[</span><span class="n" style="color: #333;">matrixSize</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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212
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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213
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<td class="diff-line-num new_line old" data-linenumber="215" 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="LC213" class="line" lang="python"> <span class="n" style="color: #333;">gapCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span><span class="p">,</span> <span class="n" style="color: #333;">deletes</span><span class="p">,</span> <span class="n" style="color: #333;">inserts</span><span class="p">,</span> <span class="n" style="color: #333;">delOpens</span><span class="p">,</span> <span class="n" style="color: #333;">insOpens</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">gapCounts</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">alignments</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"no alignments"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">countMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tranCounts</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">alignments</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">scoreFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">prob</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prob</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;">logProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">prob</span><span class="p">)</span></span>
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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">@@ -223,7 +226,7 @@ def costFromProb(scale, prob):</td>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">guessAlphabet</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"ACGT"</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">20</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;"><span class="idiff left right">"ACDEFGHIKLMNPQRSTVWY"</span></span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">20</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">proteinAlphabet20</span></span></span>
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227
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"can't handle unusual alphabets"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeMatrixHead</span><span class="p">(</span><span class="n" style="color: #333;">outFile</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet</span><span class="p">,</span> <span class="n" style="color: #333;">formatString</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">@@ -257,7 +260,6 @@ def matProbsFromCounts(counts, opts):</td>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">r</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">,</span> <span class="n" style="color: #333;">counts</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">probs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">counts</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# substitution percent identity: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# count matrix "</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">@@ -268,7 +270,6 @@ def matProbsFromCounts(counts, opts):</td>
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="s" style="color: #d14;">"(query letters = columns, reference letters = rows):"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">writeProbMatrix</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">probs</span><span class="p">,</span> <span class="s" style="color: #d14;">"# "</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">probs</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">probImbalance</span><span class="p">(</span><span class="n" style="color: #333;">endProb</span><span class="p">,</span> <span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">firstDelProb</span><span class="p">,</span> <span class="n" style="color: #333;">delExtendProb</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">@@ -282,12 +283,11 @@ def balancedEndProb(*args):</td>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">firstDelProb</span><span class="p">,</span> <span class="n" style="color: #333;">delExtendProb</span><span class="p">,</span> <span class="n" style="color: #333;">firstInsProb</span><span class="p">,</span> <span class="n" style="color: #333;">insExtendProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">delExtendProb</span><span class="p">,</span> <span class="n" style="color: #333;">insExtendProb</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">r</span><span class="idiff left"> </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">rootOfIncreasingFunction</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">probImbalance</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lowerBound</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">upperBound</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">args</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">r</span></span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">r<span class="idiff left">eturn</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rootOfIncreasingFunction</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">probImbalance</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">lowerBound</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">upperBound</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gap<span class="idiff left right">Ratio</span>sFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gap<span class="idiff left right">Prob</span>sFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">matches</span><span class="p">,</span> <span class="n" style="color: #333;">deletes</span><span class="p">,</span> <span class="n" style="color: #333;">inserts</span><span class="p">,</span> <span class="n" style="color: #333;">delOpens</span><span class="p">,</span> <span class="n" style="color: #333;">insOpens</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counts</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">alignments</span><span class="p">:</span> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"no alignments"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deletes</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">inserts</span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">gapOpens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpens</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insOpens</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">denominator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gapOpens</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># +1 pseudocount</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">@@ -295,14 +295,13 @@ def gapRatiosFromCounts(counts, opts):</td>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">gapsym</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapOpens</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">denominator</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapOpens</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">denominator</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">del<span class="idiff left right">Extend</span>Prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">gapOpens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">gaps</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">ins<span class="idiff left right">Extend</span>Prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">gapOpens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">gaps</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">del<span class="idiff left right">Grow</span>Prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">gapOpens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">gaps</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">ins<span class="idiff left right">Grow</span>Prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">gapOpens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">gaps</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpens</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">denominator</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpens</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">denominator</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">delExtendProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">deletes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delOpens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">deletes</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">insExtendProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">inserts</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insOpens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">inserts</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">delGrowProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">deletes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delOpens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">deletes</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">insGrowProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">inserts</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insOpens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">inserts</span></span>
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306
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# aligned letter pairs: %.12g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">matches</span><span class="p">)</span></span>
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307
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# deletes: %.12g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">deletes</span><span class="p">)</span></span>
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# inserts: %.12g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">inserts</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">@@ -314,29 +313,34 @@ def gapRatiosFromCounts(counts, opts):</td>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# matchProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">matchProb</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delOpenProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">delOpenProb</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insOpenProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">insOpenProb</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delExtendProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">del<span class="idiff left right">Extend</span>Prob</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insExtendProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">ins<span class="idiff left right">Extend</span>Prob</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delExtendProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">del<span class="idiff left right">Grow</span>Prob</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insExtendProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">ins<span class="idiff left right">Grow</span>Prob</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">delOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">insOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">delCloseProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delExtendProb</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gapRatiosFromProbs</span><span class="p">(</span><span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">delProbs</span><span class="p">,</span> <span class="n" style="color: #333;">insProbs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">delOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">delGrowProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delProbs</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">insOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">insGrowProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insProbs</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">delCloseProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delGrowProb</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">firstDelProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delCloseProb</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">insCloseProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins<span class="idiff left right">Extend</span>Prob</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">insCloseProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins<span class="idiff left right">Grow</span>Prob</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">firstInsProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insCloseProb</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">endProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">balancedEndProb</span><span class="p">(</span><span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">firstDelProb</span><span class="p">,</span> <span class="n" style="color: #333;">del<span class="idiff left right">Extend</span>Prob</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">firstInsProb</span><span class="p">,</span> <span class="n" style="color: #333;">ins<span class="idiff left right">Extend</span>Prob</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">endProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">balancedEndProb</span><span class="p">(</span><span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">firstDelProb</span><span class="p">,</span> <span class="n" style="color: #333;">del<span class="idiff left right">Grow</span>Prob</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">firstInsProb</span><span class="p">,</span> <span class="n" style="color: #333;">ins<span class="idiff left right">Grow</span>Prob</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># probably, endProb is negligibly less than 1</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">matchRatio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">endProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">endProb</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">firstDelRatio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">firstDelProb</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">del<span class="idiff left">ExtendRatio</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">delExtend</span>Prob</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">delRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">firstDelRatio</span><span class="p">,</span> <span class="n" style="color: #333;">del<span class="idiff left right">Extend</span>Ratio</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">del<span class="idiff left">GrowRatio</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">delGrow</span>Prob</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">delRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">firstDelRatio</span><span class="p">,</span> <span class="n" style="color: #333;">del<span class="idiff left right">Grow</span>Ratio</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">firstInsRatio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">firstInsProb</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">ins<span class="idiff left">ExtendRatio</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">insExtend</span>Prob</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">insRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">firstInsRatio</span><span class="p">,</span> <span class="n" style="color: #333;">ins<span class="idiff left right">Extend</span>Ratio</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">ins<span class="idiff left">GrowRatio</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">insGrow</span>Prob</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">insRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">firstInsRatio</span><span class="p">,</span> <span class="n" style="color: #333;">ins<span class="idiff left right">Grow</span>Ratio</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"></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">@@ -346,10 +350,8 @@ def scoreFromLetterProbs(scale, matchRatio, pairProb, rowProb, colProb):</td>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">scoreFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matchRatio</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">probRatio</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">matScoresFromProbs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">,</span> <span class="n" style="color: #333;">colProbs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">matProbs</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[[</span><span class="n" style="color: #333;">scoreFromLetterProbs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</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="LC351" class="line" lang="python"> <span class="n" style="color: #333;">rowProbs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">colProbs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">r</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">r</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[[</span><span class="n" style="color: #333;">scoreFromLetterProbs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</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="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="LC354" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">colProbs</span><span class="p">)]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">rowProbs</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gapCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">firstGapRatio</span><span class="p">,</span> <span class="n" style="color: #333;">gapExtendRatio</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The next addition gets the alignment parameter from the path</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">@@ -373,28 +375,26 @@ def scoreImbalance(scale, matScores, delCosts, insCosts):</td>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">imbalanceFromGap</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">insCosts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">homogeneousLetterFreqs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">negScoreImbalance</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">scoreImbalance</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">balancedScale</span><span class="p">(</span><span class="n" style="color: #333;">nearScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">balancedScale</span><span class="p">(</span><span class="n" style="color: #333;">imbalanceFunc</span><span class="p">,</span> <span class="n" style="color: #333;">nearScale</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Find a scale, near nearScale, with balanced length probability</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">bump</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.000001</span></span>
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreImbalance</span><span class="p">(</span><span class="n" style="color: #333;">nearScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">rootFinders</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rootOfDecreasingFunction</span><span class="p">,</span> <span class="n" style="color: #333;">rootOfIncreasingFunction</span></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">imbalanceFunc</span><span class="p">(</span><span class="n" style="color: #333;">nearScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">value</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="LC384" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nearScale</span></span>
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">oldLower</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldUpper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nearScale</span></span>
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">oldUpper</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;">nearScale</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># xxx ???</span></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">newLower</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldLower</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">bump</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">lowerValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">scoreImbalance</span></span><span class="p">(</span><span class="n" style="color: #333;">newLower</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">lowerValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">imbalanceFunc</span></span><span class="p">(</span><span class="n" style="color: #333;">newLower</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lowerValue</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="n" style="color: #333;">value</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="LC390" class="line" lang="python"> <span class="n" style="color: #333;">f<span class="idiff left">unc</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">scoreImbalance</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">value</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="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">negScoreImbalance</span></span></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">rootOfIncreasingFunction</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">func</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">newLower</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">oldLower</span></span><span class="p"><span class="idiff">,</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;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">f<span class="idiff left">inder</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">rootFinders</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">value</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="LC391" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">finder</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">imbalanceFunc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">newLower</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">oldLower</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">oldLower</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newLower</span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">newUpper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldUpper</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bump</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">upperValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">scoreImbalance</span></span><span class="p">(</span><span class="n" style="color: #333;">newUpper</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">upperValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">imbalanceFunc</span></span><span class="p">(</span><span class="n" style="color: #333;">newUpper</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">upperValue</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="n" style="color: #333;">value</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="LC396" class="line" lang="python"> <span class="n" style="color: #333;">f<span class="idiff left">unc</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">scoreImbalance</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">value</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="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">negScoreImbalance</span></span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">rootOfIncreasingFunction</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">func</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">oldUpper</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">newUpper</span></span><span class="p"><span class="idiff">,</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;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">f<span class="idiff left">inder</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">rootFinders</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">value</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="LC397" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">finder</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">imbalanceFunc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">oldUpper</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">newUpper</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"> <span class="n" style="color: #333;">oldUpper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newUpper</span></span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python"></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">@@ -403,7 +403,8 @@ def scoresAndScale(originalScale, matParams, delRatios, insRatios):</td>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matScoresFromProbs</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matParams</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">delCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">delRatios</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">insCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">balancedScale</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">balancedScale</span><span class="p">(</span><span class="n" style="color: #333;">scoreImbalance</span><span class="p">,</span> <span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">scale</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="LC409" class="line" lang="python"> <span class="n" style="color: #333;">rowFreqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">homogeneousLetterFreqs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matScores</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">colFreqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">homogeneousLetterFreqs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</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">@@ -413,20 +414,21 @@ def scoresAndScale(originalScale, matParams, delRatios, insRatios):</td>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"> <span class="s" style="color: #d14;">"doubling the scale"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">originalScale</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python"> <span class="n" style="color: #333;">firstDelCost</span><span class="p">,</span> <span class="n" style="color: #333;">delExtendCost</span><span class="p">,</span> <span class="n" style="color: #333;">firstInsCost</span><span class="p">,</span> <span class="n" style="color: #333;">insExtendCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -a"</span><span class="p">,</span> <span class="n" style="color: #333;">firstDelCost</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delExtendCost</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -A"</span><span class="p">,</span> <span class="n" style="color: #333;">firstInsCost</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insExtendCost</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -b"</span><span class="p">,</span> <span class="n" style="color: #333;">delExtendCost</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -B"</span><span class="p">,</span> <span class="n" style="color: #333;">insExtendCost</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">gapCosts</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">firstDelCost</span><span class="p">,</span> <span class="n" style="color: #333;">delExtendCost</span><span class="p">,</span> <span class="n" style="color: #333;">firstInsCost</span><span class="p">,</span> <span class="n" style="color: #333;">insExtendCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delExistCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">firstDelCost</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delExtendCost</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insExistCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">firstInsCost</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insExtendCost</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delExtendCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">delExtendCost</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insExtendCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">insExtendCost</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">isLastFormat</span><span class="p">,</span> <span class="n" style="color: #333;">outFile</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">delInit</span><span class="p">,</span> <span class="n" style="color: #333;">delGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delCosts</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">insInit</span><span class="p">,</span> <span class="n" style="color: #333;">insGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insCosts</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">delOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delGrow</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">insOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insGrow</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isLastFormat</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -a"</span><span class="p">,</span> <span class="n" style="color: #333;">delOpen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -A"</span><span class="p">,</span> <span class="n" style="color: #333;">insOpen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -b"</span><span class="p">,</span> <span class="n" style="color: #333;">delGrow</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -B"</span><span class="p">,</span> <span class="n" style="color: #333;">insGrow</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delExistCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">delOpen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insExistCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">insOpen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delExtendCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">delGrow</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insExtendCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">insGrow</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tryToMakeChildProgramsFindable</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</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">@@ -458,29 +460,46 @@ def fixedLastalArgs(opts, lastalProgName):</td>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"v"</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span></span>
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461
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span></span>
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462
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">inStream</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">inStream</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">universal_newlines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">versionFromLastal</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"lastal"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--version"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">().</span><span class="n" style="color: #333;">split</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="LC471" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">lastSplitProcess</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">splitArgs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"last-split"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-n"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m0.01"</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># xxx ???</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="p">(</span><span class="n" style="color: #333;">splitArgs</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">postmask</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">maskArgs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"last-postmask"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="p">(</span><span class="n" style="color: #333;">maskArgs</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">proc</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">doTraining</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python"> <span class="n" style="color: #333;">tryToMakeChildProgramsFindable</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">lastalProgName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readLastalProgName</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"> <span class="n" style="color: #333;">scaleIncrease</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20</span> <span class="c1" style="color: #998; font-style: italic;"># while training, up-scale the scores by this amount</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">x</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">fixedLastalArgs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">lastalProgName</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-r"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">q</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-q"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">q</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">p</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-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="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">p</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">a</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-a"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">a</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">b</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-b"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">b</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">A</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-A"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">A</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">B</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-B"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">B</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">x</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">args</span></span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">y</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"last-split"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-n"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-m0.01"</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># xxx ???</span></span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">z</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"last-postmask"</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="idiff left"> </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">subprocess</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Popen</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">stdout</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">subprocess</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">PIPE</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">universal_newlines</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">Tru</span>e</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">q</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">subprocess</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Popen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">stdin</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stdout</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">stdout</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">subprocess</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">PIPE</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="python"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">universal_newlines</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">postmask</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">q</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">subprocess</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Popen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">z</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">stdin</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">q</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stdout</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">stdout</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">subprocess</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">PIPE</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">universal_newlines</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">lastalVersion</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">versionFromHeader</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">q</span></span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="python"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">externalScale</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">scaleFromHeader</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">q</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stdout</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">lastalVersion</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">versionFromLastal</span></span><span class="p"><span class="idiff right">(</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">lastalArgs</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">fixedLastalArgs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">lastalProgName</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">r</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lastalArgs</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-r"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">r</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">q</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lastalArgs</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-q"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">q</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">p</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lastalArgs</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-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="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">p</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">a</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lastalArgs</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-a"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">a</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">b</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lastalArgs</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-b"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">b</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">A</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lastalArgs</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-A"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">A</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">B</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lastalArgs</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-B"</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">B</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">lastalArgs</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">args</span></span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">p<span class="idiff left">roc</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">process</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lastalArgs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">Non</span>e</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">proc</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">lastSplitProcess</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">proc</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">scale</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">externalScale</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">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">scale</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">math</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">log</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">else</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">externalScale</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">scaleFromHeader</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">proc</span></span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">internalScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">externalScale</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaleIncrease</span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python"> <span class="n" style="color: #333;">oldParameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="python"></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">@@ -491,18 +510,20 @@ def doTraining(opts, args):</td>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left right">lastalArgs</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="python"> <span class="n" style="color: #333;">matCounts</span><span class="p">,</span> <span class="n" style="color: #333;">gapCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countsFromLastOutput</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">q</span></span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">matchRatio</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">delRatios</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">insRatios</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">gapRatio</span>sFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">gapCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">matCounts</span><span class="p">,</span> <span class="n" style="color: #333;">gapCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countsFromLastOutput</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">proc</span></span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">gapProbs</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">gapProb</span>sFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">gapCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">matCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapRatiosFromProbs</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gapProbs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python"> <span class="n" style="color: #333;">rowProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matProbs</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">colProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matProbs</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python"> <span class="n" style="color: #333;">matParams</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">,</span> <span class="n" style="color: #333;">colProbs</span></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">sas</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresAndScale</span><span class="p">(</span><span class="n" style="color: #333;">internalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sas</span></span>
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">printGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">delCosts</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insCosts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# score matrix "</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python"> <span class="s" style="color: #d14;">"(query letters = columns, reference letters = rows):"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="python"> <span class="n" style="color: #333;">writeScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="s" style="color: #d14;">"# "</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="510" 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="531" 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">@@ -510,28 +531,22 @@ def doTraining(opts, args):</td>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python"> <span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span></span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">parameters</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">oldParameters</span><span class="p">:</span> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python"> <span class="n" style="color: #333;">oldParameters</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixedLastalArgs</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalProgName</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-t{0:.6}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-p-"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">args</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">universal_newlines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">delCosts</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="python"> <span class="n" style="color: #333;">writeScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># in python2.6, the next line must come after p.stdin.close()</span></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"> <span class="n" style="color: #333;">universal_newlines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">postmask</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="python"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">q</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="python"> <span class="n" style="color: #333;">universal_newlines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixedLastalArgs</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalProgName</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-t{0:.6}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-p-"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">args</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="p">(</span><span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">writeScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="python"> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lastSplitProcess</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">)</span></span>
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;">sas</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresAndScale</span><span class="p">(</span><span class="n" style="color: #333;">externalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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545
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sas</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">X</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -X"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">X</span><span class="p">)</span></span>
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532
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547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -Q"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span><span class="p">)</span></span>
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533
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548
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -t{0:.6}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">))</span></span>
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534
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">delCosts</span><span class="idiff left"> </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">insCosts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">stdout</span></span><span class="p">)</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">delCosts</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">insCosts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">)</span></span>
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535
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550
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -s"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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536
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551
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">S</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -S"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">S</span><span class="p">)</span></span>
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537
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# score matrix "</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="559" 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="574" 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">@@ -559,6 +574,7 @@ if __name__ == "__main__":</td>
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559
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574
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionParser</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">usage</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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560
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-v"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--verbose"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"count"</span><span class="p">,</span></span>
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561
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"show more details of intermediate steps"</span><span class="p">)</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="python"></span>
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562
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="python"> <span class="n" style="color: #333;">og</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionGroup</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">"Training options"</span><span class="p">)</span></span>
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563
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--revsym"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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564
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"force reverse-complement symmetry"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="574" 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="590" 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">@@ -574,7 +590,10 @@ if __name__ == "__main__":</td>
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574
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590
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"number of random sequence samples (default: %default)"</span><span class="p">)</span></span>
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575
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--sample-length"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2000</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"L"</span><span class="p">,</span></span>
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576
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<td class="diff-line-num new_line" data-linenumber="592" 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">
592
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"length of each sample (default: %default)"</span><span class="p">)</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--scale"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"float"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"S"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="594" 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">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"output scores in units of 1/S bits"</span><span class="p">)</span></span>
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577
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595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option_group</span><span class="p">(</span><span class="n" style="color: #333;">og</span><span class="p">)</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="python"></span>
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578
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597
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="python"> <span class="n" style="color: #333;">og</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionGroup</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">"Initial parameter options"</span><span class="p">)</span></span>
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579
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<td class="diff-line-num new_line" data-linenumber="598" 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">
598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-r"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SCORE"</span><span class="p">,</span></span>
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580
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599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"match score (default: 6 if Q>=1, else 5)"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="588" 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="607" 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">@@ -588,6 +607,7 @@ if __name__ == "__main__":</td>
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588
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-A"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COST"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"insertion existence cost"</span><span class="p">)</span></span>
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589
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608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-B"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COST"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"insertion extension cost"</span><span class="p">)</span></span>
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590
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option_group</span><span class="p">(</span><span class="n" style="color: #333;">og</span><span class="p">)</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"></span>
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591
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python"> <span class="n" style="color: #333;">og</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionGroup</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">"Alignment options"</span><span class="p">)</span></span>
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592
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-D"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"LENGTH"</span><span class="p">,</span></span>
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593
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"query letters per random alignment (default: 1e6)"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="614" 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="634" 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">@@ -614,6 +634,7 @@ if __name__ == "__main__":</td>
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614
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-Q"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"NAME"</span><span class="p">,</span></span>
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615
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635
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"input format: fastx, sanger (default=fasta)"</span><span class="p">)</span></span>
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616
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636
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option_group</span><span class="p">(</span><span class="n" style="color: #333;">og</span><span class="p">)</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="python"></span>
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617
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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"I need a lastdb index and query sequences"</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#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">@@ -51,7 +51,12 @@ void Alignment::makeXdrop( Aligners &aligners, bool isGreedy,</td>
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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;">Alphabet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">AlignmentExtras</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">extras</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;">double</span> <span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">outputType</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;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span> <span class="p">)</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">score</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;">gap</span><span class="p">.</span><span class="n" style="color: #333;">isNewFrameshifts</span><span class="p">())</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;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</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 class="c1" style="color: #998; font-style: italic;">// means that "score" is (non-integer) fullScore</span></span>
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<pre style="margin: 0;">+<span id="LC57" 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;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <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="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</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;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">seed</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;">0</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// makes things easier to understand</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">@@ -303,21 +308,21 @@ void Alignment::extend( std::vector< SegmentPair >& chunks,</td>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">isNewFrameshifts</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frame2</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;">dnaStart</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;">dnaStart</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="LC306" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">score</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">alignFrame</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="LC307" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame1</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">),</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame2</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">),</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="cpp"> <span class="idiff left right"> </span> <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;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">);</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">alignFrame</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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312
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<pre style="margin: 0;">+<span id="LC312" 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;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame1</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">),</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" 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;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame2</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">),</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" 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;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">);</span></span>
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310
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315
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<pre style="margin: 0;"> <span id="LC315" 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;">getNextChunkFrame</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="n" style="color: #333;">gapCost</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">))</span></span>
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311
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316
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<pre style="margin: 0;"> <span id="LC316" 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="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span></span>
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">gapCost</span><span class="p">));</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">FrameshiftXdropAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligners</span><span class="p">.</span><span class="n" style="color: #333;">frameshiftAligner</span><span class="p">;</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probDropLimit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">maxDrop</span><span class="p">);</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">forward</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="LC321" 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;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame1</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</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;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame2</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</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;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">probDropLimit</span><span class="p">);</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" 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;">s</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">;</span></span>
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313
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">FrameshiftXdropAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligners</span><span class="p">.</span><span class="n" style="color: #333;">frameshiftAligner</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probDropLimit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">maxDrop</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">forward</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="LC317" 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;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame1</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="LC318" 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;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame2</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">),</span></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">probDropLimit</span><span class="p">);</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">;</span></span>
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">);</span></span>
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">getColumnCodes</span><span class="p">(</span><span class="n" style="color: #333;">fxa</span><span class="p">,</span> <span class="n" style="color: #333;">columnCodes</span><span class="p">,</span> <span class="n" style="color: #333;">chunks</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;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</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/4dc09e39224756822117fb8a9fed8dbdf3619956#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">@@ -32,7 +32,7 @@ struct AlignmentText {</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">SegmentPair</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">strandNum</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;">SegmentPair</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">queryBeg</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;">SegmentPair</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">queryEnd</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;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">score</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;"><span class="idiff left right">double</span></span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">SegmentPair</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">alnSize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">SegmentPair</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">matches</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">text</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// seems to be a bit faster than std::vector<char></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" 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="40" 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">@@ -40,7 +40,7 @@ struct AlignmentText {</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentText</span><span class="p">()</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="n" style="color: #333;">AlignmentText</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNumIn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryBegIn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryEndIn</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;">char</span> <span class="n" style="color: #333;">strandIn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">scoreIn</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;">char</span> <span class="n" style="color: #333;">strandIn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">double</span></span> <span class="n" style="color: #333;">scoreIn</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;">size_t</span> <span class="n" style="color: #333;">alnSizeIn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">matchesIn</span><span class="p">,</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;">textIn</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">strandNum</span><span class="p">(</span><span class="n" style="color: #333;">queryNumIn</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="n" style="color: #333;">strandIn</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)),</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">queryBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryBegIn</span><span class="p">),</span> <span class="n" style="color: #333;">queryEnd</span><span class="p">(</span><span class="n" style="color: #333;">queryEndIn</span><span class="p">),</span> <span class="n" style="color: #333;">score</span><span class="p">(</span><span class="n" style="color: #333;">scoreIn</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">@@ -126,7 +126,7 @@ struct Alignment{</td>
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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="c1" style="color: #998; font-style: italic;">// data:</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SegmentPair</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">blocks</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// the gapless blocks of the alignment</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">double</span></span> <span class="n" style="color: #333;">score</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;">SegmentPair</span> <span class="n" style="color: #333;">seed</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// the alignment remembers its seed</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"></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;">beg1</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;">blocks</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">().</span><span class="n" style="color: #333;">beg1</span><span class="p">();</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">@@ -166,6 +166,7 @@ struct Alignment{</td>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">translationType</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC167" 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;">codonToAmino</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastEvaluer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">evaluer</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlignmentExtras</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">extras</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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtraColumns</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numColumns</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 class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isCodon</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#8758dc959aa5524be83960d0bfd56945bc432a26"><strong>src/AlignmentWrite.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">@@ -5,8 +5,10 @@</td>
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5
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5
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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 "LastEvaluer.hh"</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "MultiSequence.hh"</span></span>
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7
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7
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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 "Alphabet.hh"</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"></span>
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9
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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 <assert.h></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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></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 <cassert></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstdio> // sprintf</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,7 +34,8 @@ const char aminoTriplets[] =</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Val"</span> <span class="s" style="color: #d14;">"val"</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Trp"</span> <span class="s" style="color: #d14;">"trp"</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Tyr"</span> <span class="s" style="color: #d14;">"tyr"</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Xxx"</span> <span class="s" style="color: #d14;">"xxx"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="s" style="color: #d14;">"***"</span> <span class="s" style="color: #d14;">"***"</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Xaa"</span> <span class="s" style="color: #d14;">"xaa"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"></span>
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37
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This writes a "size_t" integer into a char buffer ending at "end".</span></span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// It writes backwards from the end, because that's easier & faster.</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">@@ -128,7 +131,7 @@ AlignmentText Alignment::write(const MultiSequence& seq1,</td>
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128
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">writeTab</span><span class="p">(</span><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;">seqNum2</span><span class="p">,</span> <span class="n" style="color: #333;">translationType</span><span class="p">,</span> <span class="n" style="color: #333;">evaluer</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">);</span></span>
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129
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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130
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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;">return</span> <span class="n" style="color: #333;">writeBlastTab</span><span class="p">(</span><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;">seqNum2</span><span class="p">,</span> <span class="n" style="color: #333;">seqData2</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">translationType</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;">codonToAmino</span><span class="p">,</span> <span class="n" style="color: #333;">evaluer</span><span class="p">,</span> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'B'</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;">codonToAmino</span><span class="p">,</span> <span class="n" style="color: #333;">evaluer</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">extras</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'B'</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="p">}</span></span>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"></span>
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134
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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;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="nf" style="color: #900; font-weight: 600;">alignedColumnCount</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SegmentPair</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">blocks</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="180" 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">@@ -180,8 +183,12 @@ static size_t writeBlocks(std::vector<char> &text,</td>
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180
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">e</span><span class="p">;</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="cpp"><span class="p">}</span></span>
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182
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">scoreFormat</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isIntegerScores</span><span class="p">)</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">isIntegerScores</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"%.0f"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"%.1f"</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="p">}</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"></span>
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183
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">writeTags</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastEvaluer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">evaluer</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">queryLength</span><span class="p">,</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">fullScore</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="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">double</span></span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">fullScore</span><span class="p">,</span></span>
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185
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">separator</span><span class="p">,</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;">out</span> <span class="p">){</span></span>
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186
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">()</span> <span class="p">){</span></span>
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187
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">epa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">evaluePerArea</span><span class="p">(</span> <span class="n" style="color: #333;">score</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">@@ -217,7 +224,7 @@ AlignmentText Alignment::writeTab(const MultiSequence& seq1,</td>
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217
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seqStart2</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;">seqBeg</span><span class="p">(</span><span class="n" style="color: #333;">seqNum2</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;">padBeg</span><span class="p">(</span><span class="n" style="color: #333;">seqNum2</span><span class="p">);</span></span>
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218
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seqLen2</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;">seqLen</span><span class="p">(</span><span class="n" style="color: #333;">seqNum2</span><span class="p">);</span></span>
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219
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">IntText</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sc</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">score</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="n" style="color: #333;"><span class="idiff left">FloatText</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sc</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">scoreFormat</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">extras</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fullScore</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 right"> </span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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221
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">n1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1</span><span class="p">.</span><span class="n" style="color: #333;">seqName</span><span class="p">(</span><span class="n" style="color: #333;">seqNum1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">strand1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">(</span><span class="n" style="color: #333;">seqNum1</span><span class="p">);</span></span>
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223
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">n2</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;">seqName</span><span class="p">(</span><span class="n" style="color: #333;">seqNum2</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="266" 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">@@ -266,9 +273,10 @@ static void putRight(Writer &w, const IntText &t, size_t width) {</td>
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266
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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>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Write an "a" line</span></span>
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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="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">writeMafLineA</span><span class="p">(</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;">out</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastEvaluer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">evaluer</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">writeMafLineA</span><span class="p">(</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;">out</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">double</span></span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastEvaluer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">evaluer</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">queryLength</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">fullScore</span><span class="p">)</span> <span class="p">{</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">out</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;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"a score=%d"</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">out</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;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"a score="</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;">out</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;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">scoreFormat</span><span class="p">(</span><span class="n" style="color: #333;">fullScore</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;">score</span><span class="p">);</span></span>
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272
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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;">return</span> <span class="n" style="color: #333;">writeTags</span><span class="p">(</span><span class="n" style="color: #333;">evaluer</span><span class="p">,</span> <span class="n" style="color: #333;">queryLength</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">fullScore</span><span class="p">,</span> <span class="sc" style="color: #d14;">' '</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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273
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"><span class="p">}</span></span>
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274
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="444" 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="452" 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">@@ -444,6 +452,7 @@ AlignmentText Alignment::writeBlastTab(const MultiSequence& seq1,</td>
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444
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">translationType</span><span class="p">,</span></span>
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445
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453
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<pre style="margin: 0;"> <span id="LC453" 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;">codonToAmino</span><span class="p">,</span></span>
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446
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454
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastEvaluer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">evaluer</span><span class="p">,</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlignmentExtras</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">extras</span><span class="p">,</span></span>
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447
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456
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtraColumns</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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448
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457
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">alnBeg1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg1</span><span class="p">();</span></span>
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449
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">alnEnd1</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="509" 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="518" 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">@@ -509,13 +518,16 @@ AlignmentText Alignment::writeBlastTab(const MultiSequence& seq1,</td>
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509
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp"> <span class="p">}</span></span>
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510
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519
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="cpp"> <span class="n" style="color: #333;">IntText</span> <span class="n" style="color: #333;">s1</span><span class="p">(</span><span class="n" style="color: #333;">seqLen1</span><span class="p">);</span></span>
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511
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="cpp"> <span class="n" style="color: #333;">IntText</span> <span class="n" style="color: #333;">s2</span><span class="p">(</span><span class="n" style="color: #333;">seqLen2</span><span class="p">);</span></span>
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512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">IntText</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sc</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">FloatText</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">sc</span></span><span class="p">;</span></span>
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513
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522
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="cpp"></span>
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514
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523
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span></span>
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515
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524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="cpp"> <span class="n" style="color: #333;">n2</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;">n1</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;">mp</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;">as</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;">mm</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;">go</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>
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516
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="cpp"> <span class="n" style="color: #333;">b2</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;">e2</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;">b1</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;">e1</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;">10</span><span class="p">;</span></span>
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517
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">())</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ev</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;">bs</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>
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<td class="diff-line-num old old_line" data-linenumber="518" 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">
518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isExtraColumns</span><span class="p">)</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">s1</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;">s2</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;">sc</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;">3</span><span class="p">;</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isExtraColumns</span><span class="p">)</span> <span class="p">{</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp"> <span class="n" style="color: #333;">sc</span><span class="p">.</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;">scoreFormat</span><span class="p">(</span><span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</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;">score</span><span class="p">);</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">s1</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;">s2</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;">sc</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;">3</span><span class="p">;</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp"> <span class="p">}</span></span>
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519
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="cpp"></span>
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520
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp"> <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;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">s</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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521
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"> <span class="n" style="color: #333;">Writer</span> <span class="n" style="color: #333;">w</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="596" 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="608" 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">@@ -596,7 +608,7 @@ static char *writeAmino(char *dest, const uchar *beg, const uchar *end,</td>
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596
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608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</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;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</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;">i</span><span class="p">)</span> <span class="p">{</span></span>
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597
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toUnmasked</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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598
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMasked</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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599
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<pre style="margin: 0;">-<span id="LC599" 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="mi" style="color: #099;">2<span class="idiff left">0</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">20</span></span><span class="p">;</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" 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="mi" style="color: #099;">2<span class="idiff left">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">21</span></span><span class="p">;</span></span>
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600
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">x</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;">isMasked</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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601
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aminoTriplets</span><span class="p">[</span><span class="n" style="color: #333;">y</span><span class="p">];</span></span>
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602
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aminoTriplets</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;">1</span><span class="p">];</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#ab919b3eb596acbd0affb15613fb99fee03165d8"><strong>src/Alphabet.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,6 +19,7 @@ const char* Alphabet::dna = "ACGT";</td>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></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;">// U=selenocysteine, O=pyrrolysine, *=stop?</span></span>
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21
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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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">protein</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACDEFGHIKLMNPQRSTVWY"</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="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">proteinWithStop</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACDEFGHIKLMNPQRSTVWY*"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>
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23
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fromString</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alphString</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;">letters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alphString</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#50bbab11fc8cfa2a0b2a909b040fb5e75e3bf421"><strong>src/Alphabet.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">@@ -23,6 +23,7 @@ struct Alphabet{</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dna</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">protein</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;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">proteinWithStop</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;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">capacity</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">256</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" 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">@@ -584,16 +584,8 @@ namespace cbrc{</td>
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alphabetSizeIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alphabetSize</span><span class="p">;</span></span>
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585
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<pre style="margin: 0;"> <span id="LC585" 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;">isExtendFwd</span><span class="p">)</span> <span class="n" style="color: #333;">alphabetSizeIncrement</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="LC586" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpen</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delGrow</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// for 1st letter in a deletion</span></span>
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpen</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insGrow</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// for 1st letter in an insert</span></span>
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delGrow</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delInit</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insGrow</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insInit</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delInitCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delNextCount</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="LC588" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insInitCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insNextCount</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="LC589" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numAntidiagonals</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span> <span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">// loop over antidiagonals</span></span>
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">seq1start</span><span class="p">(</span> <span class="n" style="color: #333;">k</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">@@ -601,9 +593,6 @@ namespace cbrc{</td>
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593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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602
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</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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603
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595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="cpp"></span>
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604
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scaledDelNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delNext</span><span class="p">;</span></span>
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605
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scaledInsNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insNext</span><span class="p">;</span></span>
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606
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="cpp"></span>
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607
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596
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span> <span class="n" style="color: #333;">k</span> <span class="p">);</span></span>
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608
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597
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bM</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="p">];</span></span>
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609
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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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bD</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="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="616" 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">@@ -616,6 +605,9 @@ namespace cbrc{</td>
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616
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fI1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fI</span><span class="p">[</span> <span class="n" style="color: #333;">vertBeg</span> <span class="p">];</span></span>
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617
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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fM2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fM</span><span class="p">[</span> <span class="n" style="color: #333;">diagBeg</span> <span class="p">];</span></span>
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618
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="cpp"></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dNextCount</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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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">iNextCount</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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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"></span>
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619
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bM0last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">numCellsAndPads</span><span class="p">(</span> <span class="n" style="color: #333;">k</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="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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620
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="cpp"></span>
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621
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613
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<pre style="margin: 0;"> <span id="LC613" 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="n" style="color: #333;">isExtendFwd</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seq1</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -640,10 +632,10 @@ namespace cbrc{</td>
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640
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">alignProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yM</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matchProb</span><span class="p">;</span></span>
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641
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">emit</span><span class="p">[</span><span class="n" style="color: #333;">letter1</span><span class="p">][</span><span class="n" style="color: #333;">letter2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alignProb</span><span class="p">;</span></span>
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642
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">toMatch</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alignProb</span><span class="p">;</span></span>
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643
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">c</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delInit</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">xSum</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">yD</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">delInit</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">c</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delNext</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">xD</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">yD</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">scaledDelNext</span></span><span class="p">;</span></span>
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645
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">c</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insInit</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">xSum</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">yI</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">insInit</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">c</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insNext</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">xI</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">yI</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">scaledInsNext</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">delInitCount</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">xSum</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">yD</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">dNextCount</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">xD</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">yD</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">insInitCount</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">xSum</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">yI</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">iNextCount</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">xI</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">yI</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bM0last</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="LC641" class="line" lang="cpp"> <span class="n" style="color: #333;">fM2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fD1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fI1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="673" 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">@@ -673,10 +665,10 @@ namespace cbrc{</td>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp"> <span class="n" style="color: #333;">countUncertainLetters</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">emit</span><span class="p">[</span><span class="n" style="color: #333;">letter1</span><span class="p">],</span> <span class="n" style="color: #333;">alignProb</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="cpp"> <span class="n" style="color: #333;">alphabetSize</span><span class="p">,</span> <span class="n" style="color: #333;">match_score</span><span class="p">[</span><span class="n" style="color: #333;">letter1</span><span class="p">],</span> <span class="n" style="color: #333;">lp2</span><span class="p">);</span></span>
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667
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">toMatch</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alignProb</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;"><span class="idiff left">c</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delInit</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">xSum</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">yD</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">delInit</span></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;"><span class="idiff left">c</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delNext</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">xD</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">yD</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">scaledDelNext</span></span><span class="p">;</span></span>
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678
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">c</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insInit</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">xSum</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">yI</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">insInit</span></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;"><span class="idiff left">c</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insNext</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">xI</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">yI</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">scaledInsNext</span></span><span class="p">;</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">delInitCount</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">xSum</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">yD</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">dNextCount</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">xD</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">yD</span></span><span class="p">;</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">insInitCount</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">xSum</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">yI</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">iNextCount</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">xI</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">yI</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bM0last</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="LC674" class="line" lang="cpp"> <span class="n" style="color: #333;">fM2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fD1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fI1</span><span class="o" style="font-weight: 600;">++</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">@@ -686,7 +678,26 @@ namespace cbrc{</td>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"> <span class="n" style="color: #333;">lp2</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">alphabetSizeIncrement</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="n" style="color: #333;">delNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">dNextCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="n" style="color: #333;">insNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">iNextCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpen</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delGrow</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// for 1st letter in a deletion</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpen</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insGrow</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// for 1st letter in an insert</span></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delGrow</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delInit</span><span class="p">;</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insGrow</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insInit</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">delInitCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delInit</span><span class="p">;</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">delNext</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">delNextCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delNext</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">insInitCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insInit</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">insNext</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">insNextCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insNext</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="cpp"> <span class="p">}</span></span>
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702
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// end namespace cbrc</span></span></pre>
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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">@@ -205,13 +205,13 @@ class GappedXdropAligner {</td>
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<pre style="margin: 0;"> <span id="LC205" 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>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Like "align3", but does "new style" DNA-protein alignment.</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alignFrame</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;"><span class="idiff left right">seq1</span></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;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left">seq2frame0</span></span><span class="p"><span class="idiff right">,</span></span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left">seq2frame1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// the</span> +1 frame</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left">seq2frame2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// the</span> +2 frame</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alignFrame</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;"><span class="idiff left right">protein</span></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;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left">frame0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// translated DNA, 0 frame</span></span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left">frame1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// translated DNA,</span> +1 frame</span></span>
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<pre style="margin: 0;">+<span id="LC211" 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;"><span class="idiff left">frame2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// translated DNA,</span> +2 frame</span></span>
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<pre style="margin: 0;"> <span id="LC212" 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="LC213" 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="LC214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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="LC214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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 class="idiff left right">Costs</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC215" 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="LC216" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Use this after alignFrame. The cost of the unaligned region</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">@@ -220,8 +220,8 @@ class GappedXdropAligner {</td>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">getNextChunkFrame</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="LC221" 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="LC222" 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="LC223" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;"><span class="idiff left">gapCost</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// cost of the gap before this chunk</span></span></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="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="LC223" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;"><span class="idiff left">costOfNearerGap</span></span><span class="p"><span class="idiff right">,</span></span></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="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeShape</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</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="LC227" class="line" lang="cpp"></span>
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<li id="aa38e532f19f245fda3e2e3b5a4ac462598ab91f">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#aa38e532f19f245fda3e2e3b5a4ac462598ab91f"><strong>src/GappedXdropAlignerFrame.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">@@ -22,33 +22,33 @@ void GappedXdropAligner::initFrame() {</td>
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<pre style="margin: 0;"> <span id="LC22" 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="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="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;">alignFrame</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;"><span class="idiff left right">seq1</span></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="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left right">seq2</span>frame0</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;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left">seq2frame1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// the +1 frame</span></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="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left">seq2frame2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// the +2 frame</span></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;">int</span> <span class="n" style="color: #333;">GappedXdropAligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">alignFrame</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;"><span class="idiff left right">protein</span></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="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frame0</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;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left">frame1</span></span><span class="p"><span class="idiff right">,</span></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="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left">frame2</span></span><span class="p"><span class="idiff right">,</span></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;">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="LC30" 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="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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 class="idiff left right">Costs</span></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;">maxScoreDrop</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC33" 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;">isForward</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="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;"><span class="idiff left">seq1</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">seq2frame0</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">seq2frame1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">--</span></span><span class="n" style="color: #333;"><span class="idiff right">seq2</span>frame2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;"><span class="idiff left">protein</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">frame0</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">frame1</span></span><span class="p"><span class="idiff">;</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;">frame2</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 class="n" style="color: #333;">const_uchar_ptr</span> <span class="n" style="color: #333;">frames</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;"><span class="idiff left">seq2frame0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq2frame1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">seq2</span>frame2</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">const_uchar_ptr</span> <span class="n" style="color: #333;">frames</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;"><span class="idiff left">frame0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">frame1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">frame2</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="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="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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delOpenScore</span> <span class="o" style="font-weight: 600;">=</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;">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>
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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;">insOpenScore</span> <span class="o" style="font-weight: 600;">=</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;">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="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;">delScore1</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;">delScore1</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;">delScore2</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;">delScore2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" 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;">delScore3</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;">delScore3</span><span class="p">;</span></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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore1</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;">insScore1</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore2</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;">insScore2</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore3</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;">insScore3</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;">delOpenScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></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>
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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;">insOpenScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></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="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;">delScore1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">delScore1</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;">delScore2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">delScore2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" 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;">delScore3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">delScore3</span><span class="p">;</span></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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">insScore1</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">insScore2</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">insScore3</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">runOfDrops</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="LC49" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">runOfEdges</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="LC50" 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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;"><span class="idiff left right">seq1e</span>nd</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="LC51" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;"><span class="idiff left right">proteinE</span>nd</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="LC52" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos6</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="LC53" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos5</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="LC54" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos4</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;">3</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -63,11 +63,11 @@ int GappedXdropAligner::alignFrame(const uchar *seq1,</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">initFrame</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="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="LC66" 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="n" style="color: #333;">seq1</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;">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;">frames</span><span class="p">[</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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="n" style="color: #333;">protein</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;">frames</span><span class="p">[</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</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;">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;">frames</span><span class="p">[</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</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>
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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="n" style="color: #333;">antidiagonal</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;"><span class="idiff left right">seq1e</span>nd</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="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">initAntidiagonal</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</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;"><span class="idiff left right">proteinE</span>nd</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="LC71" 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="LC72" 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="LC73" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -83,6 +83,7 @@ int GappedXdropAligner::alignFrame(const uchar *seq1,</td>
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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;">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="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;">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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<pre style="margin: 0;">+<span id="LC86" 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;">seqIncrement</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scorer</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;">s2</span><span class="p">];</span></span>
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87
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y5</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;">delScore1</span><span class="p">;</span></span>
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88
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y4</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;">delScore2</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -97,7 +98,6 @@ int GappedXdropAligner::alignFrame(const uchar *seq1,</td>
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97
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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;">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;">maxValue</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;">delOpenScore</span><span class="p">,</span> <span class="n" style="color: #333;">y3</span><span class="p">);</span></span>
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98
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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;">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="n" style="color: #333;">maxValue</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;">insOpenScore</span><span class="p">,</span> <span class="n" style="color: #333;">z3</span><span class="p">);</span></span>
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99
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</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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100
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<pre style="margin: 0;">-<span id="LC100" 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;">seqIncrement</span><span class="p">;</span></span>
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101
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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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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;">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;">bestScore</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="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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,7 +118,7 @@ int GappedXdropAligner::alignFrame(const uchar *seq1,</td>
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118
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">runOfEdges</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">runOfEdges</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <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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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;"><span class="idiff left right">seq1e</span>nd</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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;"><span class="idiff left right">proteinE</span>nd</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;">runOfEdges</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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123
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="p">}</span></span>
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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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,7 +130,7 @@ int GappedXdropAligner::alignFrame(const uchar *seq1,</td>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">runOfDrops</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <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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132
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</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="n" style="color: #333;"><span class="idiff left right">seq1</span></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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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">protein</span></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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134
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">frames</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;">seqIncrement</span><span class="p">;</span></span>
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135
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">frames</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;">seqIncrement</span><span class="p">;</span></span>
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136
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">frames</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -152,18 +152,18 @@ int GappedXdropAligner::alignFrame(const uchar *seq1,</td>
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152
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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;">GappedXdropAligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getNextChunkFrame</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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153
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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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154
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154
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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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;"><span class="idiff left right">gapCost</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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="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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;"><span class="idiff left right">costOfNearerGap</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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 class="idiff left right">Costs</span></span><span class="p">)</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="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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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"></span>
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159
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<pre style="margin: 0;">-<span id="LC159" 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;">delOpenScore</span> <span class="o" style="font-weight: 600;">=</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;">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>
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insOpenScore</span> <span class="o" style="font-weight: 600;">=</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;">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="LC161" 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;">delScore1</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;">delScore1</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="n" style="color: #333;">delScore2</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;">delScore2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC163" 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;">delScore3</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;">delScore3</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore1</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;">insScore1</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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore2</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;">insScore2</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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore3</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;">insScore3</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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delOpenScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></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>
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insOpenScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></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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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delScore1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">delScore1</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="n" style="color: #333;">delScore2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">delScore2</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delScore3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">delScore3</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">insScore1</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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">insScore2</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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insScore3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap<span class="idiff left right">Costs</span></span><span class="p">.</span><span class="n" style="color: #333;">insScore3</span><span class="p">;</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="cpp"></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="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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169
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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;">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="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" 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="187" 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">@@ -187,7 +187,7 @@ bool GappedXdropAligner::getNextChunkFrame(size_t &end1,</td>
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187
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"></span>
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188
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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;">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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189
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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;">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="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;"><span class="idiff left right">gapCost</span></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="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">costOfNearerGap</span></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="LC191" class="line" lang="cpp"> <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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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"> <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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -212,7 +212,7 @@ bool GappedXdropAligner::getNextChunkFrame(size_t &end1,</td>
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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;">state</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_element</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">opt</span><span class="p">;</span></span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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214
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">gapCost</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</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;">scoreHere</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">costOfNearerGap</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</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;">scoreHere</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"> <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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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#651801b243983c0404fde32d39e03c30a9dd0adc"><strong>src/GeneticCode.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">@@ -49,7 +49,8 @@ void GeneticCode::codeTableSet( const Alphabet& aaAlph, const Alphabet& dnaAlph</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">codon</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="LC51" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">genome2residue</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">UNKNOWN</span><span class="p">,</span> <span class="sc" style="color: #d14;">'X'</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;">int</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxDnaAlphabetSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">maxDnaAlphabetSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">maxDnaAlphabetSize</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;">genome2residue</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="sc" style="color: #d14;">'X'</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;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">AAs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</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;">char</span> <span class="n" style="color: #333;">aminoAcid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span> <span class="n" style="color: #333;">AAs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,13 +72,13 @@ void GeneticCode::codeTableSet( const Alphabet& aaAlph, const Alphabet& dnaAlph</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// codons containing DNA delimiters, or lowercase bases</span></span>
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<pre style="margin: 0;">-<span id="LC74" 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;"><span class="idiff left right">NumMember</span></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>
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<pre style="margin: 0;">+<span id="LC75" 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;"><span class="idiff left right">maxDnaAlphabetSize</span></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>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">codon</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;">dnaAlph</span><span class="p">.</span><span class="n" style="color: #333;">decode</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="LC77" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left right">NumMember</span></span> <span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</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;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left right">maxDnaAlphabetSize</span></span> <span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">codon</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;">dnaAlph</span><span class="p">.</span><span class="n" style="color: #333;">decode</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="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC80" 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;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left right">NumMember</span></span> <span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</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;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left right">maxDnaAlphabetSize</span></span> <span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</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;">codon</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dnaAlph</span><span class="p">.</span><span class="n" style="color: #333;">decode</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"></span>
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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;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">codon2number2</span><span class="p">(</span> <span class="n" style="color: #333;">codon</span><span class="p">,</span> <span class="n" style="color: #333;">dnaAlph</span> <span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="99" 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">@@ -99,15 +100,16 @@ void GeneticCode::codeTableSet( const Alphabet& aaAlph, const Alphabet& dnaAlph</td>
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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="p">;</span></span>
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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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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GeneticCode</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initCodons</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;">ntToNumber</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;">aaToNumber</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC104" 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;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NumMember</span><span class="p">;</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">delimiterCodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">64</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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">unknownCodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">65</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>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initCodonLookup</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lookupFromDnaTriplet</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="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;">ntToNumber</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">)</span> <span class="p">{</span></span>
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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="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;">maxDnaAlphabetSize</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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">dna</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACGTacgt"</span><span class="p">;</span></span>
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106
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">dnaMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isMaskLowercase</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="mi" style="color: #099;">8</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">delimiterCodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">64</span><span class="p">;</span></span>
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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="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">unknownCodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">65</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">genome2residue</span></span><span class="p">.</span><span class="n" style="color: #333;">assign</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;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">unknownCodon</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;"><span class="idiff left right">lookupFromDnaTriplet</span></span><span class="p">.</span><span class="n" style="color: #333;">assign</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;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">unknownCodon</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dnaMax</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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113
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dnaMax</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,12 +118,21 @@ void GeneticCode::initCodons(const uchar *ntToNumber, const uchar *aaToNumber,</td>
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116
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dna</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ntToNumber</span><span class="p">[</span><span class="n" style="color: #333;">b</span><span class="p">];</span></span>
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117
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dna</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ntToNumber</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">codonNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">16</span> <span class="o" style="font-weight: 600;">+</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="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">k</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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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">genome2residue</span></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;">n</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n</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;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">codonNumber</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">lookupFromDnaTriplet</span></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;">n</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n</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;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">codonNumber</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <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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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">setDelimiters</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">genome2residue</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">delimiterCodon</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">setDelimiters</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lookupFromDnaTriplet</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">delimiterCodon</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GeneticCode</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initCodons</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;">ntToNumber</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;">aaToNumber</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isUnmaskLowercase</span><span class="p">)</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;">initCodonLookup</span><span class="p">(</span><span class="n" style="color: #333;">genome2residue</span><span class="p">,</span> <span class="n" style="color: #333;">ntToNumber</span><span class="p">,</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isMaskLowercase</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isUnmaskLowercase</span><span class="p">)</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;">initCodonLookup</span><span class="p">(</span><span class="n" style="color: #333;">genome2residueWithoutLowercaseMasking</span><span class="p">,</span> <span class="n" style="color: #333;">ntToNumber</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <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;">uchar</span> <span class="n" style="color: #333;">unknown</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'X'</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;">uchar</span> <span class="n" style="color: #333;">delimiter</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">' '</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -136,24 +147,33 @@ void GeneticCode::initCodons(const uchar *ntToNumber, const uchar *aaToNumber,</td>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">codonToAminoAcid</span><span class="p">[</span><span class="n" style="color: #333;">delimiterCodon</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aaToNumber</span><span class="p">[</span><span class="n" style="color: #333;">delimiter</span><span class="p">];</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>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GeneticCode</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">translate</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;">beg</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dest</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="LC142" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">delimiter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genome2residue</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="LC143" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">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="LC144" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC145" 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="mi" style="color: #099;">3</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>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</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;">2</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;">j</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">3</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">translation</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;">j</span> <span class="p">);</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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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">doTranslate</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;">lookupFromDnaTriplet</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="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;">beg</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="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">)</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="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;">maxDnaAlphabetSize</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="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">delimiter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lookupFromDnaTriplet</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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149
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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;">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="mi" style="color: #099;">3</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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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</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;">2</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;">j</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" 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;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lookupFromDnaTriplet</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;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</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;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</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;">b</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="p">}</span></span>
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150
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this ensures that each reading frame has exactly the same size:</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">++</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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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="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">++</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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152
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="p">}</span></span>
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153
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"></span>
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154
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this ensures that the size of the translated sequence is exactly "size":</span></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;">if</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;">3</span> <span class="o" style="font-weight: 600;">></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;">dest</span><span class="o" style="font-weight: 600;">++</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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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">3</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;">dest</span><span class="o" style="font-weight: 600;">++</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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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">3</span> <span class="o" style="font-weight: 600;">></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;">dest</span><span class="o" style="font-weight: 600;">++</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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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">3</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;">dest</span><span class="o" style="font-weight: 600;">++</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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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"><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>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GeneticCode</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">translate</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;">beg</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</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;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</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;">doTranslate</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">genome2residue</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="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 class="n" style="color: #333;">dest</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="p">}</span></span>
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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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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GeneticCode</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">translateWithoutMasking</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;">beg</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</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;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dest</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</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;">doTranslate</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">genome2residueWithoutLowercaseMasking</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="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 class="n" style="color: #333;">dest</span><span class="p">);</span></span>
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157
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"><span class="p">}</span></span>
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158
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"></span>
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159
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#3c0366b16bdb441bbd5135e07608d67f42e74a37"><strong>src/GeneticCode.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">@@ -19,17 +19,20 @@ typedef unsigned char uchar;</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Alphabet</span><span class="p">;</span></span>
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21
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21
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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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDnaAlphabetSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">54</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GeneticCode</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="nl">private:</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">AAs</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">Base</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="LC26" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">NumMember</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">54</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// DNA member</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">UNKNOWN</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NumMember</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NumMember</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NumMember</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// unknown residue</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;">uchar</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">genome2residue</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;">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;">uchar</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">genome2residueWithoutLowercaseMasking</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;">uchar</span> <span class="n" style="color: #333;">codonToAminoAcid</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">codon2number</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;">codon</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">codon</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;">NumMember</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">NumMember</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">codon</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;">NumMember</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">codon</span><span class="p">[</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="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">codon2number</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;">codon</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC33" 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;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxDnaAlphabetSize</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;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">codon</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;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">codon</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;">codon</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="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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">codon2number2</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;">codon</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">dnaAlph</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,11 +52,16 @@ class GeneticCode{</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 64=delimiter, 65=unknown). Also setup codonToAminoAcid. Any DNA</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// triplet with non-ACGT (or with lowercase if isMaskLowercase is</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// true) gets translated to 65=unknown.</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If isMaskLowercase and isUnmaskLowercase are both true, also</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// setup translateWithoutMasking.</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;">void</span> <span class="n" style="color: #333;">initCodons</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;">ntToNumber</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;">aaToNumber</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;">bool</span> <span class="n" style="color: #333;">isMaskLowercase</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;">bool</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">isUnmaskLowercase</span></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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">translate</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;">beg</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dest</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="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;">void</span> <span class="n" style="color: #333;">translateWithoutMasking</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;">beg</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">end</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dest</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="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;">uchar</span> <span class="n" style="color: #333;">translation</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;">codon</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">genome2residue</span><span class="p">[</span> <span class="n" style="color: #333;">codon2number</span><span class="p">(</span> <span class="n" style="color: #333;">codon</span> <span class="p">)</span> <span class="p">];</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></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 "GeneticCode.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="cp" style="color: #999; font-weight: 600;">#include "alp/sls_falp_alignment_evaluer.hpp"</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="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstring></span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></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="cp" style="color: #999; font-weight: 600;">#include <random></span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define COUNTOF(a) (sizeof (a) / sizeof *(a))</span></span>
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16
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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;">namespace</span> <span class="n" style="color: #333;">cbrc</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="296" 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="300" 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">@@ -296,7 +300,7 @@ void LastEvaluer::init(const char *matrixName,</td>
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296
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FrameshiftEvalueParameters</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;">frameshiftEvalueParameters</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="LC301" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isHit</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">geneticCodeName</span><span class="p">,</span> <span class="n" style="color: #333;">matrixName</span><span class="p">,</span> <span class="n" style="color: #333;">delOpen</span><span class="p">,</span> <span class="n" style="color: #333;">delEpen</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;">frameshiftCost</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">frameshiftE</span>valuer</span><span class="p">.</span><span class="n" style="color: #333;">initParameters</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">e</span>valuer</span><span class="p">.</span><span class="n" style="color: #333;">initParameters</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC306" 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="317" 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="321" 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">@@ -317,22 +321,25 @@ void LastEvaluer::init(const char *matrixName,</td>
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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="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aaFreqs</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">letterFreqs1</span><span class="p">,</span> <span class="n" style="color: #333;">letterFreqs1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alphabetSize</span><span class="p">,</span> <span class="n" style="color: #333;">aaFreqs</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">frameshiftCost</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// with frameshifts:</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isGapped</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">initFrameshift</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">matrixSize</span><span class="p">,</span> <span class="n" style="color: #333;">codonTable</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrix</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;">ntFreqs</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;">aaFreqs</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="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">delOpen</span><span class="p">,</span> <span class="n" style="color: #333;">delEpen</span><span class="p">,</span> <span class="n" style="color: #333;">insOpen</span><span class="p">,</span> <span class="n" style="color: #333;">insEpen</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">frameshiftCost</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">lambdaTolerance</span><span class="p">,</span> <span class="n" style="color: #333;">kTolerance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">maxMegabytes</span><span class="p">,</span> <span class="n" style="color: #333;">randomSeed</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC328" 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="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">initGapless</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">matrixSize</span><span class="p">,</span> <span class="n" style="color: #333;">codonTable</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;">matrix</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;">ntFreqs</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;">aaFreqs</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="LC331" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isGapped</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">frameshiftCost</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// with frameshifts:</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FrameshiftAlignmentEvaluer</span> <span class="n" style="color: #333;">frameshiftEvaluer</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">initFrameshift</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">matrixSize</span><span class="p">,</span> <span class="n" style="color: #333;">codonTable</span><span class="p">,</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrix</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;">ntFreqs</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;">aaFreqs</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="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">delOpen</span><span class="p">,</span> <span class="n" style="color: #333;">delEpen</span><span class="p">,</span> <span class="n" style="color: #333;">insOpen</span><span class="p">,</span> <span class="n" style="color: #333;">insEpen</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;">frameshiftCost</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</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;">lambdaTolerance</span><span class="p">,</span> <span class="n" style="color: #333;">kTolerance</span><span class="p">,</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">maxMegabytes</span><span class="p">,</span> <span class="n" style="color: #333;">randomSeed</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;">const</span> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FALP_set_of_parameters</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;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">parameters</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;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentEvaluerParameters</span> <span class="n" style="color: #333;">q</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;">lambda</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">K</span><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 class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">a_I</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">b_I</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// !!! no flip</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">a_J</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">b_J</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="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">alpha_I</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">beta_I</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="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">alpha_J</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">beta_J</span><span class="p">,</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">sigma</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">tau</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">initParameters</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// without frameshifts:</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;">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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">txFreqs</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</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;">makeTxFreqs</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txFreqs</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;">ntFreqs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">codonTable</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="LC343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isGapped</span><span class="p">)</span> <span class="p">{</span></span>
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337
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">set_gapped_computation_parameters_simplified</span><span class="p">(</span><span class="n" style="color: #333;">maxSeconds</span><span class="p">);</span></span>
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338
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">initGapped</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrix</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;">txFreqs</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;">aaFreqs</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 unfold js-unfold new_line" data-linenumber="349" 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">@@ -342,6 +349,14 @@ void LastEvaluer::init(const char *matrixName,</td>
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349
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<pre style="margin: 0;"> <span id="LC349" 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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350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">initGapless</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrix</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;">txFreqs</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;">aaFreqs</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="LC351" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ALP_set_of_parameters</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">parameters</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;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentEvaluerParameters</span> <span class="n" style="color: #333;">q</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;">lambda</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">K</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;">p</span><span class="p">.</span><span class="n" style="color: #333;">a_J</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">b_J</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">a_I</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">b_I</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// !!! flip (I, J)</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;">p</span><span class="p">.</span><span class="n" style="color: #333;">alpha_J</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">beta_J</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">9</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;">p</span><span class="p">.</span><span class="n" style="color: #333;">alpha_I</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">beta_I</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;">p</span><span class="p">.</span><span class="n" style="color: #333;">sigma</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">tau</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">initParameters</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// ordinary alignment:</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isGapped</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">insOpen</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">delOpen</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">insEpen</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">delEpen</span><span class="p">)</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">@@ -402,31 +417,74 @@ void LastEvaluer::init(const char *matrixName,</td>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">theMinScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">area</span><span class="p">)</span> <span class="p">{</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// do log of evalue separately, to reduce the risk of overflow:</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">area</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">evalue</span><span class="p">))</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">lambda</span><span class="p">;</span></span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">));</span></span>
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409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">LastEvaluer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initFrameshift</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">proteinLetterFreqs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numProteinLetters</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tranDnaLetterFreqs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numTranDnaLetters</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbosity</span><span class="p">)</span> <span class="p">{</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;">FrameshiftXdropAligner</span> <span class="n" style="color: #333;">aligner</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">proteinLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">200</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// xxx long enough to avoid edge effects ???</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tranDnaLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proteinLength</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numOfAlignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">50</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// suggested by Y-K Yu, R Bundschuh, T Hwa, 2002</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbosity</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">numOfAlignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mt19937_64</span> <span class="n" style="color: #333;">randGen</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC434" 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;">discrete_distribution</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">pDist</span><span class="p">(</span><span class="n" style="color: #333;">proteinLetterFreqs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="n" style="color: #333;">proteinLetterFreqs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numProteinLetters</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC436" 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;">discrete_distribution</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">tDist</span><span class="p">(</span><span class="n" style="color: #333;">tranDnaLetterFreqs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">tranDnaLetterFreqs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numTranDnaLetters</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"></span>
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439
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<pre style="margin: 0;">+<span id="LC439" 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;">uchar</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seqs</span><span class="p">(</span><span class="n" style="color: #333;">proteinLength</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tranDnaLength</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">protein</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</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="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tranDna</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">protein</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">proteinLength</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probRatioSum</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="LC445" 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;">numOfAlignments</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="LC446" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">proteinLength</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="n" style="color: #333;">protein</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;">pDist</span><span class="p">(</span><span class="n" style="color: #333;">randGen</span><span class="p">);</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tranDnaLength</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="n" style="color: #333;">tranDna</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;">tDist</span><span class="p">(</span><span class="n" style="color: #333;">randGen</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">maxSumOfProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">protein</span><span class="p">,</span> <span class="n" style="color: #333;">proteinLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="n" style="color: #333;">tranDna</span><span class="p">,</span> <span class="n" style="color: #333;">tranDnaLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="n" style="color: #333;">probRatioSum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbosity</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"simScore: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">log</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;">scale</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">LastEvaluer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">area</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="LC412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ALP_set_of_parameters</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">theMinScore</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">K</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">area</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC415" 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;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FALP_set_of_parameters</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;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">theMinScore</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">K</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">area</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC418" 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="LC419" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</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="LC455" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// max likelihood k = 1 / (m * n * avg[exp(-lambda * score)])</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfAlignments</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">proteinLength</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tranDnaLength</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">probRatioSum</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbosity</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"lambda k m n: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">proteinLength</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">tranDnaLength</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp"> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentEvaluerParameters</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span 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 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 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="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">initParameters</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="LC465" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">LastEvaluer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">area</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="LC468" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ALP_set_of_parameters</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// do log of evalue separately, to reduce the risk of overflow:</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">K</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">area</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">evalue</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="n" style="color: #333;">lambda</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">LastEvaluer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">queryLettersPerRandomAlignment</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="LC424" 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;">isGood</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</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="LC474" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">LastEvaluer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">queryLettersPerRandomAlignment</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="LC475" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">huge</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1e9</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryLettersPerRandomAlignment</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">huge</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC427" 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;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">area</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">huge</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">evaluePerArea</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ALP_set_of_parameters</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryLettersPerRandomAlignment</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">databaseSeqNum</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beg</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="LC479" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">databaseSeqLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">K</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"></span>
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481
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<pre style="margin: 0;">+<span id="LC481" 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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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</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>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mid</span><span class="p">;</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">evalue</span><span class="p">(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="n" style="color: #333;">huge</span><span class="p">,</span> <span class="n" style="color: #333;">databaseSeqLen</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">huge</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">x</span><span class="p">)</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span><span class="p">;</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" 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;">mid</span><span class="p">;</span></span>
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="cpp"> <span class="p">}</span></span>
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="cpp"><span class="p">}</span></span>
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490
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<pre style="margin: 0;"> <span id="LC490" 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">@@ -434,9 +492,6 @@ void LastEvaluer::writeCommented(std::ostream& out) const {</td>
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">())</span> <span class="p">{</span></span>
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ALP_set_of_parameters</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">();</span></span>
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494
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"# lambda="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" K="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">K</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC437" 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;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FALP_set_of_parameters</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;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"# lambda="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" K="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">K</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC497" 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">@@ -444,19 +499,12 @@ void LastEvaluer::writeParameters(std::ostream &out) const {</td>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">streamsize</span> <span class="n" style="color: #333;">prec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">precision</span><span class="p">(</span><span class="mi" style="color: #099;">17</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ALP_set_of_parameters</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// !!! flip (I, J) order, to match AlignmentEvaluer::initParameters</span></span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">K</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">a_I</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">b_I</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">a_J</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">b_J</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">alpha_I</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">beta_I</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">alpha_J</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">beta_J</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">sigma</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">tau</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC453" 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;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FALP_set_of_parameters</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;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">K</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">a_I</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">b_I</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">a_J</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">b_J</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">alpha_I</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">beta_I</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">alpha_J</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">beta_J</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">alpha_I</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">beta_I</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">sigma</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">tau</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="cpp"> <span class="p">}</span></span>
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510
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">precision</span><span class="p">(</span><span class="n" style="color: #333;">prec</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#8ad69f8f5b121bdf5620a1b9db78266650ef63ed"><strong>src/LastEvaluer.hh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,12 +18,14 @@</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define LAST_EVALUER_HH</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ScoreMatrixRow.hh"</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "mcf_frameshift_xdrop_aligner.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "alp/sls_alignment_evaluer.hpp"</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "alp/sls_falp_alignment_evaluer.hpp"</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;">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="LC26" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <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="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GeneticCode</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="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">LastEvaluer</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">@@ -54,6 +56,14 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">geneticCodeName</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;">int</span> <span class="n" style="color: #333;">verbosity</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// "new-style" frameshifts, sum-of-paths scores</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// scale=lambda</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// The Freqs need not sum to 1</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;">void</span> <span class="n" style="color: #333;">initFrameshift</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">proteinLetterFreqs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numProteinLetters</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tranDnaLetterFreqs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numTranDnaLetters</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;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbosity</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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setSearchSpace</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">databaseLength</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// number of database letters</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;">double</span> <span class="n" style="color: #333;">databaseMaxSeqLength</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// length of longest seq</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;">double</span> <span class="n" style="color: #333;">numOfStrands</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// 1 or 2</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">@@ -66,37 +76,26 @@ public:</td>
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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 class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC78" 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;">bool</span> <span class="n" style="color: #333;">isGood</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGood</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Don't call this in the "bad" state:</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evaluePerArea</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</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="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">evaluePerArea</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">evaluePerArea</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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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="LC82" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evaluePerArea</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">evaluePerArea</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Don't call this in the "bad" state or before calling setSearchSpace:</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">area</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">queryLength</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="LC80" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">databaseSeqNum</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">area</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">queryLength</span><span class="p">,</span> <span class="n" style="color: #333;">databaseSeqLen</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">area</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">queryLength</span><span class="p">,</span> <span class="n" style="color: #333;">databaseSeqLen</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">area</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">queryLength</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">databaseSeqNum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">area</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">queryLength</span><span class="p">,</span> <span class="n" style="color: #333;">databaseSeqLen</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>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Don't call this in the "bad" state:</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">bitScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</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="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">bitScore</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">frameshiftEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">bitScore</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">bitScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">bitScore</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">In the "good" state: returns the minimum score with E-value <=</span></span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">"evalue", which is always > 0. Otherwise: returns -1</span>.</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;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">area</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="LC92" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">Returns max(0, score with E-value == "evalue").</span></span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">Don't call this in the "bad" state</span>.</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;"><span class="idiff left right">double</span></span> <span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">area</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="LC95" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// In the "good" state, after calling setSearchSpace: returns the</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// minimum positive score with E-value <= 1 per this many query</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// letters. In the "bad" state: returns -1.</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;">int</span> <span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">queryLettersPerRandomAlignment</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="LC96" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Returns max(0, score with E-value == 1 per this many query letters).</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Don't call this in the "bad" state or before calling setSearchSpace.</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">queryLettersPerRandomAlignment</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="LC99" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Writes some parameters preceded by "#". Does nothing in the "bad" state.</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeCommented</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out</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">@@ -106,7 +105,6 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"><span class="nl">private:</span></span>
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108
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AlignmentEvaluer</span> <span class="n" style="color: #333;">evaluer</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;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FrameshiftAlignmentEvaluer</span> <span class="n" style="color: #333;">frameshiftEvaluer</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">databaseSeqLen</span><span class="p">;</span></span>
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111
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">databaseSeqNum</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"><span class="p">};</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#4b7be8c3b80efc62977b307791d1a304c23e1fa4"><strong>src/LastalArguments.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">@@ -3,12 +3,14 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "LastalArguments.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "stringify.hh"</span></span>
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5
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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 "getoptUtil.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="cp" style="color: #999; font-weight: 600;">#include <math.h></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="cp" style="color: #999; font-weight: 600;">#include <algorithm> // max</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sstream></span></span>
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9
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdexcept></span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cctype></span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cmath> // log</span></span>
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12
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstring> // strtok</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstdlib> // EXIT_SUCCESS</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="561" 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">@@ -561,7 +563,7 @@ static int percent(int val, int percentage) {</td>
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561
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">percentage</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">percentage</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">LastalArguments</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setDefaultsFromMatrix</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">minScore</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">LastalArguments</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setDefaultsFromMatrix</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">double</span></span> <span class="n" style="color: #333;">minScore</span><span class="p">,</span></span>
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565
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxEvalueDefault</span><span class="p">)</span> <span class="p">{</span></span>
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxEvalue</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;">maxEvalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxEvalueDefault</span><span class="p">;</span></span>
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567
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">minScoreGapped</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;">minScoreGapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minScoreGapless</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">@@ -572,11 +574,15 @@ can't calculate E-values: maybe the mismatch or gap costs are too weak.\n\</td>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="cpp"><span class="s" style="color: #d14;">To proceed without E-values, set a score threshold with option -e."</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="cpp"> <span class="n" style="color: #333;">minScoreGapped</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="LC576" class="line" lang="cpp"> <span class="p">}</span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="p">)</span> <span class="n" style="color: #333;">minScoreGapless</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minScoreGapped</span><span class="p">;</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp"></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">minScoreGapped</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">INT_MAX</span><span class="p">)</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"> <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="s" style="color: #d14;">"the alignment score threshold is too big"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">minScoreGapless</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="n" style="color: #333;">minScoreGapped</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="cpp"></span>
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">temperature</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">temperature</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">lambda</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">defaultMaxScoreDrop</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;"><span class="idiff left">minScoreGapped</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><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="LC585" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">defaultMaxScoreDrop</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;"><span class="idiff left">ceil</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">minScoreGapped</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.0</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// xxx</span></span></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="cpp"> <span class="n" style="color: #333;">defaultMaxScoreDrop</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;">defaultMaxScoreDrop</span><span class="p">,</span> <span class="n" style="color: #333;">maxDropGapless</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxDropFinalSuffix</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'%'</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/4dc09e39224756822117fb8a9fed8dbdf3619956#c41d15f61c8e13ecbdb96a800b59fc069d2c6695"><strong>src/LastalArguments.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">@@ -2,16 +2,17 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This struct holds the command line arguments for lastal.</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></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;">#ifndef LASTALARGUMENTS_HH</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define LASTALARGUMENTS_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;">#ifndef LASTAL<span class="idiff left right">_</span>ARGUMENTS_HH</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define LASTAL<span class="idiff left right">_</span>ARGUMENTS_HH</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"></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 "SequenceFormat.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <climits></span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits.h></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stddef.h></span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iosfwd></span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stddef.h> // size_t</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;">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="LC18" 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">@@ -39,7 +40,7 @@ struct LastalArguments{</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isCaseSensitiveSeeds</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isVolumes</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">refMinimizerWindow</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;">unsigned</span> <span class="n" style="color: #333;">realNumOfThreads</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;">void</span> <span class="n" style="color: #333;">setDefaultsFromMatrix</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">minScore</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;">void</span> <span class="n" style="color: #333;">setDefaultsFromMatrix</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">double</span></span> <span class="n" style="color: #333;">minScore</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;">double</span> <span class="n" style="color: #333;">maxEvalueDefault</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="c1" style="color: #998; font-style: italic;">// write the parameter settings, starting each line with "#":</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">@@ -80,7 +81,7 @@ struct LastalArguments{</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maskLowercase</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxEvalue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">queryLettersPerRandomAlignment</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">minScoreGapped</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">double</span></span> <span class="n" style="color: #333;">minScoreGapped</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;">minScoreGapless</span><span class="p">;</span></span>
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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;">matchScore</span><span class="p">;</span></span>
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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;">mismatchCost</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">@@ -121,5 +122,6 @@ struct LastalArguments{</td>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">inputStart</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// index in argv of first input filename</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"><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="LC124" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// end namespace cbrc</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif // LASTALARGUMENTS_HH</span></span></pre>
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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>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<li id="54925a3b3158a751c06af7acce6d06070e5ac813">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#54925a3b3158a751c06af7acce6d06070e5ac813"><strong>src/LastdbArguments.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">@@ -27,6 +27,7 @@ using namespace cbrc;</td>
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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;">LastdbArguments</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LastdbArguments</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">isProtein</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</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;">isAddStops</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">isKeepLowercase</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</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;">tantanSetting</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="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">isCaseSensitive</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,6 +73,7 @@ Advanced Options (default settings):\n\</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"><span class="s" style="color: #d14;">-s: volume size (unlimited)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="s" style="color: #d14;">-Q: input format: fastx, keep, sanger, solexa, illumina (default=fasta)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"><span class="s" style="color: #d14;">-q: interpret the sequences as proteins and append */STOP</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"><span class="s" style="color: #d14;">-P: number of parallel threads ("</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">numOfThreads</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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77
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"><span class="s" style="color: #d14;">-m: seed patterns (1=match, 0=anything, @=transition)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</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">@@ -92,7 +94,7 @@ Report bugs to: last-align (ATmark) googlegroups (dot) com\n\</td>
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92
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"><span class="s" style="color: #d14;">LAST home page: http://last.cbrc.jp/</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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93
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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94
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"></span>
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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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">sOpts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"hVpR:cm:d:S:s:w:W:P:u:a:i:b:B:C:xvQ:"</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="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">sOpts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"hVp<span class="idiff left right">q</span>R:cm:d:S:s:w:W:P:u:a:i:b:B:C:xvQ:"</span><span class="p">;</span></span>
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96
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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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97
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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;">int</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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98
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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;">while</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myGetopt</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">sOpts</span><span class="p">))</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 class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" 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">@@ -108,6 +110,9 @@ LAST home page: http://last.cbrc.jp/\n\</td>
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108
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">:</span></span>
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109
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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;">isProtein</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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110
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'q'</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;">isAddStops</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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111
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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;">case</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">:</span></span>
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112
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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;">if</span><span class="p">(</span> <span class="n" style="color: #333;">optarg</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="sc" style="color: #d14;">'0'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">optarg</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="sc" style="color: #d14;">'1'</span> <span class="p">)</span> <span class="n" style="color: #333;">badopt</span><span class="p">(</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span> <span class="p">);</span></span>
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113
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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;">if</span><span class="p">(</span> <span class="n" style="color: #333;">optarg</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="sc" style="color: #d14;">'0'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">optarg</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="sc" style="color: #d14;">'2'</span> <span class="p">)</span> <span class="n" style="color: #333;">badopt</span><span class="p">(</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</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 +31,7 @@ struct LastdbArguments{</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// options:</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;">bool</span> <span class="n" style="color: #333;">isProtein</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;">bool</span> <span class="n" style="color: #333;">isAddStops</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;">bool</span> <span class="n" style="color: #333;">isKeepLowercase</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tantanSetting</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;">bool</span> <span class="n" style="color: #333;">isCaseSensitive</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#166cfea9495f22785b4b042c1f067c32d00762cb"><strong>src/MultiSequence.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">@@ -9,13 +9,15 @@</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">MultiSequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initForAppending</span><span class="p">(</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">padSizeIn</span> <span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">MultiSequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initForAppending</span><span class="p">(</span><span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">padSizeIn</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAppendStopSymbol</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"> <span class="n" style="color: #333;">padSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">padSizeIn</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">padSize</span><span class="p">,</span> <span class="sc" style="color: #d14;">' '</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;">ends</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">padSize</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">names</span><span class="p">.</span><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="LC18" class="line" lang="cpp"> <span class="n" style="color: #333;">nameEnds</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="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="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">qualityScoresPerLetter</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="LC20" class="line" lang="cpp"> <span class="n" style="color: #333;">isAppendingStopSymbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isAppendStopSymbol</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>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">MultiSequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reinitForAppending</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">@@ -98,7 +100,12 @@ MultiSequence::appendFromFasta( std::istream& stream, indexT maxSeqLen ){</td>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snextc</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isRoomToAppendPad</span><span class="p">(</span><span class="n" style="color: #333;">maxSeqLen</span><span class="p">))</span> <span class="n" style="color: #333;">finish</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;">seq</span><span class="p">.</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxSeqLen</span> <span class="o" style="font-weight: 600;">&&</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">padSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">isAppendingStopSymbol</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxSeqLen</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;">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="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isAppendingStopSymbol</span><span class="p">)</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><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="sc" style="color: #d14;">'*'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">finish</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">stream</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#de5a928be30a99dcb150a5f687171caed2e9c00c"><strong>src/MultiSequence.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">@@ -24,7 +24,7 @@ class MultiSequence{</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">LAST_INT_TYPE</span> <span class="n" style="color: #333;">indexT</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// initialize with leftmost delimiter pad, ready for appending sequences</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initForAppending</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">indexT</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">padSizeIn</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initForAppending</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">indexT</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">padSizeIn</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">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">isAppendStopSymbol</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// re-initialize, but keep the last sequence if it is unfinished</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reinitForAppending</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -141,6 +141,7 @@ class MultiSequence{</td>
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141
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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;">VectorOrMmap</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;">qualityScores</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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">qualityScoresPerLetter</span><span class="p">;</span></span>
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143
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isReadingFastq</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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAppendingStopSymbol</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Read a fasta/fastq header: read the whole line but store just the</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1st word</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#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">@@ -311,14 +311,21 @@ static void calculateScoreStatistics(const std::string& matrixName,</td>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">gaplessEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">init</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 class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">scoreMat</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <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 class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">fsCost</span><span class="p">,</span> <span class="n" style="color: #333;">geneticCode</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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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">isNewFrameshifts</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isGapped</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" 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;">Piece</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">del</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</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>
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<pre style="margin: 0;">-<span id="LC316" 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;">Piece</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</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>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">canonicalMatrixName</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">scoreMat</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">,</span> <span class="n" style="color: #333;">isGapped</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC319" 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 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="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">fsCost</span><span class="p">,</span> <span class="n" style="color: #333;">geneticCode</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">geneticCodeFile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbosity</span><span class="p">);</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">isNewFrameshifts</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isGapped</span><span class="p">)</span> <span class="p">{</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">temperature</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="p">;</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">alphSize2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">isCodonCols</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">64</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">initFrameshift</span><span class="p">(</span><span class="n" style="color: #333;">fwdMatrices</span><span class="p">.</span><span class="n" style="color: #333;">ratios</span><span class="p">,</span> <span class="n" style="color: #333;">p1</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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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs2</span><span class="p">(),</span> <span class="n" style="color: #333;">alphSize2</span><span class="p">,</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">(),</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbosity</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC320" 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="LC321" 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;">Piece</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">del</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</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>
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<pre style="margin: 0;">+<span id="LC322" 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;">Piece</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</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>
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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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">canonicalMatrixName</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">scoreMat</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">,</span> <span class="n" style="color: #333;">isGapped</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC325" 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 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="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">fsCost</span><span class="p">,</span> <span class="n" style="color: #333;">geneticCode</span><span class="p">,</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">geneticCodeFile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbosity</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <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;">countT</span> <span class="n" style="color: #333;">m</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;">refMaxSeqLen</span><span class="p">,</span> <span class="n" style="color: #333;">refLetters</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">setSearchSpace</span><span class="p">(</span><span class="n" style="color: #333;">refLetters</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">numOfStrands</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;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbosity</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">writeParameters</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</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">@@ -453,8 +460,14 @@ static const ScoreMatrixRow *getQueryPssm(const LastAligner &aligner,</td>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">Phase</span><span class="p">{</span> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">Enum</span><span class="p">{</span> <span class="n" style="color: #333;">gapless</span><span class="p">,</span> <span class="n" style="color: #333;">gapped</span><span class="p">,</span> <span class="k" style="font-weight: 600;">final</span> <span class="p">};</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">isFullScoreThreshold</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">isNewFrameshifts</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">isMaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span> <span class="o" style="font-weight: 600;">></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;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</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="LC468" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</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="LC469" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">e</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isFullScoreThreshold</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</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="LC471" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">Dispatcher</span><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="751" 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">@@ -751,8 +764,9 @@ void alignGapped( LastAligner& aligner,</td>
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">minScoreGapped</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC754" 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;">aln</span><span class="p">.</span><span class="n" style="color: #333;">isOptimal</span><span class="p">(</span> <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;">dis</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span></span>
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755
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="cpp"> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <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="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC767" 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;">isFullScoreThreshold</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="cpp"> <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;">isOptimal</span><span class="p">(</span><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;">dis</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="cpp"> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <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="p">{</span></span>
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If retained, non-"optimal" alignments can hide "optimal"</span></span>
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// alignments, e.g. during non-redundantization.</span></span>
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772
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="830" 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="844" 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">@@ -830,8 +844,8 @@ static void eraseWeakAlignments(LastAligner &aligner, AlignmentPot &gappedAlns,</td>
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830
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844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="cpp"> <span class="n" style="color: #333;">Dispatcher</span> <span class="n" style="color: #333;">dis</span><span class="p">(</span><span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gapless</span><span class="p">,</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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831
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845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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832
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846
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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833
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<pre style="margin: 0;">-<span id="LC833" 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;">a</span><span class="p">.</span><span class="n" style="color: #333;">hasGoodSegment</span><span class="p">(</span><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;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">minScoreGapped</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">m</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">gapCosts</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="cpp"> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <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="p">{</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" 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;">a</span><span class="p">.</span><span class="n" style="color: #333;">hasGoodSegment</span><span class="p">(</span><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;"><span class="idiff left">ceil</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">minScoreGapped</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">m</span></span><span class="p">,</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <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="p">{</span></span>
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849
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentPot</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mark</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">);</span></span>
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="cpp"> <span class="p">}</span></span>
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851
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<pre style="margin: 0;"> <span id="LC851" 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">@@ -911,44 +925,69 @@ void makeQualityPssm( LastAligner& aligner,</td>
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925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="cpp"> <span class="p">}</span></span>
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926
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<pre style="margin: 0;"> <span id="LC926" class="line" lang="cpp"><span class="p">}</span></span>
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927
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">unmaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span></span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SubstitutionMatrices</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrices</span><span class="p">,</span></span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">querySeq</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="cpp"> <span class="n" style="color: #333;">makeQualityPssm</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">isCodonCols</span><span class="p">())</span> <span class="p">{</span></span>
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933
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<pre style="margin: 0;">+<span id="LC933" 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;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqReader</span><span class="p">();</span></span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="cpp"> <span class="n" style="color: #333;">geneticCode</span><span class="p">.</span><span class="n" style="color: #333;">translateWithoutMasking</span><span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">),</span></span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="cpp"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padEnd</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">),</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="cpp"> <span class="p">}</span></span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">remaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SubstitutionMatrices</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrices</span><span class="p">,</span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">querySeq</span><span class="p">)</span> <span class="p">{</span></span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="cpp"> <span class="n" style="color: #333;">makeQualityPssm</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">isCodonCols</span><span class="p">())</span> <span class="p">{</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" 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;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqReader</span><span class="p">();</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="cpp"> <span class="n" style="color: #333;">geneticCode</span><span class="p">.</span><span class="n" style="color: #333;">translate</span><span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">),</span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="cpp"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padEnd</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">),</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="cpp"> <span class="p">}</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="cpp"><span class="p">}</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="cpp"></span>
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950
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<pre style="margin: 0;"> <span id="LC950" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Scan one query sequence against one database volume</span></span>
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951
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<pre style="margin: 0;"> <span id="LC951" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">scan</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC916" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SubstitutionMatrices</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">uchar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">querySeq</span><span class="p">)</span> <span class="p">{</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SubstitutionMatrices</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">uchar</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;">querySeq</span><span class="p">)</span> <span class="p">{</span></span>
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917
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953
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<pre style="margin: 0;"> <span id="LC953" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">// we just want match counts</span></span>
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954
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="cpp"> <span class="n" style="color: #333;">countMatches</span><span class="p">(</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span> <span class="p">);</span></span>
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919
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955
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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956
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="cpp"> <span class="p">}</span></span>
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957
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC922" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">isMask</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">maskLowercase</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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923
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<pre style="margin: 0;">-<span id="LC923" class="line" lang="cpp"> <span class="n" style="color: #333;">makeQualityPssm</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">isMask</span></span><span class="p">);</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maskMode</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">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">maskLowercase</span></span><span class="p">;</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"> <span class="n" style="color: #333;">makeQualityPssm</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">maskMode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="924" 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">
924
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="cpp"></span>
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925
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<td class="diff-line-num new_line" data-linenumber="961" 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">
961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="cpp"> <span class="n" style="color: #333;">SegmentPairPot</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="926" 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">
926
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<td class="diff-line-num new_line" data-linenumber="962" 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">
962
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="cpp"> <span class="n" style="color: #333;">alignGapless</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="927" 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">
927
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<td class="diff-line-num new_line" data-linenumber="963" 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">
963
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// we just want gapless alignments</span></span>
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<td class="diff-line-num old_line" data-linenumber="928" 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">
928
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964
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<pre style="margin: 0;"> <span id="LC964" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gaplessAlns</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;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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929
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="930" 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">
930
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<td class="diff-line-num new_line old" data-linenumber="966" 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="LC930" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">maskLowercase</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">maskLowercase</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="931" 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">
931
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">makeQualityPssm</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">aligner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">queryNum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matrices</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">querySeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="932" 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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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">maskMode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">maskMode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">isFullScoreThreshold</span></span><span class="p"><span class="idiff right">())</span>)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="967" 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">
967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">unmaskLowercase</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">aligner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">queryNum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matrices</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">querySeq</span></span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="932" 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">
932
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968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="933" 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">
933
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<td class="diff-line-num new_line" data-linenumber="969" 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">
969
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<pre style="margin: 0;"> <span id="LC969" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentPot</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="934" 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">
934
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<td class="diff-line-num new_line" data-linenumber="970" 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">
970
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="935" 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">
935
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<td class="diff-line-num new_line old" data-linenumber="971" 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="LC935" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropFinal</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropGapped</span> <span class="p">){</span></span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropFinal</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropGapped</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">maskMode</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;">isFullScoreThreshold</span><span class="p">()))</span> <span class="p">{</span></span>
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936
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<td class="diff-line-num new_line" data-linenumber="973" 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">
973
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="cpp"> <span class="n" style="color: #333;">alignGapped</span><span class="p">(</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="937" 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">
937
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<td class="diff-line-num new_line" data-linenumber="974" 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">
974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="cpp"> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gapped</span> <span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="938" 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">
938
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975
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="cpp"> <span class="n" style="color: #333;">erase_if</span><span class="p">(</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">,</span> <span class="n" style="color: #333;">SegmentPairPot</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isNotMarkedAsGood</span> <span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="976" 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">
976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maskMode</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;">isFullScoreThreshold</span><span class="p">())</span></span>
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<td class="diff-line-num new old_line" data-linenumber="939" 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="977" 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">
977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="cpp"> <span class="n" style="color: #333;">unmaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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939
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<td class="diff-line-num new_line" data-linenumber="978" 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">
978
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<pre style="margin: 0;"> <span id="LC978" class="line" lang="cpp"> <span class="p">}</span></span>
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940
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979
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<pre style="margin: 0;"> <span id="LC979" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="941" 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">
941
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<td class="diff-line-num new_line" data-linenumber="980" 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">
980
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<pre style="margin: 0;"> <span id="LC980" class="line" lang="cpp"> <span class="n" style="color: #333;">alignGapped</span><span class="p">(</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="942" 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">
942
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<td class="diff-line-num new_line" data-linenumber="981" 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">
981
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<pre style="margin: 0;"> <span id="LC981" class="line" lang="cpp"> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">final</span> <span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="943" 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">
943
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<td class="diff-line-num new_line" data-linenumber="982" 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">
982
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gappedAlns</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;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="944" 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">
944
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<td class="diff-line-num new_line" data-linenumber="983" 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">
983
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<pre style="margin: 0;"> <span id="LC983" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="945" 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">
945
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<td class="diff-line-num new_line old" data-linenumber="984" 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="LC945" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">maskLowercase</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="946" 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">
946
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<td class="diff-line-num new_line old" data-linenumber="984" 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="LC946" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">makeQualityPssm</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">aligner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">queryNum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matrices</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">querySeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">true</span></span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="947" 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="984" 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">
984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">maskMode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">isFullScoreThreshold</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="947" 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="985" 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">
985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">remaskLowercase</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">aligner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">queryNum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matrices</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">querySeq</span></span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="947" 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">
947
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<td class="diff-line-num new_line" data-linenumber="986" 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">
986
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<pre style="margin: 0;"> <span id="LC986" class="line" lang="cpp"> <span class="n" style="color: #333;">eraseWeakAlignments</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="948" 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">
948
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<td class="diff-line-num new_line" data-linenumber="987" 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">
987
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<pre style="margin: 0;"> <span id="LC987" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG2</span><span class="p">(</span><span class="s" style="color: #d14;">"lowercase-filtered alignments="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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949
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988
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<pre style="margin: 0;"> <span id="LC988" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gappedAlns</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;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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950
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989
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<pre style="margin: 0;"> <span id="LC989" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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951
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">makeQualityPssm</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">aligner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">queryNum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matrices</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">querySeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">);</span></span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">unmaskLowercase</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">aligner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">queryNum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matrices</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">querySeq</span></span><span class="p">);</span></span>
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952
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991
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<pre style="margin: 0;"> <span id="LC991" class="line" lang="cpp"> <span class="p">}</span></span>
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953
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992
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="cpp"></span>
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993
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<pre style="margin: 0;"> <span id="LC993" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span> <span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">// we want non-redundant alignments</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="961" 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">@@ -961,9 +1000,9 @@ void scan(LastAligner& aligner, size_t queryNum,</td>
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1000
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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="cpp"><span class="p">}</span></span>
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1001
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="cpp"></span>
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963
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1002
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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tantanMaskOneQuery</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">querySeq</span><span class="p">)</span> <span class="p">{</span></span>
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964
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<pre style="margin: 0;">-<span id="LC964" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">b<span class="idiff left right">eg</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">);</span></span>
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965
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<pre style="margin: 0;">-<span id="LC965" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">e<span class="idiff left right">nd</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqEnd</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">);</span></span>
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966
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<pre style="margin: 0;">-<span id="LC966" class="line" lang="cpp"> <span class="n" style="color: #333;">tantanMasker</span><span class="p">.</span><span class="n" style="color: #333;">mask</span><span class="p">(</span><span class="n" style="color: #333;">querySeq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b<span class="idiff left">eg</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">querySeq</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">end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">a</span>lph</span><span class="p">.</span><span class="n" style="color: #333;">numbersToLowercase</span><span class="p">);</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1004" 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">
1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqEnd</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="967" 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="1005" 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">
1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="cpp"> <span class="n" style="color: #333;">tantanMasker</span><span class="p">.</span><span class="n" style="color: #333;">mask</span><span class="p">(</span><span class="n" style="color: #333;">querySeq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">querySeq</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">e</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">queryA</span>lph</span><span class="p">.</span><span class="n" style="color: #333;">numbersToLowercase</span><span class="p">);</span></span>
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967
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1006
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<pre style="margin: 0;"> <span id="LC1006" class="line" lang="cpp"><span class="p">}</span></span>
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968
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1007
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<pre style="margin: 0;"> <span id="LC1007" class="line" lang="cpp"></span>
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969
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1008
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tantanMaskTranslatedQuery</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">querySeq</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="984" 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">@@ -984,28 +1023,43 @@ static void tantanMaskTranslatedQuery(size_t queryNum, uchar *querySeq) {</td>
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984
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1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// after optionally translating and/or masking the query</span></span>
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985
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1024
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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">translateAndScan</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span></span>
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986
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1025
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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SubstitutionMatrices</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrices</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="987" 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">
987
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<pre style="margin: 0;">-<span id="LC987" 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;">querySeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqReader</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">);</span></span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">querySeqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqWriter</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1027" 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">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="cpp"> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">querySeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querySeqs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">);</span></span>
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988
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1028
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<pre style="margin: 0;"> <span id="LC1028" 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;">uchar</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">modifiedQuery</span><span class="p">;</span></span>
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989
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1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padLen</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">);</span></span>
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990
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1030
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="cpp"></span>
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991
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<pre style="margin: 0;">-<span id="LC991" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isTranslated</span><span class="p">()</span> <span class="p">){</span></span>
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992
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<pre style="margin: 0;">-<span id="LC992" class="line" lang="cpp"> <span class="n" style="color: #333;">modifiedQuery</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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<td class="diff-line-num old old_line" data-linenumber="993" 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">
993
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<pre style="margin: 0;">-<span id="LC993" class="line" lang="cpp"> <span class="n" style="color: #333;">geneticCode</span><span class="p">.</span><span class="n" style="color: #333;">translate</span><span class="p">(</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span> <span class="o" style="font-weight: 600;">+</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;">modifiedQuery</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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994
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<pre style="margin: 0;">-<span id="LC994" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">isCodonCols</span><span class="p">()</span> <span class="p">){</span></span>
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995
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="cpp"> <span class="n" style="color: #333;">tantanMaskTranslatedQuery</span><span class="p">(</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modifiedQuery</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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1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isTranslated</span><span class="p">())</span> <span class="p">{</span></span>
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1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">isCodonCols</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1033" 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">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isKeepLowercase</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1034" 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">
1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="cpp"> <span class="n" style="color: #333;">err</span><span class="p">(</span><span class="s" style="color: #d14;">"can't keep lowercase & find simple repeats & use codons"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1035" 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">
1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1036" 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">
1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="cpp"> <span class="n" style="color: #333;">tantanMaskOneQuery</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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996
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<td class="diff-line-num new_line" data-linenumber="1037" 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">
1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1038" 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">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="cpp"> <span class="n" style="color: #333;">modifiedQuery</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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<td class="diff-line-num new new_line" data-linenumber="1039" 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">
1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="cpp"> <span class="n" style="color: #333;">geneticCode</span><span class="p">.</span><span class="n" style="color: #333;">translate</span><span class="p">(</span><span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span> <span class="o" style="font-weight: 600;">+</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;">modifiedQuery</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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997
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1040
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="cpp"> <span class="n" style="color: #333;">querySeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modifiedQuery</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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998
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<td class="diff-line-num new_line old" data-linenumber="1041" 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="LC998" 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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999
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<pre style="margin: 0;">-<span id="LC999" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</span> <span class="p">){</span></span>
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1000
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<td class="diff-line-num new_line old" data-linenumber="1041" 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="LC1000" class="line" lang="cpp"> <span class="n" style="color: #333;">modifiedQuery</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">size</span> <span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1001" 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">
1001
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<pre style="margin: 0;">-<span id="LC1001" class="line" lang="cpp"> <span class="n" style="color: #333;">tantanMaskOneQuery</span><span class="p">(</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modifiedQuery</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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<td class="diff-line-num old old_line" data-linenumber="1002" 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">
1002
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<td class="diff-line-num new_line old" data-linenumber="1041" 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="LC1002" class="line" lang="cpp"> <span class="n" style="color: #333;">querySeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modifiedQuery</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">isCodonCols</span><span class="p">())</span> <span class="p">{</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cpp"> <span class="n" style="color: #333;">tantanMaskTranslatedQuery</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1043" 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">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1044" 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">
1044
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<pre style="margin: 0;">+<span id="LC1044" 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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<td class="diff-line-num new new_line" data-linenumber="1045" 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">
1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1046" 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">
1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isKeepLowercase</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1047" 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">
1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="cpp"> <span class="n" style="color: #333;">modifiedQuery</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="cpp"> <span class="n" style="color: #333;">querySeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modifiedQuery</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="cpp"> <span class="p">}</span></span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="cpp"> <span class="n" style="color: #333;">tantanMaskOneQuery</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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1003
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1051
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="cpp"> <span class="p">}</span></span>
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1004
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1052
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="cpp"> <span class="p">}</span></span>
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1005
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1053
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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="cpp"></span>
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1006
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1054
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">oldNumOfAlns</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;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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1007
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1055
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="cpp"> <span class="n" style="color: #333;">scan</span><span class="p">(</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span> <span class="p">);</span></span>
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1008
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<td class="diff-line-num new_line" data-linenumber="1056" 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">
1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="cpp"> <span class="n" style="color: #333;">cullFinalAlignments</span><span class="p">(</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">textAlns</span><span class="p">,</span> <span class="n" style="color: #333;">oldNumOfAlns</span> <span class="p">);</span></span>
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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="cpp"></span>
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isKeepLowercase</span><span class="p">)</span> <span class="p">{</span></span>
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1059
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<pre style="margin: 0;">+<span id="LC1059" 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="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</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;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqEnd</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</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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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="cpp"> <span class="n" style="color: #333;">querySeqs</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;">queryAlph</span><span class="p">.</span><span class="n" style="color: #333;">numbersToUppercase</span><span class="p">[</span><span class="n" style="color: #333;">querySeqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]];</span></span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="cpp"> <span class="p">}</span></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="cpp"> <span class="p">}</span></span>
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1009
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1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="cpp"><span class="p">}</span></span>
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1010
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1064
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="cpp"></span>
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1011
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1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">alignOneQuery</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1103" 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="1157" 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">@@ -1103,7 +1157,7 @@ int calcMinScoreGapless(double numLettersInReference) {</td>
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1103
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1157
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<pre style="margin: 0;"> <span id="LC1157" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// This attempts to ensure that the gapped alignment phase will be</span></span>
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1104
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1158
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<pre style="margin: 0;"> <span id="LC1158" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// reasonably fast relative to the gapless alignment phase.</span></span>
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1105
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1159
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<pre style="margin: 0;"> <span id="LC1159" class="line" lang="cpp"></span>
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1106
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<pre style="margin: 0;">-<span id="LC1106" 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;">gaplessEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">minScoreGapped</span></span><span class="p">;</span></span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" 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;">gaplessEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">ceil</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">minScoreGapped</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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1107
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1161
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<pre style="margin: 0;"> <span id="LC1161" class="line" lang="cpp"></span>
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1108
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1162
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<pre style="margin: 0;"> <span id="LC1162" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxGaplessAlignmentsPerQueryPosition</span><span class="p">;</span></span>
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1109
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1163
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<pre style="margin: 0;"> <span id="LC1163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxGaplessAlignmentsPerQueryPosition</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// ?</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1172" 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">@@ -1118,8 +1172,9 @@ int calcMinScoreGapless(double numLettersInReference) {</td>
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1118
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1172
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<pre style="margin: 0;"> <span id="LC1172" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// trial-and-error. It should depend on the relative speeds of</span></span>
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1119
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1173
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<pre style="margin: 0;"> <span id="LC1173" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// gapless and gapped extensions.</span></span>
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1120
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1174
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<pre style="margin: 0;"> <span id="LC1174" class="line" lang="cpp"></span>
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1121
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<pre style="margin: 0;">-<span id="LC1121" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaplessEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">numLettersInReference</span><span class="p">);</span></span>
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1122
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<pre style="margin: 0;">-<span id="LC1122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">minScoreGapped</span><span class="p">);</span></span>
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1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gaplessEvaluer</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">numLettersInReference</span><span class="p">);</span></span>
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1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">minScoreGapped</span><span class="p">));</span></span>
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1123
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1178
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<pre style="margin: 0;"> <span id="LC1178" class="line" lang="cpp"><span class="p">}</span></span>
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1124
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1179
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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="cpp"></span>
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1125
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1180
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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Read one database volume</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1251" 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="1306" 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">@@ -1251,10 +1306,7 @@ void lastal( int argc, char** argv ){</td>
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1251
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1306
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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="cpp"> <span class="n" style="color: #333;">isKeepRefLowercase</span><span class="p">,</span> <span class="n" style="color: #333;">refTantanSetting</span><span class="p">,</span></span>
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1252
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1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="cpp"> <span class="n" style="color: #333;">isCaseSensitiveSeeds</span><span class="p">,</span> <span class="n" style="color: #333;">isMultiVolume</span><span class="p">,</span></span>
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1253
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1308
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<pre style="margin: 0;"> <span id="LC1308" class="line" lang="cpp"> <span class="n" style="color: #333;">refMinimizerWindow</span><span class="p">,</span> <span class="n" style="color: #333;">aligners</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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1254
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<pre style="margin: 0;">-<span id="LC1254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</span> <span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1255" 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">
1255
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<td class="diff-line-num new_line old" data-linenumber="1309" 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="LC1255" class="line" lang="cpp"> <span class="n" style="color: #333;">tantanMasker</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span> <span class="n" style="color: #333;">isProtein</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</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 old_line" data-linenumber="1256" 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">
1256
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<td class="diff-line-num new_line old" data-linenumber="1309" 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="LC1256" class="line" lang="cpp"> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span> <span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1257" 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">
1257
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<td class="diff-line-num new_line old" data-linenumber="1309" 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="LC1257" class="line" lang="cpp"> <span class="n" style="color: #333;">makeScoreMatrix</span><span class="p">(</span> <span class="n" style="color: #333;">matrixName</span><span class="p">,</span> <span class="n" style="color: #333;">matrixFile</span> <span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1258" 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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1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="cpp"> <span class="n" style="color: #333;">makeScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">matrixName</span><span class="p">,</span> <span class="n" style="color: #333;">matrixFile</span><span class="p">);</span></span>
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1258
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<td class="diff-line-num new_line" data-linenumber="1310" 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">
1310
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<pre style="margin: 0;"> <span id="LC1310" class="line" lang="cpp"> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">delOpenCosts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">delGrowCosts</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1259" 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">
1259
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<td class="diff-line-num new_line" data-linenumber="1311" 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">
1311
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<pre style="margin: 0;"> <span id="LC1311" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">insOpenCosts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">insGrowCosts</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1260" 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">
1260
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<td class="diff-line-num new_line" data-linenumber="1312" 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">
1312
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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">frameshiftCosts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gapPairCost</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1267" 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="1319" 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">@@ -1267,25 +1319,38 @@ void lastal( int argc, char** argv ){</td>
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1267
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<td class="diff-line-num new_line" data-linenumber="1319" 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">
1319
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<pre style="margin: 0;"> <span id="LC1319" class="line" lang="cpp"> <span class="n" style="color: #333;">geneticCode</span><span class="p">.</span><span class="n" style="color: #333;">fromString</span><span class="p">(</span><span class="n" style="color: #333;">GeneticCode</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringFromName</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">geneticCodeFile</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="1268" 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">
1268
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<td class="diff-line-num new_line" data-linenumber="1320" 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">
1320
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">isCodonCols</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1269" 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">
1269
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<td class="diff-line-num new_line" data-linenumber="1321" 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">
1321
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="cpp"> <span class="n" style="color: #333;">geneticCode</span><span class="p">.</span><span class="n" style="color: #333;">initCodons</span><span class="p">(</span><span class="n" style="color: #333;">queryAlph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">,</span></span>
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1270
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<td class="diff-line-num new_line old" data-linenumber="1322" 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="LC1270" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1271" 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="1322" 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">
1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">maskLowercase</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">);</span></span>
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1271
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<td class="diff-line-num new_line" data-linenumber="1323" 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">
1323
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<pre style="margin: 0;"> <span id="LC1323" 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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1272
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<td class="diff-line-num new_line" data-linenumber="1324" 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">
1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="cpp"> <span class="n" style="color: #333;">geneticCode</span><span class="p">.</span><span class="n" style="color: #333;">codeTableSet</span><span class="p">(</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">queryAlph</span> <span class="p">);</span></span>
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1273
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1325
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<pre style="margin: 0;"> <span id="LC1325" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1274" 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">
1274
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<td class="diff-line-num new_line" data-linenumber="1326" 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">
1326
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="cpp"> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">initForAppending</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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1275
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<td class="diff-line-num new_line old" data-linenumber="1327" 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="LC1275" class="line" lang="cpp"> <span class="p">}</span></span>
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1276
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<td class="diff-line-num new_line old" data-linenumber="1327" 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="LC1276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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1327
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<pre style="margin: 0;">+<span id="LC1327" 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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1328
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<pre style="margin: 0;"> <span id="LC1328" class="line" lang="cpp"> <span class="n" style="color: #333;">queryAlph</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alph</span><span class="p">;</span></span>
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1278
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1329
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<pre style="margin: 0;"> <span id="LC1329" class="line" lang="cpp"> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">initForAppending</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1279
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1330
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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="cpp"> <span class="p">}</span></span>
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1280
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1331
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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="cpp"></span>
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1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</span><span class="p">)</span> <span class="p">{</span></span>
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1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAtRichDna</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</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="1334" 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">
1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">isCodonCols</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1335" 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">
1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="cpp"> <span class="n" style="color: #333;">tantanMasker</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">isAtRichDna</span><span class="p">,</span> <span class="n" style="color: #333;">queryAlph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">,</span> <span class="n" style="color: #333;">queryAlph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">);</span></span>
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1336
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<pre style="margin: 0;">+<span id="LC1336" 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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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="cpp"> <span class="n" style="color: #333;">tantanMasker</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">isProtein</span><span class="p">,</span> <span class="n" style="color: #333;">isAtRichDna</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">);</span></span>
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1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="cpp"> <span class="p">}</span></span>
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1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="cpp"> <span class="p">}</span></span>
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1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="cpp"></span>
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1281
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1341
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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1282
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1342
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="cpp"> <span class="n" style="color: #333;">calculateScoreStatistics</span><span class="p">(</span><span class="n" style="color: #333;">matrixName</span><span class="p">,</span> <span class="n" style="color: #333;">refLetters</span><span class="p">,</span> <span class="n" style="color: #333;">refMaxSeqLen</span><span class="p">);</span></span>
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1283
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1343
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="cpp"> <span class="p">}</span></span>
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1284
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1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="cpp"></span>
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1285
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<pre style="margin: 0;">-<span id="LC1285" 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="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxEvalue</span> <span class="o" style="font-weight: 600;">></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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxEvalue</span><span class="p">,</span> <span class="mf" style="color: #099;">1e18</span><span class="p">)</span></span>
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1286
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<pre style="margin: 0;">-<span id="LC1286" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">queryLettersPerRandomAlignment</span><span class="p">);</span></span>
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1287
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<pre style="margin: 0;">-<span id="LC1287" class="line" lang="cpp"></span>
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1288
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<pre style="margin: 0;">-<span id="LC1288" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eg2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="mf" style="color: #099;">1e18</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">evaluePerArea</span><span class="p">(</span><span class="n" style="color: #333;">minScore</span><span class="p">)</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="LC1345" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minScore</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="LC1346" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eg2</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="LC1347" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">isGood</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="cpp"> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxEvalue</span> <span class="o" style="font-weight: 600;">></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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxEvalue</span><span class="p">,</span> <span class="mf" style="color: #099;">1e18</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">queryLettersPerRandomAlignment</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1350" 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;">isFullScoreThreshold</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="cpp"> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="mf" style="color: #099;">1.0</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="LC1352" class="line" lang="cpp"> <span class="n" style="color: #333;">eg2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1e18</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">evaluePerArea</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="LC1353" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1354" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">setDefaultsFromMatrix</span><span class="p">(</span><span class="n" style="color: #333;">fwdMatrices</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">(),</span> <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">eg2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="cpp"> <span class="n" style="color: #333;">minScoreGapless</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calcMinScoreGapless</span><span class="p">(</span><span class="n" style="color: #333;">refLetters</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#de4252990d12a909e50ff0b994d1715eae0ea5fd"><strong>src/lastdb.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,6 +27,7 @@ typedef unsigned long long countT;</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Set up an alphabet (e.g. DNA or protein), based on the user options</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;">void</span> <span class="nf" style="color: #900; font-weight: 600;">makeAlphabet</span><span class="p">(</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastdbArguments</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">args</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC29" 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;">args</span><span class="p">.</span><span class="n" style="color: #333;">userAlphabet</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">)</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">fromString</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">userAlphabet</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;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isAddStops</span> <span class="p">)</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">fromString</span><span class="p">(</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">proteinWithStop</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isProtein</span> <span class="p">)</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">fromString</span><span class="p">(</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">protein</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">fromString</span><span class="p">(</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">dna</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC33" 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="343" 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="344" 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">@@ -343,7 +344,7 @@ void lastdb( int argc, char** argv ){</td>
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343
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span><span class="s" style="color: #d14;">"wordLength="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">wordsFinder</span><span class="p">.</span><span class="n" style="color: #333;">wordLength</span><span class="p">);</span></span>
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344
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"></span>
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345
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">MultiSequence</span> <span class="n" style="color: #333;">multi</span><span class="p">;</span></span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">multi</span><span class="p">.</span><span class="n" style="color: #333;">initForAppending</span><span class="p">(</span><span class="mi" style="color: #099;">1</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;">multi</span><span class="p">.</span><span class="n" style="color: #333;">initForAppending</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">isAddStops</span></span><span class="p">);</span></span>
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347
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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;">alph</span><span class="p">.</span><span class="n" style="color: #333;">tr</span><span class="p">(</span><span class="n" style="color: #333;">multi</span><span class="p">.</span><span class="n" style="color: #333;">seqWriter</span><span class="p">(),</span> <span class="n" style="color: #333;">multi</span><span class="p">.</span><span class="n" style="color: #333;">seqWriter</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">multi</span><span class="p">.</span><span class="n" style="color: #333;">seqBeg</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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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">volumeNumber</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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349
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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;">countT</span> <span class="n" style="color: #333;">sequenceCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="365" 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="366" 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">@@ -365,7 +366,7 @@ void lastdb( int argc, char** argv ){</td>
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365
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequenceCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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366
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367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="cpp"> <span class="n" style="color: #333;">maxSeqLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxLettersPerVolume</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">wordsFinder</span><span class="p">,</span></span>
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367
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp"> <span class="n" style="color: #333;">multi</span><span class="p">.</span><span class="n" style="color: #333;">qualsPerLetter</span><span class="p">(),</span> <span class="n" style="color: #333;">seeds</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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368
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="cpp"> <span class="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;">args</span><span class="p">.</span><span class="n" style="color: #333;">isProtein</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">userAlphabet</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" 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;">args</span><span class="p">.</span><span class="n" style="color: #333;">isProtein</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isAddStops</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">userAlphabet</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span></span>
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369
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">isDubiousDna</span><span class="p">(</span><span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">multi</span><span class="p">))</span> <span class="p">{</span></span>
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370
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">programName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">": that's some funny-lookin DNA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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371
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#b8658dba55bc28b741dfef5e4ea001b2623bdb9e"><strong>src/mcf_frameshift_xdrop_aligner.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">@@ -6,6 +6,7 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <assert.h></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 <math.h></span></span>
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8
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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="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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<pre style="margin: 0;"> <span id="LC10" 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="LC11" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC12" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -366,14 +367,141 @@ void FrameshiftXdropAligner::count(bool isRightwardExtension,</td>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</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;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ins1</span><span class="p">;</span></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ins2</span><span class="p">;</span></span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ins3</span><span class="p">;</span></span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</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;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb3</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">insNext</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</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;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delNext</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// deleted whole codons</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insNext</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// inserted whole codons</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">del3</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// in-frame opens/closes</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</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;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ins3</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// in-frame opens/closes</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"></span>
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373
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">del1</span><span class="p">;</span></span>
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374
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">del2</span><span class="p">;</span></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">del3</span><span class="p">;</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb3</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">delNext</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">del3</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;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ins1</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="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ins2</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="p">}</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">FrameshiftXdropAligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">maxSumOfProbRatios</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;">protein</span><span class="p">,</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">proteinLength</span><span class="p">,</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="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;">tranDna</span><span class="p">,</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tranDnaLength</span><span class="p">,</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">)</span> <span class="p">{</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delProb1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb1</span><span class="p">;</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delProb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb2</span><span class="p">;</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delProb3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb3</span><span class="p">;</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insProb1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb1</span><span class="p">;</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insProb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb2</span><span class="p">;</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insProb3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb3</span><span class="p">;</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"></span>
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396
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<pre style="margin: 0;">+<span id="LC396" 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;">proteinSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proteinLength</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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397
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<pre style="margin: 0;">+<span id="LC397" 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;">tranDnaSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tranDnaLength</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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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="n" style="color: #333;">xFwdProbs</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">tranDnaSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">proteinSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tranDnaSize</span><span class="p">);</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">delRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xFwdProbs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">newRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delRow</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tranDnaSize</span><span class="p">;</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Y1</span><span class="p">,</span> <span class="n" style="color: #333;">Y2</span><span class="p">,</span> <span class="n" style="color: #333;">Y3</span><span class="p">,</span> <span class="n" style="color: #333;">Z1</span><span class="p">,</span> <span class="n" style="color: #333;">Z2</span><span class="p">,</span> <span class="n" style="color: #333;">Z3</span><span class="p">;</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</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;">Z3</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="404" 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">
404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tranDnaSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="405" 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">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z1</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;">insProb1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z2</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;">insProb2</span><span class="p">;</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insProb3</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="408" 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">
408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</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;">z2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</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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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</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;">b</span><span class="p">;</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="n" style="color: #333;">delRow</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;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delOpenProb</span><span class="p">;</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="n" style="color: #333;">Z3</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="LC412" class="line" lang="cpp"> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z1</span><span class="p">;</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</span><span class="p">;</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="p">}</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"></span>
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416
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<pre style="margin: 0;">+<span id="LC416" 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;">1</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;">proteinSize</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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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="n" style="color: #333;">protein</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]];</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">oldRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newRow</span><span class="p">;</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tranDnaSize</span><span class="p">;</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="n" style="color: #333;">Y2</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;">Z3</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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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="p">{</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delRow</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb3</span><span class="p">;</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">y3</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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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</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;">b</span><span class="p">;</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;">delRow</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;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y3</span><span class="p">;</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span><span class="p">;</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC431" 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;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tranDnaSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">Y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y2</span><span class="p">;</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">Y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span><span class="p">;</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delRow</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldRow</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;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">substitutionRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDna</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;">1</span><span class="p">]];</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y1</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;">delProb1</span><span class="p">;</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y2</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;">delProb2</span><span class="p">;</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb3</span><span class="p">;</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z1</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;">insProb1</span><span class="p">;</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z2</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;">insProb2</span><span class="p">;</span></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insProb3</span><span class="p">;</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</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;">y1</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;">y3</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;">z2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</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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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</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;">b</span><span class="p">;</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"> <span class="n" style="color: #333;">delRow</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;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y3</span><span class="p">;</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"> <span class="n" style="color: #333;">Z3</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="LC446" class="line" lang="cpp"> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxValue</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="LC452" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</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;">Z3</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="LC454" 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="n" style="color: #333;">tranDnaSize</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">--</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z1</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;">insProb1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z2</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;">insProb2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insProb3</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</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;">z2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</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="LC459" class="line" lang="cpp"> <span class="n" style="color: #333;">maxValue</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;">maxValue</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;">newRow</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="LC460" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</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;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="n" style="color: #333;">delRow</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;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delOpenProb</span><span class="p">;</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="n" style="color: #333;">Z3</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="LC463" class="line" lang="cpp"> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC467" 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="n" style="color: #333;">proteinLength</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="n" style="color: #333;">protein</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="LC469" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">oldRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newRow</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">tranDnaSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"> <span class="n" style="color: #333;">Y2</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;">Z3</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="LC472" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"> <span class="p">{</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDnaLength</span><span class="p">];</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb3</span><span class="p">;</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">y3</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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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"> <span class="n" style="color: #333;">maxValue</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;">maxValue</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;">newRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDnaLength</span><span class="p">]);</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDnaLength</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp"> <span class="n" style="color: #333;">delRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDnaLength</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y3</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"></span>
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483
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<pre style="margin: 0;">+<span id="LC483" 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="n" style="color: #333;">tranDnaLength</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">--</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;)</span> <span class="p">{</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="n" style="color: #333;">Y1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"> <span class="n" style="color: #333;">Y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span><span class="p">;</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delRow</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldRow</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;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">substitutionRow</span><span class="p">[</span><span class="n" style="color: #333;">tranDna</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]];</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y1</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;">delProb1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y2</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;">delProb2</span><span class="p">;</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Y3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delProb3</span><span class="p">;</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z1</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;">insProb1</span><span class="p">;</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z2</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;">insProb2</span><span class="p">;</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insProb3</span><span class="p">;</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</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;">y1</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;">y3</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;">z2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</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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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">maxValue</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;">maxValue</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;">newRow</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"> <span class="n" style="color: #333;">newRow</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;">b</span><span class="p">;</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"> <span class="n" style="color: #333;">delRow</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;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y3</span><span class="p">;</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"> <span class="n" style="color: #333;">Z3</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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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z1</span><span class="p">;</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"> <span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z3</span><span class="p">;</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"> <span class="p">}</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">maxValue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC507" 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/4dc09e39224756822117fb8a9fed8dbdf3619956#7b7b86f617ae717ef44a71c27b54fe7b613973d1"><strong>src/mcf_frameshift_xdrop_aligner.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">@@ -54,6 +54,12 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">xFwdProbs</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;">xBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">totalNumOfCells</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">7</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="LC55" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// tranDna should point to translated DNA: frame 012012012...</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;">double</span> <span class="n" style="color: #333;">maxSumOfProbRatios</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;">protein</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">proteinLength</span><span class="p">,</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="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;">tranDna</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tranDnaLength</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;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</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="nl">private:</span></span>
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<pre style="margin: 0;"> <span id="LC64" 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;">Prob</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">xFwdProbs</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;">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;">Prob</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">yFwdProbs</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/4dc09e39224756822117fb8a9fed8dbdf3619956#f9ba055bb143316361a1f420366c034ad9589728"><strong>src/mcf_substitution_matrix_stats.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">@@ -18,6 +18,8 @@ const struct {</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="p">}</span> <span class="n" style="color: #333;">substitutionMatrixScales</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</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 class="s" style="color: #d14;">"BL62"</span><span class="p">,</span> <span class="mf" style="color: #099;">3.0861133577701141</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"BL80"</span><span class="p">,</span> <span class="mf" style="color: #099;">2.8253295934982616</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 class="s" style="color: #d14;">"MIQS"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"PAM10"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"PAM30"</span><span class="p">,</span> <span class="mf" style="color: #099;">2.8848596855435313</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>
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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">@@ -100,21 +102,30 @@ void SubstitutionMatrixStats::calcBias(const const_int_ptr *scoreMatrix,</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubstitutionMatrixStats</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">calcUnbiased</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrixName</span><span class="p">,</span></span>
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101
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_int_ptr</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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102
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</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="LC105" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">realSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"></span>
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103
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">COUNTOF</span><span class="p">(</span><span class="n" style="color: #333;">substitutionMatrixScales</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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104
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">matrixName</span><span class="p">,</span> <span class="n" style="color: #333;">substitutionMatrixScales</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">calcFromScale</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">scoreMatrix</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">substitutionMatrixScales</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">scale</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left right">return</span></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;"><span class="idiff left">scale</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">substitutionMatrixScales</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">scale</span></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;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">size</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">20</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">realSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">20</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="p">}</span></span>
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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="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">cbrc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LambdaCalculator</span> <span class="n" style="color: #333;">c</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">calculate</span><span class="p">(</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">size</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;">mLambda</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC113" 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;">isBad</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">calcFromScale</span><span class="p">(</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">realSize</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC117" 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="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">cbrc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LambdaCalculator</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">calculate</span><span class="p">(</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">realSize</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;">mLambda</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">();</span></span>
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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;">isBad</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">mBias</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="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">mLetterProbs1</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs1</span><span class="p">(),</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs1</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left right">s</span>ize</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">mLetterProbs2</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs2</span><span class="p">(),</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs2</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left right">s</span>ize</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;">mLetterProbs1</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs1</span><span class="p">(),</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs1</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left right">realS</span>ize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">mLetterProbs2</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs2</span><span class="p">(),</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">letterProbs2</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left right">realS</span>ize</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>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">mLetterProbs1</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">mLetterProbs1</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">realSize</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">mLetterProbs2</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">mLetterProbs2</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">realSize</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SubstitutionMatrixStats</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">flipDnaStrands</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">complement</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"11<span class="idiff left right">45</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;">"11<span class="idiff left right">67</span>"</span></span></pre>
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