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GitLab

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<h3>

Nilesh Patra pushed to branch master

at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/649febce00d36a9bea89dda4805e112d5f9d052e">649febce</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-11T02:56:23+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1145</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/a86dc0d1495dfb4a3002249fcba4ca6f22cf7fc4">a86dc0d1</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-11T02:56:23+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/25043627750ce080ba2db6a8554376ba6dcb3c5e">25043627</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-11T02:56:25+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1145'

Update to upstream version '1145'

with Debian dir c9929103cb5326fea16f17460ac3d39c784c60ac</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/ecb816aebfd4f2ff823ad8c831db121fee56d7e8">ecb816ae</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-11T02:58:36+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/5c0d82d459d98ffaac17546c38e70b2500d73072">5c0d82d4</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-11T02:58:49+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>24 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#57bf262130f956caf76c405086f0815caf4e0a89">

ChangeLog.txt

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#3aa5932f37417bf29a460d19625313d84f634221">

debian/patches/helpMakefiles.patch

</a>

</li>

<li class="file-stats">

<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">

debian/patches/simde

</a>

</li>

<li class="file-stats">

<a href="#4db689a65e7ef5a4449dcfaf14aed62c7a3556a1">

doc/last-split.html

</a>

</li>

<li class="file-stats">

<a href="#5f5e686e75cf05fe83c2679635e96a5c9230bd0f">

doc/last-split.txt

</a>

</li>

<li class="file-stats">

<a href="#5e55dbeefff2057b414960d9467d183920e31b8a">

src/Alignment.cc

</a>

</li>

<li class="file-stats">

<a href="#bd17e03c676d289c9cc5bb117da6d9d2bde74764">

src/Alignment.hh

</a>

</li>

<li class="file-stats">

<a href="#8758dc959aa5524be83960d0bfd56945bc432a26">

src/AlignmentWrite.cc

</a>

</li>

<li class="file-stats">

<a href="#76a46dca9f85ee73b2a8d67a89f4b9bf80c34b4b">

src/Centroid.cc

</a>

</li>

<li class="file-stats">

<a href="#7cc18ac8f8022614b0ff31ec1eeb4152cd88880e">

src/Centroid.hh

</a>

</li>

<li class="file-stats">

<a href="#8f014a93cf121af8fe88d03244d4d4b173d32a6d">

src/GappedXdropAligner.cc

</a>

</li>

<li class="file-stats">

<a href="#30d72e7e81ec011dcda59c2395cb78f718d054e4">

src/GappedXdropAligner2qual.cc

</a>

</li>

<li class="file-stats">

<a href="#fe292bc81098de48178ce05c67f141fe55186348">

src/GappedXdropAlignerDna.cc

</a>

</li>

<li class="file-stats">

<a href="#aa38e532f19f245fda3e2e3b5a4ac462598ab91f">

src/GappedXdropAlignerFrame.cc

</a>

</li>

<li class="file-stats">

<a href="#35f9fe39feef01a50cdd57a941b460c37cbaffba">

src/GappedXdropAlignerPssm.cc

</a>

</li>

<li class="file-stats">

<a href="#4b7be8c3b80efc62977b307791d1a304c23e1fa4">

src/LastalArguments.cc

</a>

</li>

<li class="file-stats">

<a href="#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">

src/lastal.cc

</a>

</li>

<li class="file-stats">

<a href="#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">

src/makefile

</a>

</li>

<li class="file-stats">

<a href="#b8658dba55bc28b741dfef5e4ea001b2623bdb9e">

<span class="new-file">

+

src/mcf_frameshift_xdrop_aligner.cc

</span>

</a>

</li>

<li class="file-stats">

<a href="#7b7b86f617ae717ef44a71c27b54fe7b613973d1">

<span class="new-file">

+

src/mcf_frameshift_xdrop_aligner.hh

</span>

</a>

</li>

<li class="file-stats">

<a href="#8266f3ec3e8e19e5efa1a2f239f8ba579e89eb00">

src/mcf_gap_costs.cc

</a>

</li>

<li class="file-stats">

<a href="#f4c2aa5ffe5ddbfe5093d67a91ae22b61c035703">

src/mcf_gap_costs.hh

</a>

</li>

<li class="file-stats">

<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">

src/version.hh

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="57bf262130f956caf76c405086f0815caf4e0a89">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2020-11-06  Martin C. Frith  <Martin C. Frith></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">      * src/mcf_frameshift_xdrop_aligner.hh:</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">      Try to appease C++ compilers</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">      [62a147543f2b] [tip]</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">      * doc/last-split.txt:</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">      Add awk mismap trick to doc</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">      [aabc3e86c600]</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">     * src/GappedXdropAlignerFrame.cc:</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">     Refactor</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

13

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">     [10c6c0ff4ac2]</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">     * src/GappedXdropAligner.cc, src/GappedXdropAligner2qual.cc,</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">     src/GappedXdropAlignerDna.cc, src/GappedXdropAlignerFrame.cc,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">     src/GappedXdropAlignerPssm.cc:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">     Refactor</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">     [0bff03a84a63]</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">     * src/Alignment.cc, src/Alignment.hh, src/AlignmentWrite.cc,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">     src/LastalArguments.cc, src/lastal.cc, src/makefile,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">     src/mcf_frameshift_xdrop_aligner.cc,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">     src/mcf_frameshift_xdrop_aligner.hh, test/last-test.out, test/last-</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(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="LC25" class="line" lang="plaintext">     test.sh:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">     Add probabilities for new-style frameshifts</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">     [8b133765d82e]</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">2020-11-05  Martin C. Frith  <Martin C. Frith></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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30

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">     * src/Alignment.hh, src/Centroid.cc, src/Centroid.hh:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">     Refactor</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">     [8291399ebe14]</span>

</pre>

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34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(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="LC35" class="line" lang="plaintext">     * src/Alignment.hh, src/AlignmentWrite.cc, test/last-test.out, test</span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">     /last-test.sh:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">     Fix protein-codon alignment probabilities</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">     [86ac07a750ac]</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

39

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(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="LC40" class="line" lang="plaintext">2020-11-04  Martin C. Frith  <Martin C. Frith></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="plaintext">     * src/Centroid.cc, src/lastal.cc, src/mcf_gap_costs.cc,</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(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="LC43" class="line" lang="plaintext">     src/mcf_gap_costs.hh:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(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="LC44" class="line" lang="plaintext">     Refactor</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

45

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">     [8383c3867429]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="plaintext">     * src/Alignment.cc, src/Alignment.hh, src/lastal.cc, src/makefile:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">     Refactor</span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">     [115ac5aa5bee]</span>

</pre>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">     * src/Alignment.cc, src/AlignmentWrite.cc:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">     Refactor</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">     [defdc3f2ccdd]</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

54

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(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="LC55" class="line" lang="plaintext">     * src/Alignment.cc:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

56

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">     Refactor</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">     [7b420067c0fa]</span>

</pre>

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58

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

59

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">     * src/Alignment.cc, src/Alignment.hh, src/AlignmentWrite.cc,</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

60

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">     src/Centroid.cc, src/Centroid.hh, src/lastal.cc:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

61

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">     Refactor</span>

</pre>

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62

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">     [60f728268532]</span>

</pre>

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63

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>

</pre>

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1

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<td class="diff-line-num new_line" data-linenumber="64" 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">

64

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">2020-10-14  Martin C. Frith  <Martin C. Frith></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" data-linenumber="65" 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">

65

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="66" 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">

66

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">     * scripts/last-dotplot:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">     last-dotplot: fix crash on long annotation names</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line old" data-linenumber="68" 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="LC5" class="line" lang="plaintext">      [04663552433d]<span class="idiff left right"> [tip]</span></span>

</pre>

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68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">     [04663552433d]</span>

</pre>

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6

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<td class="diff-line-num new_line" data-linenumber="69" 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">

69

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line" data-linenumber="70" 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">

70

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">     * scripts/last-dotplot:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line" data-linenumber="71" 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">

71

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">     last-dotplot: fix crash on annotation names</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">last-align (1145-1) unstable; urgency=medium</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * New upstream version</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com>  Wed, 11 Nov 2020 02:58:49 +0530</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

</pre>

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1

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<td class="diff-line-num new_line" data-linenumber="8" 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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">last-align (1133-1) unstable; urgency=medium</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="9" 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">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre>

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3

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<td class="diff-line-num new_line" data-linenumber="10" 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">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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<br>

</li>

<li id="3aa5932f37417bf29a460d19625313d84f634221">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#3aa5932f37417bf29a460d19625313d84f634221"><strong>debian/patches/helpMakefiles.patch</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" 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="75" 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">@@ -75,5 +75,5 @@</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) -MM alp/*.cpp | sed 's|.*:|alp/&|' >> m</span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) -MM -I. split/*.cc | sed 's|.*:|split/&|' | $(fix8) >> m</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff">  mv m makefile</span>

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<td class="diff-line-num old old_line" data-linenumber="78" 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="LC78" class="line" lang="diff"> Alignment.o Alignment.o8: Alignment.cc Alignment.hh <span class="idiff left right">ScoreMatrixRow.hh SegmentPai</span>r.hh \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff">  mcf_<span class="idiff left right">gap_costs.hh Alphabet.hh Centroid.hh GappedXdropAligner</span>.hh \</span></pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> Alignment.o Alignment.o8: Alignment.cc Alignment.hh <span class="idiff left right">Centroid.hh GappedXdropAligne</span>r.hh \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff">  mcf_<span class="idiff left right">contiguous_queue.hh mcf_reverse_queue.hh mcf_gap_costs</span>.hh \</span></pre>

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<br>

</li>

<li id="4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -159,7 +159,7 @@ equivalents automatically</td>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="diff"> #endif</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="160" 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">

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/GappedXdropAligner.cc</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/GappedXdropAligner.cc</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" 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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<td class="diff-line-num new_line old" data-linenumber="162" 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="LC162" class="line" lang="diff"><span class="p">@@ -14<span class="idiff left right">2,17 +142</span>,13 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="163" style="width: 35px; color: rgba(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="162" style="width: 35px; color: rgba(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="LC162" class="line" lang="diff"><span class="p">@@ -14<span class="idiff left right">0,17 +140</span>,13 @@</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="diff">     if (isAffine) {</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="164" 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">

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="diff">       for (int i = 0; i < numCells; i += simdLen) {</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="165" 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">

165

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<td class="diff-line-num new_line" data-linenumber="165" 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">

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="diff">         SimdInt s = simdSet(</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="179" 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="179" 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">@@ -179,7 +179,7 @@ equivalents automatically</td>

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<td class="diff-line-num old_line" data-linenumber="179" 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">

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<td class="diff-line-num new_line" data-linenumber="179" 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">

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="diff">         SimdInt y = simdSub(simdLoad(y1+i), mDelGrowCost);</span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/GappedXdropAlignerPssm.cc</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="181" 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">

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<td class="diff-line-num new_line" data-linenumber="181" 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">

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/GappedXdropAlignerPssm.cc</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="182" 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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<td class="diff-line-num new_line old" data-linenumber="182" 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="LC182" class="line" lang="diff"><span class="p">@@ -9<span class="idiff left right">3,17 +93</span>,13 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="p">@@ -9<span class="idiff left right">1,17 +91</span>,13 @@</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="diff">     if (isAffine) {</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="184" 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">

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<td class="diff-line-num new_line" data-linenumber="184" 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">

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="diff">       for (int i = 0; i < numCells; i += simdLen) {</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="185" 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">

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<td class="diff-line-num new_line" data-linenumber="185" 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">

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="diff">         SimdInt s = simdSet(</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="318" 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="318" 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">@@ -318,7 +318,7 @@ equivalents automatically</td>

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<td class="diff-line-num old_line" data-linenumber="318" 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">

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<td class="diff-line-num new_line" data-linenumber="318" 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">

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="diff">                  scorer[3][3], scorer[3][2], scorer[3][1], scorer[3][0],</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="319" 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">

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<td class="diff-line-num new_line" data-linenumber="319" 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">

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="diff">                  scorer[2][3], scorer[2][2], scorer[2][1], scorer[2][0],</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="320" 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">

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<td class="diff-line-num new_line" data-linenumber="320" 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">

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="diff">                  scorer[1][3], scorer[1][2], scorer[1][1], scorer[1][0],</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="321" 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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<td class="diff-line-num new_line old" data-linenumber="321" 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="LC321" class="line" lang="diff"><span class="p">@@ -12<span class="idiff left right">8,8 +124</span>,6 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(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="321" style="width: 35px; color: rgba(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="LC321" class="line" lang="diff"><span class="p">@@ -12<span class="idiff left right">6,8 +122</span>,6 @@</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="322" 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">

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<td class="diff-line-num new_line" data-linenumber="322" 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">

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="323" 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">

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<td class="diff-line-num new_line" data-linenumber="323" 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">

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="diff">       for (int i = 0; i < numCells; i += simdBytes) {</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="324" 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">

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<td class="diff-line-num new_line" data-linenumber="324" 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">

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="diff">         SimdInt s = simdSet1(</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="327" 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="327" 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">@@ -327,7 +327,7 @@ equivalents automatically</td>

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<td class="diff-line-num old_line" data-linenumber="327" 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">

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<td class="diff-line-num new_line" data-linenumber="327" 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">

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="diff">                              scorer[s1[31]][s2[31]],</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="328" 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">

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="diff">                              scorer[s1[30]][s2[30]],</span>

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<td class="diff-line-num old_line" data-linenumber="329" 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">

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="diff">                              scorer[s1[29]][s2[29]],</span>

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<td class="diff-line-num old old_line" data-linenumber="330" 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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<td class="diff-line-num new_line old" data-linenumber="330" 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="LC330" class="line" lang="diff"><span class="p">@@ -14<span class="idiff left right">6,7 +140</span>,6 @@</span></span>

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<td class="diff-line-num new old_line" data-linenumber="331" style="width: 35px; color: rgba(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="330" style="width: 35px; color: rgba(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="LC330" class="line" lang="diff"><span class="p">@@ -14<span class="idiff left right">4,7 +138</span>,6 @@</span></span>

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<td class="diff-line-num old_line" data-linenumber="331" 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">

331

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<td class="diff-line-num new_line" data-linenumber="331" 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">

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="diff">                              scorer[s1[18]][s2[18]],</span>

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<td class="diff-line-num old_line" data-linenumber="332" 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">

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<td class="diff-line-num new_line" data-linenumber="332" 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">

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="diff">                              scorer[s1[17]][s2[17]],</span>

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<td class="diff-line-num old_line" data-linenumber="333" 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">

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<td class="diff-line-num new_line" data-linenumber="333" 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">

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="diff">                              scorer[s1[16]][s2[16]],</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="335" 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="335" 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">@@ -335,7 +335,7 @@ equivalents automatically</td>

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<td class="diff-line-num old_line" data-linenumber="335" 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">

335

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335

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="diff">                              scorer[s1[15]][s2[15]],</span>

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<td class="diff-line-num old_line" data-linenumber="336" 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">

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="diff">                              scorer[s1[14]][s2[14]],</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="337" 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">

337

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<td class="diff-line-num new_line" data-linenumber="337" 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">

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="diff">                              scorer[s1[13]][s2[13]],</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="338" 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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<td class="diff-line-num new_line old" data-linenumber="338" 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="LC338" class="line" lang="diff"><span class="p">@@ -16<span class="idiff left right">2,7 +155</span>,6 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="339" style="width: 35px; color: rgba(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="338" style="width: 35px; color: rgba(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="LC338" class="line" lang="diff"><span class="p">@@ -16<span class="idiff left right">0,7 +153</span>,6 @@</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="339" 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">

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="diff">                              scorer[s1[3]][s2[3]],</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="340" 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">

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<td class="diff-line-num new_line" data-linenumber="340" 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">

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="diff">                              scorer[s1[2]][s2[2]],</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="341" 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">

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<td class="diff-line-num new_line" data-linenumber="341" 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">

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="diff">                              scorer[s1[1]][s2[1]],</span>

</pre>

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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -343,7 +343,7 @@ equivalents automatically</td>

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<td class="diff-line-num 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">

343

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<td class="diff-line-num new_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">

343

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="diff">                              scorer[s1[0]][s2[0]]);</span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="345" 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">

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<td class="diff-line-num new_line" data-linenumber="345" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC345" class="line" lang="diff">         SimdInt x = simdAdds1(simdLoad(x2+i), mScoreRise12);</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="346" 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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<td class="diff-line-num new_line old" data-linenumber="346" 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">

</td>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="diff"><span class="p">@@ -27<span class="idiff left right">8,5 +270</span>,3 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="346" style="width: 35px; color: rgba(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="LC346" class="line" lang="diff"><span class="p">@@ -27<span class="idiff left right">7,5 +269</span>,3 @@</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="diff"> }</span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="diff"> }</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="351" 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="351" 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">@@ -351,7 +351,7 @@ equivalents automatically</td>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Alignment.cc</span></span>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Alignment.cc</span></span>

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">57,13 +357</span>,11 @@</span></span>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">74,13 +374</span>,11 @@</span></span>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="diff">                                   del.openCost, del.growCost,</span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="diff">                                   ins.openCost, ins.growCost,</span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="diff">                                   gap.pairCost, gap.isAffine, maxDrop, smMax)</span>

</pre>

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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -365,7 +365,7 @@ equivalents automatically</td>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="diff">     :           aligner.align(seq1 + start1, seq2 + start2,</span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="diff">                               isForward, globality, sm,</span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="diff">                               del.openCost, del.growCost,</span>

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<pre style="margin: 0;">-<span id="LC368" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">383,14 +381</span>,12 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">400,14 +398</span>,12 @@</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="diff">       while( greedyAligner.getNextChunk( end1, end2, size ) )</span>

</pre>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="diff">         chunks.push_back( SegmentPair( end1 - size, end2 - size, size ) );</span>

</pre>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="diff">     }</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">@@ -500,6 +500,14 @@ Error probability &lt;= 10 ^ -((ASCII value - 33) / 10)</td>

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<pre style="margin: 0;"> <span id="LC500" class="line" lang="html">you run last-split twice, as in the genome alignment recipes, the</span>

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<pre style="margin: 0;"> <span id="LC501" class="line" lang="html">mismap is the lowest combined error probability from both <span class="ni" style="color: #800080;">&quot;</span>p<span class="ni" style="color: #800080;">&quot;</span> lines.)<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC502" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"tips"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Tips<span class="nt" style="color: #000080;"></h2></span></span>

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>To omit alignments with mismap probability <span class="ni" style="color: #800080;">&gt;</span> <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> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>10^-6<span class="nt" style="color: #000080;"></span></tt></span> (say), you can</span>

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<pre style="margin: 0;">+<span id="LC506" class="line" lang="html">use the <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> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-m<span class="nt" style="color: #000080;"></span></tt></span> option (see below), or do this:<span class="nt" style="color: #000080;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC508" class="line" lang="html">awk -F= '/^a/ {i = $3 <span class="ni" style="color: #800080;">&lt;</span>= 1e-6} i' out.maf <span class="ni" style="color: #800080;">&gt;</span> out2.maf</span>

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>

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<pre style="margin: 0;">+<span id="LC510" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>

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<pre style="margin: 0;"> <span id="LC511" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"split-versus-spliced-alignment"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Split versus spliced alignment<span class="nt" style="color: #000080;"></h2></span></span>

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<pre style="margin: 0;"> <span id="LC513" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Here is a split alignment:<span class="nt" style="color: #000080;"></p></span></span>

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</li>

<li id="5f5e686e75cf05fe83c2679635e96a5c9230bd0f">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#5f5e686e75cf05fe83c2679635e96a5c9230bd0f"><strong>doc/last-split.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">@@ -111,6 +111,14 @@ The "mismap" is simply the lowest probability from the "p" line.  (If</td>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext">you run last-split twice, as in the genome alignment recipes, the</span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext">mismap is the lowest combined error probability from both "p" lines.)</span>

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113

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">Tips</span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">----</span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">To omit alignments with mismap probability > ``10^-6`` (say), you can</span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">use the ``-m`` option (see below), or do this::</span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

120

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">  awk -F= '/^a/ {i = $3 <= 1e-6} i' out.maf > out2.maf</span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

121

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

114

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<td class="diff-line-num new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

122

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext">Split versus spliced alignment</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

115

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<td class="diff-line-num new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

123

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext">------------------------------</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

116

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<td class="diff-line-num new_line" data-linenumber="124" 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">

124

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext"></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="5e55dbeefff2057b414960d9467d183920e31b8a">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#5e55dbeefff2057b414960d9467d183920e31b8a"><strong>src/Alignment.cc</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" 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="2" 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">@@ -2,54 +2,36 @@</td>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

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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 "Alignment.hh"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

</td>

<td class="diff-line-num new_line" data-linenumber="4" 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">

4

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Alphabet.hh"</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="5" 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">

5

</td>

<td class="diff-line-num new_line old" data-linenumber="5" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Centroid.hh"</span></span>

</pre>

</td>

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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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<td class="diff-line-num new_line" data-linenumber="5" 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">

5

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<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>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="7" 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">

7

</td>

<td class="diff-line-num new_line old" data-linenumber="6" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "GreedyXdropAligner.hh"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="8" 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">

8

</td>

<td class="diff-line-num new_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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "TwoQualityScoreMatrix.hh"</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="9" 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">

9

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<td class="diff-line-num new_line old" data-linenumber="7" 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">

</td>

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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>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_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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<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">

8

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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 <assert.h></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" 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">

10

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<td class="diff-line-num new_line" data-linenumber="9" 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">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" 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">

11

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<td class="diff-line-num new_line" data-linenumber="10" 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">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// make C++ tolerable:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" 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">

12

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<td class="diff-line-num new_line" data-linenumber="11" 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">

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;">#define IT(type) std::vector<type>::iterator</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" 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">

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<td class="diff-line-num new_line" data-linenumber="12" 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">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" 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">

14

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<td class="diff-line-num new_line" data-linenumber="13" 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">

13

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<pre style="margin: 0;"> <span id="LC13" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" 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">

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<td class="diff-line-num new_line" data-linenumber="14" 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">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" 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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<td class="diff-line-num new_line old" data-linenumber="15" 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="LC16" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fromSegmentPair</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SegmentPair</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sp</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" 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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<td class="diff-line-num new_line old" data-linenumber="15" 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="LC17" class="line" lang="cpp">  <span class="n" style="color: #333;">blocks</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;">sp</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" 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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<td class="diff-line-num new_line old" data-linenumber="15" 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="LC18" 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;">sp</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" 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="LC19" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" 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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<td class="diff-line-num new_line old" data-linenumber="15" 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="LC21" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addExpectedCounts</span><span class="p">(</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;">expectedCounts</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" 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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<td class="diff-line-num new_line old" data-linenumber="15" 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="LC22" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpectedCount</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ec</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="15" 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="LC23" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(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="15" style="width: 35px; color: rgba(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="LC15" 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;">addExpectedCounts</span><span class="p">(</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;">totalCounts</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpectedCount</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ec</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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">

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<td class="diff-line-num new_line" data-linenumber="16" 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">

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<pre style="margin: 0;"> <span id="LC16" 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;">scoreMatrixRowSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" 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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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC25" 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;">alph</span><span class="p">.</span><span class="n" style="color: #333;">numbersToUppercase</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" 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">

26

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC26" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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">

27

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<td class="diff-line-num new_line" data-linenumber="17" 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">

17

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<pre style="margin: 0;"> <span id="LC17" 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;">scoreMatrixRowSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" 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">

28

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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC28" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">numbersToUppercase</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" 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">

29

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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC29" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" 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">

30

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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC30" class="line" lang="cpp">      <span class="n" style="color: #333;">expectedCounts</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;">alph</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;">y</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ec</span><span class="p">.</span><span class="n" style="color: #333;">emit</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">totalCounts</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ec</span><span class="p">.</span><span class="n" style="color: #333;">emit</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">totalCounts</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" 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">

31

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<td class="diff-line-num new_line" data-linenumber="20" 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">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" 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">

32

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<td class="diff-line-num new_line" data-linenumber="21" 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">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" 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">

33

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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC33" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" 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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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC34" 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;">numEmissionCounts</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="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" 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">

35

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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC35" 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;">transitionCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">[</span> <span class="n" style="color: #333;">numEmissionCounts</span> <span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" 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">

36

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<td class="diff-line-num new_line old" data-linenumber="22" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" 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">

37

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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC37" class="line" lang="cpp">  <span class="n" style="color: #333;">transitionCounts</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;">ec</span><span class="p">.</span><span class="n" style="color: #333;">toMatch</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" 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">

38

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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC38" 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;">ec</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;">ec</span><span class="p">.</span><span class="n" style="color: #333;">delInit</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// deleted letter count</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" 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">

39

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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC39" 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;">ec</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;">ec</span><span class="p">.</span><span class="n" style="color: #333;">insInit</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// inserted letter count</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" 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">

40

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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC40" 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;">ec</span><span class="p">.</span><span class="n" style="color: #333;">delInit</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// deletion open/close count</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" 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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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC41" 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;">ec</span><span class="p">.</span><span class="n" style="color: #333;">insInit</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// insertion open/close count</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(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="22" style="width: 35px; color: rgba(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="LC22" class="line" lang="cpp">  <span class="n" style="color: #333;">totalCounts</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;">ec</span><span class="p">.</span><span class="n" style="color: #333;">toMatch</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(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="LC23" class="line" lang="cpp">  <span class="n" style="color: #333;">totalCounts</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;">ec</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;">ec</span><span class="p">.</span><span class="n" style="color: #333;">delInit</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// deleted letter count</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(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="24" style="width: 35px; color: rgba(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="LC24" class="line" lang="cpp">  <span class="n" style="color: #333;">totalCounts</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;">ec</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;">ec</span><span class="p">.</span><span class="n" style="color: #333;">insInit</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// inserted letter count</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(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="25" style="width: 35px; color: rgba(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="LC25" class="line" lang="cpp">  <span class="n" style="color: #333;">totalCounts</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;">ec</span><span class="p">.</span><span class="n" style="color: #333;">delInit</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// deletion open/close count</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(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="LC26" class="line" lang="cpp">  <span class="n" style="color: #333;">totalCounts</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;">ec</span><span class="p">.</span><span class="n" style="color: #333;">insInit</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// insertion open/close count</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" 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">

42

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<td class="diff-line-num new_line" data-linenumber="27" 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">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" 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">

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<td class="diff-line-num new_line" data-linenumber="28" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" 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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<td class="diff-line-num new_line old" data-linenumber="29" 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="LC44" 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;">countSeedMatches</span><span class="p">(</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;">expectedCounts</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" 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">

45

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<td class="diff-line-num new_line old" data-linenumber="29" 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="LC45" 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;">seq1beg</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;">seq1end</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" 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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<td class="diff-line-num new_line old" data-linenumber="29" 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="LC46" 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;">seq2beg</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;">alph</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" 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">

47

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<td class="diff-line-num new_line old" data-linenumber="29" 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="LC47" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">seq1end</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" 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">

48

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<td class="diff-line-num new_line old" data-linenumber="29" 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="LC48" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">x1</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;">numbersToUppercase</span><span class="p">[</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="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" 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">

49

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<td class="diff-line-num new_line old" data-linenumber="29" 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="LC49" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">x2</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;">numbersToUppercase</span><span class="p">[</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2beg</span><span class="o" style="font-weight: 600;">++</span> <span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" 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">

50

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">x1</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="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">x2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">[</span> <span class="n" style="color: #333;">x1</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="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">x2</span> <span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addSeedCounts</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">                     <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">counts</span><span class="p">)</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;">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;">size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp">    <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;">seq1</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;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]];</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp">  <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;">counts</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">size</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="c1" style="color: #998; font-style: italic;">// Does x precede and touch y in both sequences?</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" 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="39" 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">@@ -57,12 +39,12 @@ static bool isNext( const SegmentPair& x, const SegmentPair& y ){</td>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">end1</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">beg1</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">end2</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">beg2</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><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="LC60" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">centroid</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp">                      <span class="n" style="color: #333;">GreedyXdropAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span> <span class="n" style="color: #333;">Aligners</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligners</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

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<td class="diff-line-num new_line" data-linenumber="43" 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">

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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="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="63" 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">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp">                      <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="64" 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">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp">                      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMin</span><span class="p">,</span></span>

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<td class="diff-line-num new_line old" data-linenumber="46" 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="LC65" class="line" lang="cpp">                      <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mcf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC46" 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;">probMatrix</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>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp">                      <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp">                      <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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp">                           <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TwoQualityScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp">                           <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qual1</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;">qual2</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" 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="55" 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">@@ -73,21 +55,17 @@ void Alignment::makeXdrop( Centroid& centroid,</td>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC56" 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="LC57" 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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<pre style="margin: 0;">-<span id="LC76" 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;">numEmissionCounts</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC77" 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;">numTransitionCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" 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;">expectedCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="79" 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="LC79" class="line" lang="cpp">    <span class="n" style="color: #333;">expectedCounts</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span> <span class="n" style="color: #333;">numEmissionCounts</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numTransitionCounts</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="80" 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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<td class="diff-line-num new_line old" data-linenumber="58" 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="LC80" class="line" lang="cpp">    <span class="n" style="color: #333;">countSeedMatches</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp">                 <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">beg1</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;">seed</span><span class="p">.</span><span class="n" style="color: #333;">end1</span><span class="p">(),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="82" 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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<td class="diff-line-num new_line old" data-linenumber="58" 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="LC82" 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;">seed</span><span class="p">.</span><span class="n" style="color: #333;">beg2</span><span class="p">(),</span> <span class="n" style="color: #333;">alph</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="83" 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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<td class="diff-line-num new_line old" data-linenumber="58" 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="LC83" class="line" lang="cpp">    <span class="n" style="color: #333;">expectedCounts</span><span class="p">[</span> <span class="n" style="color: #333;">numEmissionCounts</span> <span class="p">]</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;">size</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// match count</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numOfTransitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frameSize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC59" 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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(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="LC60" class="line" lang="cpp">    <span class="n" style="color: #333;">ec</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numOfTransitions</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(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="LC61" class="line" lang="cpp">    <span class="n" style="color: #333;">addSeedCounts</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;">seed</span><span class="p">.</span><span class="n" style="color: #333;">beg1</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;">seed</span><span class="p">.</span><span class="n" style="color: #333;">beg2</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="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ec</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="62" 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">

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="85" 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">

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<td class="diff-line-num new_line" data-linenumber="63" 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">

63

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="64" 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">

64

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// extend a gapped alignment in the left/reverse direction from the seed:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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<td class="diff-line-num new_line" data-linenumber="65" 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">

65

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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="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">columnAmbiguityCodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">columnAmbiguityCodes</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" 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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<td class="diff-line-num new_line old" data-linenumber="66" 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="LC88" class="line" lang="cpp">  <span class="n" style="color: #333;">extend</span><span class="p">(</span> <span class="n" style="color: #333;">blocks</span><span class="p">,</span> <span class="n" style="color: #333;">columnAmbiguityCodes</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">centroid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">greedyAligner</span></span><span class="p">,</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp">  <span class="n" style="color: #333;">extend</span><span class="p">(</span> <span class="n" style="color: #333;">blocks</span><span class="p">,</span> <span class="n" style="color: #333;">columnAmbiguityCodes</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">aligners</span></span><span class="p">,</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp">     <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">beg1</span><span class="p">(),</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">beg2</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" 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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<td class="diff-line-num new_line old" data-linenumber="68" 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="LC90" class="line" lang="cpp">     <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="n" style="color: #333;">smMin</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span></span>

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp">     <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="n" style="color: #333;">smMin</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">probMatrix</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">scale</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span></span>

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<td class="diff-line-num new_line" data-linenumber="69" 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">

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp">     <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span> <span class="n" style="color: #333;">qual1</span><span class="p">,</span> <span class="n" style="color: #333;">qual2</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp">     <span class="n" style="color: #333;">extras</span><span class="p">,</span> <span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">outputType</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" 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="83" 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">@@ -105,9 +83,9 @@ void Alignment::makeXdrop( Centroid& centroid,</td>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// extend a gapped alignment in the right/forward direction from the seed:</span></span>

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<pre style="margin: 0;"> <span id="LC84" 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;">forwardBlocks</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="85" 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">

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">forwardAmbiguities</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="86" 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="LC108" class="line" lang="cpp">  <span class="n" style="color: #333;">extend</span><span class="p">(</span> <span class="n" style="color: #333;">forwardBlocks</span><span class="p">,</span> <span class="n" style="color: #333;">forwardAmbiguities</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">centroid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">greedyAligner</span></span><span class="p">,</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp">  <span class="n" style="color: #333;">extend</span><span class="p">(</span> <span class="n" style="color: #333;">forwardBlocks</span><span class="p">,</span> <span class="n" style="color: #333;">forwardAmbiguities</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">aligners</span></span><span class="p">,</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">     <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">end1</span><span class="p">(),</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">end2</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="110" 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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<td class="diff-line-num new_line old" data-linenumber="88" 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="LC110" class="line" lang="cpp">    <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="n" style="color: #333;">smMin</span><span class="p">,</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">     <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="n" style="color: #333;">smMin</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">probMatrix</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">scale</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">     <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span> <span class="n" style="color: #333;">qual1</span><span class="p">,</span> <span class="n" style="color: #333;">qual2</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp">     <span class="n" style="color: #333;">extras</span><span class="p">,</span> <span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">outputType</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="113" 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">

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<td class="diff-line-num new_line" data-linenumber="91" 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">

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="162" 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="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -162,7 +140,7 @@ void Alignment::makeXdrop( Centroid& centroid,</td>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// cost of the gap between x and y</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">gapCost</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SegmentPair</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SegmentPair</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">y</span><span class="p">,</span></span>

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<td class="diff-line-num new_line old" data-linenumber="143" 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="LC165" class="line" lang="cpp">             <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">mcf</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></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;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(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="LC143" 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;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="166" 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">

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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">isNewFrameshifts</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">gapSize1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">beg1</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">end1</span><span class="p">();</span></span>

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<td class="diff-line-num new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">gapSize2</span><span class="p">,</span> <span class="n" style="color: #333;">frameshift2</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="174" 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="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>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -174,7 +152,7 @@ static int gapCost(const SegmentPair &x, const SegmentPair &y,</td>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isOptimal</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp">                     <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span></span>

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<td class="diff-line-num new_line old" data-linenumber="155" 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="LC177" class="line" lang="cpp">                     <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">mcf</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></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;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC155" 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;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<td class="diff-line-num new_line" data-linenumber="156" 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">

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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;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp">                           <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TwoQualityScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC158" 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;">qual1</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;">qual2</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="diff-line-num unfold js-unfold old_line" data-linenumber="216" 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="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -216,7 +194,7 @@ bool Alignment::isOptimal( const uchar* seq1, const uchar* seq2, int globality,</td>

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">hasGoodSegment</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC196" 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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">mcf</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></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;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC197" 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;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssm2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TwoQualityScoreMatrix</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sm2qual</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC200" 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;">qual1</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;">qual2</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="diff-line-num unfold js-unfold old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="251" 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">@@ -273,27 +251,46 @@ static void getColumnCodes(const Centroid& centroid, std::vector<char>& codes,</td>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC254" 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;">getColumnCodes</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="255" style="width: 35px; color: rgba(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="LC255" class="line" lang="cpp">                     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">codes</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp">                     <span class="k" style="font-weight: 600;">const</span> <span class="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;">chunks</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC257" 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;">chunks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SegmentPair</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;">chunks</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC259" 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="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">k</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="LC260" 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;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">matchProb</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">beg1</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="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">beg2</span><span class="p">()</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="mi" style="color: #099;">3</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp">      <span class="n" style="color: #333;">codes</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">asciiProbability</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">    <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="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="264" style="width: 35px; color: rgba(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="LC264" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isNext</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;">chunks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isNext</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">chunks</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">end1</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">end2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isNext</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">chunks</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">beg2</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chunks</span><span class="p">[</span><span class="n" style="color: #333;">j</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>

</pre>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">beg1</span><span class="p">()</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="LC268" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">beg2</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">end2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp">    <span class="n" style="color: #333;">codes</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">codes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">n1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">n2</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extend</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;">SegmentPair</span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">chunks</span><span class="p">,</span></span>

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<td class="diff-line-num new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp">                  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">columnCodes</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp">                  <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">centroid</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="cpp">                  <span class="n" style="color: #333;">GreedyXdropAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">                  <span class="n" style="color: #333;">Aligners</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligners</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMin</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxDrop</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mcf</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">GapCosts</span></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">gap</span></span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">                  <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">const_dbl_ptr</span></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">probMat</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">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">scale</span></span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxDrop</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">GapCosts</span></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">gap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="cpp"><span class="idiff left right">                        </span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TwoQualityScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"><span class="idiff left right">                   </span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TwoQualityScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC284" 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;">qual1</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;">qual2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC285" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC286" 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="LC291" 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;">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>

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<pre style="margin: 0;">-<span id="LC292" 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;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">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;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC288" 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;">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;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp">  <span class="n" style="color: #333;">Centroid</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">centroid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligners</span><span class="p">.</span><span class="n" style="color: #333;">centroid</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp">  <span class="n" style="color: #333;">GappedXdropAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aligner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">aligner</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp">  <span class="n" style="color: #333;">GreedyXdropAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">greedyAligner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligners</span><span class="p">.</span><span class="n" style="color: #333;">greedyAligner</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</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="LC296" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</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;">4</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isGreedy</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">globality</span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">pssm2</span> <span class="p">);</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -313,7 +310,27 @@ void Alignment::extend( std::vector< SegmentPair >& chunks,</td>

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<pre style="margin: 0;"> <span id="LC310" 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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<pre style="margin: 0;"> <span id="LC311" 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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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp">                               <span class="n" style="color: #333;">gapCost</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC313" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(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="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="316" style="width: 35px; color: rgba(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="320" style="width: 35px; color: rgba(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="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="316" style="width: 35px; color: rgba(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="321" style="width: 35px; color: rgba(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="LC321" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="316" style="width: 35px; color: rgba(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="322" style="width: 35px; color: rgba(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="LC322" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="316" style="width: 35px; color: rgba(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="323" style="width: 35px; color: rgba(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="LC323" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="324" style="width: 35px; color: rgba(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="LC324" 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;">ec</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="316" style="width: 35px; color: rgba(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="325" style="width: 35px; color: rgba(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="LC325" 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;">subsCounts</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="326" style="width: 35px; color: rgba(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="LC326" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp">      <span class="n" style="color: #333;">subsCounts</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;">ec</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;">scoreMatrixRowSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="316" style="width: 35px; color: rgba(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="328" style="width: 35px; color: rgba(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="LC328" 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;">tranCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="316" style="width: 35px; color: rgba(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="329" style="width: 35px; color: rgba(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="LC329" class="line" lang="cpp">    <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">subsCounts</span><span class="p">,</span> <span class="n" style="color: #333;">tranCounts</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="316" style="width: 35px; color: rgba(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="330" style="width: 35px; color: rgba(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="LC330" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="316" style="width: 35px; color: rgba(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="331" style="width: 35px; color: rgba(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="LC331" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="316" 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">

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="317" style="width: 35px; color: rgba(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="333" style="width: 35px; color: rgba(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="LC333" class="line" lang="cpp">      <span class="n" style="color: #333;">assert</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;">4</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC334" 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;">1</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;">1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC335" 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;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">align3</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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<td class="diff-line-num new_line" data-linenumber="336" 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">

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<pre style="margin: 0;"> <span id="LC336" 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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="434" 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">@@ -417,7 +434,7 @@ void Alignment::extend( std::vector< SegmentPair >& chunks,</td>

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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp">      <span class="n" style="color: #333;">ExpectedCount</span> <span class="n" style="color: #333;">ec</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;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">computeExpectedCounts</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;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">start2</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;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">gap</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 class="n" style="color: #333;">ec</span> <span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC420" class="line" lang="cpp">      <span class="n" style="color: #333;">addExpectedCounts</span><span class="p">(</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">extras</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">expectedCounts</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ec</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alph</span></span><span class="idiff right"> </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;">addExpectedCounts</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">&</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">expectedCounts</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ec</span></span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="439" 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">

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC440" class="line" lang="cpp"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="bd17e03c676d289c9cc5bb117da6d9d2bde74764">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#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">@@ -4,25 +4,28 @@</td>

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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 ALIGNMENT_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 ALIGNMENT_HH</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ScoreMatrixRow.hh"</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"></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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Centroid.hh"</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "GreedyXdropAligner.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" 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">

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<td class="diff-line-num new_line" data-linenumber="10" 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">

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 "SegmentPair.hh"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" 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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<td class="diff-line-num new_line old" data-linenumber="11" 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="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "mcf_gap_costs.hh"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" 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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<td class="diff-line-num new_line old" data-linenumber="11" 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="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stddef.h>  // size_t</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" 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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<td class="diff-line-num new_line old" data-linenumber="11" 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="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="12" style="width: 35px; color: rgba(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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "mcf_frameshift_xdrop_aligner.hh"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="12" style="width: 35px; color: rgba(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="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" 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">

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<td class="diff-line-num new_line" data-linenumber="13" 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">

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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 <vector></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" 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">

13

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<td class="diff-line-num new_line" data-linenumber="14" 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">

14

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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></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" 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">

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<td class="diff-line-num new_line" data-linenumber="15" 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">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" 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">

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<td class="diff-line-num new_line" data-linenumber="16" 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">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

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<td class="diff-line-num new_line" data-linenumber="17" 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">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" 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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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC17" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">uchar</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" 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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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC18" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" 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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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GreedyXdropAligner</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

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<td class="diff-line-num new_line" data-linenumber="18" 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">

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<pre style="margin: 0;"> <span id="LC18" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" 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">

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<td class="diff-line-num new_line" data-linenumber="19" 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">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MultiSequence</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" 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">

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<td class="diff-line-num new_line" data-linenumber="20" 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">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" 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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<td class="diff-line-num new_line old" data-linenumber="21" 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="LC23" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Centroid</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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">

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<td class="diff-line-num new_line" data-linenumber="21" 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">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TwoQualityScoreMatrix</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">Aligners</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp">  <span class="n" style="color: #333;">Centroid</span> <span class="n" style="color: #333;">centroid</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp">  <span class="n" style="color: #333;">FrameshiftXdropAligner</span> <span class="n" style="color: #333;">frameshiftAligner</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp">  <span class="n" style="color: #333;">GreedyXdropAligner</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="p">};</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">AlignmentText</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// This holds the final text representation of an alignment, along</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// with data for sorting it.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" 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="73" 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">@@ -70,18 +73,21 @@ struct AlignmentExtras {</td>

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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="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">Alignment</span><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// make a single-block alignment:</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;">void</span> <span class="n" style="color: #333;">fromSegmentPair</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SegmentPair</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sp</span> <span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">fromSegmentPair</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SegmentPair</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sp</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp">    <span class="n" style="color: #333;">blocks</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;">sp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="LC78" 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;">sp</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp">  <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;">// Make an Alignment by doing gapped X-drop extension in both</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// directions starting from a seed SegmentPair.  The resulting</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Alignment might not be "optimal" (see below).</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// If outputType > 3: calculates match probabilities.</span></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;">// If outputType > 4: does gamma-centroid alignment.</span></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">centroid</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp">             <span class="n" style="color: #333;">GreedyXdropAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span> <span class="n" style="color: #333;">Aligners</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligners</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">             <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp">             <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMin</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp">             <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mcf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(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="89" style="width: 35px; color: rgba(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="LC89" 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;">probMatrix</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(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="90" style="width: 35px; color: rgba(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="LC90" 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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDrop</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>

</pre>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp">             <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TwoQualityScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC93" 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;">qual1</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;">qual2</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">@@ -94,7 +100,7 @@ struct Alignment{</td>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// If "globality" is non-zero, skip the prefix and suffix checks.</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;">bool</span> <span class="n" style="color: #333;">isOptimal</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">mcf</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></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;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC103" 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;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TwoQualityScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC106" 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;">qual1</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;">qual2</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="diff-line-num unfold js-unfold new_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>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,7 +108,7 @@ struct Alignment{</td>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Does the Alignment have any segment with score >= minScore?</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hasGoodSegment</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC110" 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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">mcf</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></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;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC111" 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;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssm2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TwoQualityScoreMatrix</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sm2qual</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC114" 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;">qual1</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;">qual2</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">@@ -130,13 +136,13 @@ struct Alignment{</td>

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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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">extend</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;">SegmentPair</span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">chunks</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">columnCodes</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cpp">         <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">centroid</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cpp">         <span class="n" style="color: #333;">GreedyXdropAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp">         <span class="n" style="color: #333;">Aligners</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligners</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp">         <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp">         <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMin</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mcf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMax</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">smMin</span><span class="p">,</span></span>

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(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="LC144" 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;">probMat</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>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxDrop</span><span class="p">,</span> <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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm2</span><span class="p">,</span></span>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="147" 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">

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp">               <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TwoQualityScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sm2qual</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="142" 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">

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<td class="diff-line-num new_line" data-linenumber="148" 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">

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<pre style="margin: 0;"> <span id="LC148" 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;">qual1</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;">qual2</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" 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="175" 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">@@ -169,6 +175,9 @@ struct Alignment{</td>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC176" 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;">writeBotSeq</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;">dest</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;">seq</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;">alph</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp">              <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">qualsPerBase</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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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC179" 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;">writeColumnProbs</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;">dest</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;">probSymbols</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp">                   <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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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC183" 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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<br>

</li>

<li id="8758dc959aa5524be83960d0bfd56945bc432a26">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#8758dc959aa5524be83960d0bfd56945bc432a26"><strong>src/AlignmentWrite.cc</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="302" 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">@@ -302,14 +302,33 @@ static char *writeMafHeadQ(char *out,</td>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Write a "c" line</span></span>

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<pre style="margin: 0;"> <span id="LC304" 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;">writeMafLineC</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="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cLine</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">counts</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</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;">0</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="LC308" class="line" lang="cpp">  <span class="n" style="color: #333;">cLine</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">counts</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC306" 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;">bool</span> <span class="n" style="color: #333;">isCodon</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC308" 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;">isCodon</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>

</pre>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">numOfSubstitutions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span></span>

</pre>

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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;">numOfTransitions</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;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">numOfSubstitutions</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(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="LC311" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfCounts</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alphSize2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numOfTransitions</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp">  <span class="n" style="color: #333;">cLine</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">numOfCounts</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC313" 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;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cLine</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

312

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<td class="diff-line-num new_line old" data-linenumber="315" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC312" class="line" lang="cpp">    <span class="n" style="color: #333;">e</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;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">" %.3g"</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

315

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

316

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<pre style="margin: 0;">+<span id="LC316" 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;">alph</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="317" style="width: 35px; color: rgba(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="LC317" 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;">alph</span><span class="p">.</span><span class="n" style="color: #333;">numbersToLowercase</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

318

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<pre style="margin: 0;">+<span id="LC318" 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;">alphSize2</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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;">unsigned</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isCodon</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;">alph</span><span class="p">.</span><span class="n" style="color: #333;">numbersToLowercase</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="320" style="width: 35px; color: rgba(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="LC320" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">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;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="321" style="width: 35px; color: rgba(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="LC321" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">i</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;">counts</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;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

322

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">j</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;">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;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="323" style="width: 35px; color: rgba(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="LC323" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">i</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;">j</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;">counts</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;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="324" style="width: 35px; color: rgba(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="LC324" class="line" lang="cpp">      <span class="n" style="color: #333;">e</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;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">" %.3g"</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="325" style="width: 35px; color: rgba(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="LC325" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="326" style="width: 35px; color: rgba(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="LC326" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="327" style="width: 35px; color: rgba(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="LC327" class="line" lang="cpp"></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC328" 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;">numOfTransitions</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="LC329" class="line" lang="cpp">    <span class="n" style="color: #333;">e</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;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">" %.3g"</span><span class="p">,</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">numOfSubstitutions</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp">  <span class="p">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="313" style="width: 35px; color: rgba(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="LC331" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\n'</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;">cLine</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">-</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cLine</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="LC334" 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="324" 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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -324,7 +343,7 @@ AlignmentText Alignment::writeMaf(const MultiSequence& seq1,</td>

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<pre style="margin: 0;"> <span id="LC343" 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 class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isCodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">translationType</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="LC345" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">fullScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">column<span class="idiff left right">AmbiguityCode</span>s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">columnAmbiguityCodes</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="328" style="width: 35px; color: rgba(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="LC346" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">column<span class="idiff left right">ProbSymbol</span>s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">columnAmbiguityCodes</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC348" 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>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC349" 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="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="384" 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">@@ -365,14 +384,14 @@ AlignmentText Alignment::writeMaf(const MultiSequence& seq1,</td>

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365

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<td class="diff-line-num new_line" data-linenumber="384" 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">

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">sLineLen</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;">pLineBlankLen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numColumns</span><span class="p">(</span><span class="n" style="color: #333;">frameSize2</span><span class="p">,</span> <span class="n" style="color: #333;">isCodon</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>

</pre>

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<td class="diff-line-num old_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">

366

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<td class="diff-line-num new_line" data-linenumber="385" 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">

385

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="367" 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">

367

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<td class="diff-line-num new_line" data-linenumber="386" 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">

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cLine</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="368" 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">

368

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<td class="diff-line-num new_line old" data-linenumber="387" 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="LC368" class="line" lang="cpp">  <span class="n" style="color: #333;">writeMafLineC</span><span class="p">(</span><span class="n" style="color: #333;">cLine</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="369" style="width: 35px; color: rgba(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="387" style="width: 35px; color: rgba(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="LC387" class="line" lang="cpp">  <span class="n" style="color: #333;">writeMafLineC</span><span class="p">(</span><span class="n" style="color: #333;">cLine</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">expectedCounts</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alph</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">isCodon</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="369" 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">

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<td class="diff-line-num new_line" data-linenumber="388" 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">

388

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="370" 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">

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<td class="diff-line-num new_line" data-linenumber="389" 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">

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">qualsPerBase1</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;">qualsPerLetter</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="371" 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">

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<td class="diff-line-num new_line" data-linenumber="390" 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">

390

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">qualsPerBase2</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;">qualsPerLetter</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="372" 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">

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<td class="diff-line-num new_line" data-linenumber="391" 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">

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isQuals1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualsPerBase1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">translationType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="373" 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">

373

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<td class="diff-line-num new_line" data-linenumber="392" 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">

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isQuals2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualsPerBase2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">translationType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="374" 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">

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<td class="diff-line-num new_line" data-linenumber="393" 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">

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="375" 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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<td class="diff-line-num new_line old" data-linenumber="394" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC375" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">sLineNum</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;">isQuals1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">isQuals2</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">column<span class="idiff left right">AmbiguityCode</span>s</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="376" style="width: 35px; color: rgba(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="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">sLineNum</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;">isQuals1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">isQuals2</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">column<span class="idiff left right">ProbSymbol</span>s</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="376" 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">

376

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<td class="diff-line-num new_line" data-linenumber="395" 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">

395

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">textLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aLineLen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sLineLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sLineNum</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cLine</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="377" 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">

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<td class="diff-line-num new_line" data-linenumber="396" 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">

396

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC396" 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;">textLen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="378" 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">

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="421" 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">@@ -402,17 +421,17 @@ AlignmentText Alignment::writeMaf(const MultiSequence& seq1,</td>

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<pre style="margin: 0;"> <span id="LC421" 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="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cpp">  <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="423" 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">

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line old" data-linenumber="424" 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="LC405" 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;">dest</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="424" 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="LC406" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="407" 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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<td class="diff-line-num new_line old" data-linenumber="424" 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="LC407" 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;">columnAmbiguityCodes</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_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">

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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;">columnProbSymbols</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC425" 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;">dest</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="426" 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">

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp">    <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'p'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">' '</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="409" 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">

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<td class="diff-line-num new_line" data-linenumber="427" 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">

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp">    <span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">fill</span><span class="p">(</span><span class="n" style="color: #333;">pLineBlankLen</span><span class="p">,</span> <span class="sc" style="color: #d14;">' '</span><span class="p">);</span></span>

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<td class="diff-line-num new_line old" data-linenumber="428" 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="LC410" class="line" lang="cpp">    <span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">columnAmbiguityCodes</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">columnAmbiguityCodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC411" class="line" lang="cpp">    <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="412" style="width: 35px; color: rgba(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="428" style="width: 35px; color: rgba(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="LC428" class="line" lang="cpp">    <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">pointer</span><span class="p">();</span></span>

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<td class="diff-line-num new old_line" data-linenumber="412" style="width: 35px; color: rgba(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="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp">    <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writeColumnProbs</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">columnProbSymbols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">frameSize2</span><span class="p">,</span> <span class="n" style="color: #333;">isCodon</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="412" style="width: 35px; color: rgba(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="430" style="width: 35px; color: rgba(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="LC430" 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="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="412" 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">

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<td class="diff-line-num new_line" data-linenumber="431" 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">

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp">  <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="413" 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">

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<td class="diff-line-num new_line" data-linenumber="432" 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">

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="414" style="width: 35px; color: rgba(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="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

433

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<pre style="margin: 0;">+<span id="LC433" 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;">dest</span><span class="p">);</span></span>

</pre>

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414

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<td class="diff-line-num new_line" data-linenumber="434" 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">

434

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<pre style="margin: 0;"> <span id="LC434" 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;">cLine</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cLine</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">cLine</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="415" 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">

415

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<td class="diff-line-num new_line old" data-linenumber="435" 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="LC415" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="416" 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">

416

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<td class="diff-line-num new_line" data-linenumber="435" 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">

435

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<pre style="margin: 0;"> <span id="LC435" class="line" lang="cpp">  <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// blank line afterwards</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="417" 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">

417

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<td class="diff-line-num new_line" data-linenumber="436" 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">

436

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<pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="418" 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">

418

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<td class="diff-line-num new_line" data-linenumber="437" 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">

437

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">AlignmentText</span><span class="p">(</span><span class="n" style="color: #333;">seqNum2</span><span class="p">,</span> <span class="n" style="color: #333;">alnBeg2</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd2</span><span class="p">,</span> <span class="n" style="color: #333;">strand2</span><span class="p">,</span> <span class="n" style="color: #333;">score</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;">text</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="649" 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="668" 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">@@ -649,3 +668,42 @@ char *Alignment::writeBotSeq(char *dest, const uchar *seq,</td>

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<td class="diff-line-num old_line" data-linenumber="649" 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">

649

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<td class="diff-line-num new_line" data-linenumber="668" 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">

668

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="650" 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">

650

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<td class="diff-line-num new_line" data-linenumber="669" 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">

669

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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dest</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="651" 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">

651

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<td class="diff-line-num new_line" data-linenumber="670" 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">

670

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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

671

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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

672

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<pre style="margin: 0;">+<span id="LC672" 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;">writeProbSymbols</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;">dest</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;">probSymbols</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

673

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<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp">                        <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">aaLen</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

674

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC674" 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;">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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

675

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC675" 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;">aaLen</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

676

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC676" 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;">probSymbols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

677

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dest</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="678" style="width: 35px; color: rgba(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="LC678" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="679" style="width: 35px; color: rgba(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="LC679" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

680

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<pre style="margin: 0;">+<span id="LC680" 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;">Alignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeColumnProbs</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;">dest</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;">probSymbols</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

681

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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp">                            <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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

682

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<pre style="margin: 0;">+<span id="LC682" 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;">aaLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isCodon</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>

</pre>

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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

684

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<pre style="margin: 0;">+<span id="LC684" 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;">blocks</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

685

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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SegmentPair</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;">blocks</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="686" style="width: 35px; color: rgba(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="LC686" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</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;">0</span><span class="p">)</span> <span class="p">{</span>  <span class="c1" style="color: #998; font-style: italic;">// between each pair of aligned blocks:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="687" style="width: 35px; color: rgba(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="LC687" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SegmentPair</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;">blocks</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="688" style="width: 35px; color: rgba(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="LC688" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="689" style="width: 35px; color: rgba(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="LC689" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">topLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">beg1</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">end1</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="690" style="width: 35px; color: rgba(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="LC690" class="line" lang="cpp">      <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writeProbSymbols</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="n" style="color: #333;">probSymbols</span><span class="p">,</span> <span class="n" style="color: #333;">topLen</span><span class="p">,</span> <span class="n" style="color: #333;">aaLen</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="691" style="width: 35px; color: rgba(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="LC691" class="line" lang="cpp">      <span class="n" style="color: #333;">probSymbols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">topLen</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

692

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

694

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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp">      <span class="n" style="color: #333;">setFrameCoords</span><span class="p">(</span><span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">shift</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">end2</span><span class="p">(),</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">beg2</span><span class="p">(),</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="n" style="color: #333;">isCodon</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

695

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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">rawLen</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

696

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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">botLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rawLen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">aaLen</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;">aaLen</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

697

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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">shift</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="sc" style="color: #d14;">'-'</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

698

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp">      <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writeProbSymbols</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="n" style="color: #333;">probSymbols</span><span class="p">,</span> <span class="n" style="color: #333;">botLen</span><span class="p">,</span> <span class="n" style="color: #333;">aaLen</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

699

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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp">      <span class="n" style="color: #333;">probSymbols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">botLen</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

700

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<pre style="margin: 0;">+<span id="LC700" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">rawLen</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">aaLen</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="sc" style="color: #d14;">'-'</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

701

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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">rawLen</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">aaLen</span> <span class="o" style="font-weight: 600;">==</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;">dest</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

702

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

703

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

704

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<pre style="margin: 0;">+<span id="LC704" class="line" lang="cpp">    <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writeProbSymbols</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="n" style="color: #333;">probSymbols</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">aaLen</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

705

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC705" class="line" lang="cpp">    <span class="n" style="color: #333;">probSymbols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

706

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC706" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

707

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC707" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

708

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<pre style="margin: 0;">+<span id="LC708" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dest</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="652" style="width: 35px; color: rgba(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="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

709

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC709" class="line" lang="cpp"><span class="p">}</span></span></pre>

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</li>

<li id="76a46dca9f85ee73b2a8d67a89f4b9bf80c34b4b">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#76a46dca9f85ee73b2a8d67a89f4b9bf80c34b4b"><strong>src/Centroid.cc</strong></a>

<hr>

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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 +3,11 @@</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"></span>

</pre>

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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 "Centroid.hh"</span></span>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "GappedXdropAlignerInl.hh"</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"></span>

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<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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>

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<td class="diff-line-num old_line" data-linenumber="7" 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">

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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 <cassert></span></span>

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<td class="diff-line-num new_line" data-linenumber="9" 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">

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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 <cmath> // for exp</span></span>

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<td class="diff-line-num new_line" data-linenumber="10" 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">

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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 <cfloat>   // for DBL_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 <cstdlib>  // for abs</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 <iomanip></span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="13" 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">

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<pre style="margin: 0;"> <span id="LC12" 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;">double</span> <span class="n" style="color: #333;">DINF</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DBL_MAX</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="13" 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">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,14 +113,14 @@ namespace cbrc{</td>

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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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">forward</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp">                   <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp">                   <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</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="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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</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="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp">    <span class="n" style="color: #333;">initForwardMatrix</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="121" 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="LC121" 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;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">openCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC122" 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;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">growCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC123" 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;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">openCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="120" 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="LC124" 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;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">growCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="125" style="width: 35px; color: rgba(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="LC120" 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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">openProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="125" style="width: 35px; color: rgba(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="LC121" 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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">growProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="125" style="width: 35px; color: rgba(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="LC122" 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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">openProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="125" style="width: 35px; color: rgba(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="LC123" 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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">growProb</span></span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="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="LC126" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -231,14 +230,14 @@ namespace cbrc{</td>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// compute posterior probabilities while executing backward algorithm</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC234" 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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">const</span> <span class="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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC234" 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;">isExtendFwd</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="LC235" class="line" lang="cpp">    <span class="n" style="color: #333;">initBackwardMatrix</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC238" 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;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">openCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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<pre style="margin: 0;">-<span id="LC239" 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;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">growCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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<pre style="margin: 0;">-<span id="LC240" 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;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">openCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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<pre style="margin: 0;">-<span id="LC241" 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;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">growCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC237" 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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">openProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">growProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC239" 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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">openProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC240" 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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">growProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC242" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC243" 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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="516" 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">@@ -516,21 +515,6 @@ namespace cbrc{</td>

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC516" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC519" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Return an ASCII code representing an error probability.  The</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC520" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// printable codes are 33--126, but here we use a maximum of 125, so</span></span>

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<pre style="margin: 0;">-<span id="LC521" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// that 126 is reserved for special cases.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC522" 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="n" style="color: #333;">asciiProbability</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probCorrect</span> <span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC523" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">probCorrect</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>

</pre>

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524

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC524" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//assert( probCorrect <= 1 );  // can fail: floating point is imperfect</span></span>

</pre>

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525

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC525" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">probCorrect</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="526" 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">

526

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC526" 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;">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;">e</span><span class="p">,</span> <span class="mf" style="color: #099;">1e-10</span> <span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// avoid overflow errors</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="527" 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">

527

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC527" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</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;">log10</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC528" class="line" lang="cpp">    <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="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// round fractions down</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="529" 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">

529

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<pre style="margin: 0;">-<span id="LC529" class="line" lang="cpp">    <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;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">33</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="530" 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">

530

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC530" class="line" lang="cpp">    <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="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;">j</span><span class="p">,</span> <span class="mi" style="color: #099;">125</span> <span class="p">);</span></span>

</pre>

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531

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<pre style="margin: 0;">-<span id="LC531" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre>

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532

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC532" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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533

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<pre style="margin: 0;">-<span id="LC533" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="534" 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">

534

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518

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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getMatchAmbiguities</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="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">ambiguityCodes</span><span class="p">,</span></span>

</pre>

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519

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="cpp">                               <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq2end</span><span class="p">,</span></span>

</pre>

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520

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<pre style="margin: 0;"> <span id="LC520" class="line" lang="cpp">                               <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">length</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="584" 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="568" 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">@@ -584,7 +568,7 @@ namespace cbrc{</td>

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<pre style="margin: 0;"> <span id="LC568" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">computeExpectedCounts</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC569" class="line" lang="cpp">                                   <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC570" class="line" lang="cpp">                                   <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></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="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="LC571" 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="LC572" class="line" lang="cpp">                                   <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">alphabetSize</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC573" class="line" lang="cpp">                                   <span class="n" style="color: #333;">ExpectedCount</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">c</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="LC574" class="line" lang="cpp">    <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">start1</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="600" 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">@@ -600,10 +584,10 @@ 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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<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="LC603" 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;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">openCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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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;">delGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">growCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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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;">insOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">openCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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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="n" style="color: #333;">insGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">EXP</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">gap</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">growCost</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">T</span></span><span class="p"><span class="idiff right">)</span>;</span></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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">openProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

588

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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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">delProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">growProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="607" style="width: 35px; color: rgba(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="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

589

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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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">openProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

590

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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;"><span class="idiff left">gapCosts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insProbPieces</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">growProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_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">

607

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<td class="diff-line-num new_line" data-linenumber="591" 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">

591

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC591" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_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">

608

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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="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="609" 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">

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<td class="diff-line-num new_line" data-linenumber="593" 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">

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;">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>

</pre>

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<br>

</li>

<li id="7cc18ac8f8022614b0ff31ec1eeb4152cd88880e">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#7cc18ac8f8022614b0ff31ec1eeb4152cd88880e"><strong>src/Centroid.hh</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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">@@ -3,10 +3,16 @@</td>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"></span>

</pre>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef CENTROID_HH</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line" data-linenumber="5" 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">

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;">#define CENTROID_HH</span></span>

</pre>

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<td class="diff-line-num new old_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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<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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"></span>

</pre>

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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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<td class="diff-line-num new_line" data-linenumber="7" 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">

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 "GappedXdropAligner.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line" data-linenumber="8" 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">

8

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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 "mcf_gap_costs.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line" data-linenumber="9" 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">

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 "SegmentPair.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" 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">

9

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<td class="diff-line-num new_line" data-linenumber="10" 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">

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 "OneQualityScoreMatrix.hh"</span></span>

</pre>

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<td class="diff-line-num new old_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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<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">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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 <assert.h></span></span>

</pre>

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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 <math.h></span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream> // for debug</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" 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">@@ -56,17 +62,17 @@ namespace cbrc{</td>

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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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">doForwardBackwardAlgorithm</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp">                               <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp">                               <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span> <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="LC65" class="line" lang="cpp">                               <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span> <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="LC66" class="line" lang="cpp">                               <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp">      <span class="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>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp">      <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">start2</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isPssm</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">pssmExp2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</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="LC70" class="line" lang="cpp">      <span class="n" style="color: #333;">numAntidiagonals</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;">numAntidiagonals</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;">scale</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp">      <span class="n" style="color: #333;">forward</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;">pssm</span><span class="p">,</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">      <span class="n" style="color: #333;">forward</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;">pssm</span><span class="p">,</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</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;">globality</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp">      <span class="n" style="color: #333;">mD</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</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="LC74" class="line" lang="cpp">      <span class="n" style="color: #333;">mI</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</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="LC69" class="line" lang="cpp">      <span class="n" style="color: #333;">backward</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;">pssm</span><span class="p">,</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp">      <span class="n" style="color: #333;">backward</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;">pssm</span><span class="p">,</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</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;">globality</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="LC77" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dp</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">gamma</span> <span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" 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="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<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 +103,7 @@ namespace cbrc{</td>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Added by MH (2008/10/10) : compute expected counts for transitions and emissions</span></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">computeExpectedCounts</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">alphabetSize</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC106" 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="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">alphabetSize</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp">                         <span class="n" style="color: #333;">ExpectedCount</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</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="LC108" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="109" 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">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp">  <span class="nl">private:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -138,11 +144,11 @@ namespace cbrc{</td>

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<td class="diff-line-num old_line" data-linenumber="138" 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">

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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="139" 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">

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<td class="diff-line-num new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">forward</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="141" 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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<td class="diff-line-num new_line old" data-linenumber="147" 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="LC141" 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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="142" style="width: 35px; color: rgba(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="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" 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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="142" 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">

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<td class="diff-line-num new_line" data-linenumber="148" 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">

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="143" 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">

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<td class="diff-line-num new_line" data-linenumber="149" 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">

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="150" 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">

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" 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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<td class="diff-line-num new_line old" data-linenumber="151" 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="LC145" 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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="146" style="width: 35px; color: rgba(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="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="147" 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">

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<td class="diff-line-num new_line" data-linenumber="153" 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">

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initForwardMatrix</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="148" 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">

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<td class="diff-line-num new_line" data-linenumber="154" 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">

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initBackwardMatrix</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="156" 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="162" 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">@@ -156,6 +162,20 @@ namespace cbrc{</td>

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<td class="diff-line-num new_line" data-linenumber="162" 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">

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="157" 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">

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<td class="diff-line-num new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp">  <span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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<td class="diff-line-num new_line" data-linenumber="164" 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">

164

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

165

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Return an ASCII code representing an error probability.  The</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

166

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// printable codes are 33--126, but here we use a maximum of 125, so</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(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="LC167" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// that 126 is reserved for special cases.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(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="LC168" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">asciiProbability</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probCorrect</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(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="LC169" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">probCorrect</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//assert(probCorrect <= 1);  // can fail: floating point is imperfect</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(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="LC171" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">probCorrect</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(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="LC172" 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;">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;">e</span><span class="p">,</span> <span class="mf" style="color: #099;">1e-10</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// avoid overflow errors</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">log10</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp">    <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="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// round fractions down</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp">    <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;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">33</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp">    <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="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;">j</span><span class="p">,</span> <span class="mi" style="color: #099;">125</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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<td class="diff-line-num new_line" data-linenumber="179" 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">

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="160" 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">

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<td class="diff-line-num new_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">

180

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>

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<br>

</li>

<li id="8f014a93cf121af8fe88d03244d4d4b173d32a6d">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#8f014a93cf121af8fe88d03244d4d4b173d32a6d"><strong>src/GappedXdropAligner.cc</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" 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="74" 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">@@ -74,7 +74,7 @@ int GappedXdropAligner::align(const uchar *seq1,</td>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill</span><span class="p">(</span><span class="n" style="color: #333;">insExtensionCost</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="75" 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">

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="76" 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">

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<td class="diff-line-num new_line" data-linenumber="76" 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">

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="77" 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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<td class="diff-line-num new_line old" data-linenumber="77" 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="LC77" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="78" style="width: 35px; color: rgba(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="77" style="width: 35px; color: rgba(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="LC77" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numCells</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">1</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

78

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<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="79" 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">

79

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<td class="diff-line-num new_line" data-linenumber="79" 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">

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="80" 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">

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<td class="diff-line-num new_line" data-linenumber="80" 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">

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,9 +103,7 @@ int GappedXdropAligner::align(const uchar *seq1,</td>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="104" 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">

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" 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">

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="106" 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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<td class="diff-line-num new_line old" data-linenumber="106" 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="LC106" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" 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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<td class="diff-line-num new_line old" data-linenumber="107" 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="LC108" class="line" lang="cpp"></span>

</pre>

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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;">const_int_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pssmQueue</span><span class="p">.</span><span class="n" style="color: #333;">fromEnd</span><span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">simdLen</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2queue</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<td class="diff-line-num new_line" data-linenumber="109" 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">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="127" 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">@@ -129,7 +127,7 @@ int GappedXdropAligner::align(const uchar *seq1,</td>

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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</span><span class="p">];</span></span>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">z1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">z2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="131" 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">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp">      <span class="n" style="color: #333;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="132" 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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<td class="diff-line-num new_line old" data-linenumber="130" 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="LC132" class="line" lang="cpp">            <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1<span class="idiff left right">beg</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(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="130" style="width: 35px; color: rgba(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="LC130" class="line" lang="cpp">            <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1<span class="idiff left">end</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">numCells</span></span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="134" 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">

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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="135" 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">

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<td class="diff-line-num new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter1</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="200" 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="198" 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">@@ -200,6 +198,7 @@ int GappedXdropAligner::align(const uchar *seq1,</td>

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<td class="diff-line-num old_line" data-linenumber="200" 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">

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<td class="diff-line-num new_line" data-linenumber="198" 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">

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp">    <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="199" 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">

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="202" 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">

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<td class="diff-line-num new_line" data-linenumber="200" 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">

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INF</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(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="LC201" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="203" 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">

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<td class="diff-line-num new_line" data-linenumber="202" 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">

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1end</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">];</span></span>

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<td class="diff-line-num old_line" data-linenumber="205" 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">

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp">      <span class="n" style="color: #333;">pssmQueue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">simdLen</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" 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="212" 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">@@ -213,10 +212,10 @@ int GappedXdropAligner::align(const uchar *seq1,</td>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp">      <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="214" 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">

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp">      <span class="n" style="color: #333;">isDelimiter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC216" 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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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="219" 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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<td class="diff-line-num new_line old" data-linenumber="219" 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="LC219" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq1end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="221" 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">

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"></span>

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<br>

</li>

<li id="30d72e7e81ec011dcda59c2395cb78f718d054e4">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#30d72e7e81ec011dcda59c2395cb78f718d054e4"><strong>src/GappedXdropAligner2qual.cc</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" 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="27" 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">@@ -27,7 +27,7 @@ int GappedXdropAligner::align2qual(const uchar *seq1,</td>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp">                                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMatchScore</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numCells</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">1</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="32" 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">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" 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="41" 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">@@ -41,15 +41,13 @@ int GappedXdropAligner::align2qual(const uchar *seq1,</td>

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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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</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;">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="LC44" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" 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="LC48" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC49" 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;">isForward</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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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q1</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;">qual1</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;">qual1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq2pos</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">qual2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">qual2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq2pos</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC45" 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="LC46" 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;">q1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">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;">seq2</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual2</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">    <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">    <span class="n" style="color: #333;">qual2</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="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;">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;">2</span><span class="p">,</span> <span class="n" style="color: #333;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">thisPos</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp">    <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" 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="71" 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">@@ -73,7 +71,7 @@ int GappedXdropAligner::align2qual(const uchar *seq1,</td>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">z1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">z2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp">      <span class="n" style="color: #333;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp">             <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1<span class="idiff left right">beg</span></span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">             <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1<span class="idiff left">end</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">numCells</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC76" 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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter1</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" 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="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>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -154,14 +152,19 @@ int GappedXdropAligner::align2qual(const uchar *seq1,</td>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp">    <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INF</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC155" 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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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1end</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INF</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="162" style="width: 35px; color: rgba(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="LC160" 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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<td class="diff-line-num new old_line" data-linenumber="162" style="width: 35px; color: rgba(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="LC161" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos</span><span class="p">;</span></span>

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164

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<td class="diff-line-num new_line old" data-linenumber="164" 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="LC164" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">seq1end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" style="width: 35px; color: rgba(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="LC164" class="line" lang="cpp">      <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" style="width: 35px; color: rgba(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="LC165" class="line" lang="cpp">      <span class="n" style="color: #333;">qual1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" style="width: 35px; color: rgba(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="166" style="width: 35px; color: rgba(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="LC166" class="line" lang="cpp">      <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" style="width: 35px; color: rgba(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="167" style="width: 35px; color: rgba(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="LC167" class="line" lang="cpp">      <span class="n" style="color: #333;">qual2</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="165" 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">

165

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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="169" 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">

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="170" 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">

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"></span>

</pre>

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<br>

</li>

<li id="fe292bc81098de48178ce05c67f141fe55186348">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#fe292bc81098de48178ce05c67f141fe55186348"><strong>src/GappedXdropAlignerDna.cc</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" 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="54" 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">@@ -54,7 +54,7 @@ int GappedXdropAligner::alignDna(const uchar *seq1,</td>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp">            <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">            <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">scorer</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>

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<td class="diff-line-num new_line" data-linenumber="56" 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">

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="57" 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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<td class="diff-line-num new_line old" data-linenumber="57" 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="LC57" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numCells</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">1</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="58" 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">

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<td class="diff-line-num new_line" data-linenumber="58" 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">

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" 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">

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<td class="diff-line-num new_line" data-linenumber="59" 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">

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="83" 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="83" 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">@@ -83,9 +83,7 @@ int GappedXdropAligner::alignDna(const uchar *seq1,</td>

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<td class="diff-line-num old_line" data-linenumber="83" 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">

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="84" 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">

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<td class="diff-line-num new_line" data-linenumber="84" 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">

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="85" 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">

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</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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<td class="diff-line-num old old_line" data-linenumber="86" 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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<td class="diff-line-num new_line old" data-linenumber="86" 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="LC86" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="88" 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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<td class="diff-line-num new_line old" data-linenumber="87" 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="LC88" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="89" 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">

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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">fromEnd</span><span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seqLoadLen</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="90" 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">

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2queue</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>

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<td class="diff-line-num old_line" data-linenumber="91" 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">

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="199" 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="197" 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">@@ -199,6 +197,7 @@ int GappedXdropAligner::alignDna(const uchar *seq1,</td>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp">    <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="198" 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">

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x0</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">droppedTinyScore</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC200" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="202" 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">

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<td class="diff-line-num new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1end</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="203" 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">

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp">      <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toUnmasked</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp">      <span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seqLoadLen</span><span class="p">);</span></span>

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<td class="diff-line-num 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>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="216" 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">@@ -217,10 +216,10 @@ int GappedXdropAligner::alignDna(const uchar *seq1,</td>

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217

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp">  <span class="n" style="color: #333;">isDna</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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 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="LC220" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="221" style="width: 35px; color: rgba(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="LC219" 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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<td class="diff-line-num new old_line" data-linenumber="221" style="width: 35px; color: rgba(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="LC220" 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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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq1end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp">  <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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<br>

</li>

<li id="aa38e532f19f245fda3e2e3b5a4ac462598ab91f">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#aa38e532f19f245fda3e2e3b5a4ac462598ab91f"><strong>src/GappedXdropAlignerFrame.cc</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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="30" 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">@@ -30,7 +30,10 @@ int GappedXdropAligner::alignFrame(const uchar *seq1,</td>

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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="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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<td class="diff-line-num old old_line" data-linenumber="33" 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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<td class="diff-line-num new_line old" data-linenumber="33" 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="LC33" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <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;">seq2frame0</span><span class="p">,</span> <span class="n" style="color: #333;">seq2frame1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2frame2</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(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="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(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="34" style="width: 35px; color: rgba(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="LC34" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">seq1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">seq2frame0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">seq2frame1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">seq2frame2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(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="35" style="width: 35px; color: rgba(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="LC35" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(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="36" style="width: 35px; color: rgba(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="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;">seq2frame0</span><span class="p">,</span> <span class="n" style="color: #333;">seq2frame1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2frame2</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" 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">

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<td class="diff-line-num new_line" data-linenumber="37" 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">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" 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">

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<td class="diff-line-num new_line" data-linenumber="38" 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">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" 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">

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<td class="diff-line-num new_line" data-linenumber="39" 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">

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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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" 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="47" 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">@@ -44,7 +47,7 @@ int GappedXdropAligner::alignFrame(const uchar *seq1,</td>

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<td class="diff-line-num new_line" data-linenumber="47" 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">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="45" 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">

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<td class="diff-line-num new_line" data-linenumber="48" 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">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="46" 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">

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<td class="diff-line-num new_line" data-linenumber="49" 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">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" 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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<td class="diff-line-num new_line old" data-linenumber="50" 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="LC47" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="48" style="width: 35px; color: rgba(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="50" style="width: 35px; color: rgba(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="LC50" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numCells</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">1</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" 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">

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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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;">seq1end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="49" 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">

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<td class="diff-line-num new_line" data-linenumber="52" 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">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="50" 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">

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<td class="diff-line-num new_line" data-linenumber="53" 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">

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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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,13 +63,9 @@ 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>

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" 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="LC64" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="66" 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="LC65" class="line" lang="cpp"></span>

</pre>

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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;">seq2</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>

</pre>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="68" 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="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;">s1</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;">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="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="69" 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="LC69" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="70" style="width: 35px; color: rgba(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="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="70" style="width: 35px; color: rgba(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="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="70" style="width: 35px; color: rgba(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="LC68" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="70" 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">

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<td class="diff-line-num new_line" data-linenumber="69" 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">

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" 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">

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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;">seq1end</span><span class="p">,</span> <span class="n" style="color: #333;">thisPos</span><span class="p">,</span> <span class="n" style="color: #333;">numCells</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="71" 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">

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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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,9 +113,11 @@ int GappedXdropAligner::alignFrame(const uchar *seq1,</td>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp">    <span class="n" style="color: #333;">vertPos1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp">    <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"></span>

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<td class="diff-line-num new old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="117" 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">

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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;">X0</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INF</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">runOfEdges</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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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<td class="diff-line-num old_line" data-linenumber="120" 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">

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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;">seq1end</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;">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="LC123" 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="127" 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="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -127,8 +128,12 @@ int GappedXdropAligner::alignFrame(const uchar *seq1,</td>

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<pre style="margin: 0;"> <span id="LC128" 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="LC129" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">runOfDrops</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">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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<td class="diff-line-num old old_line" data-linenumber="130" 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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<td class="diff-line-num new_line old" data-linenumber="131" 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="LC130" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="131" 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="LC131" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq1end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(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="LC133" class="line" lang="cpp">  <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(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="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

132

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<td class="diff-line-num new_line" data-linenumber="137" 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">

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos6</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="138" 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">

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos5</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="134" 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">

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<td class="diff-line-num new_line" data-linenumber="139" 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">

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos4</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="35f9fe39feef01a50cdd57a941b460c37cbaffba">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#35f9fe39feef01a50cdd57a941b460c37cbaffba"><strong>src/GappedXdropAlignerPssm.cc</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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="25" 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">@@ -25,7 +25,7 @@ int GappedXdropAligner::alignPssm(const uchar *seq,</td>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SimdInt</span> <span class="n" style="color: #333;">mInsGrowCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simdFill</span><span class="p">(</span><span class="n" style="color: #333;">insExtensionCost</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" 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">

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<td class="diff-line-num new_line" data-linenumber="26" 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">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isForward</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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">

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<td class="diff-line-num new_line" data-linenumber="27" 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">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" 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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<td class="diff-line-num new_line old" data-linenumber="28" 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="LC28" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq1beg</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="29" style="width: 35px; color: rgba(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="28" style="width: 35px; color: rgba(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="LC28" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numCells</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">1</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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">

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<td class="diff-line-num new_line" data-linenumber="30" 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">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" 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">

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<td class="diff-line-num new_line" data-linenumber="31" 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">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="54" 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">@@ -54,9 +54,7 @@ int GappedXdropAligner::alignPssm(const uchar *seq,</td>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="55" 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">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</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;">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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<td class="diff-line-num new_line old" data-linenumber="57" 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="LC57" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="58" 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">

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">fromEnd</span><span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">simdLen</span><span class="p">);</span></span>

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<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;">const_int_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pssmQueue</span><span class="p">.</span><span class="n" style="color: #333;">fromEnd</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" 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="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,7 +78,7 @@ int GappedXdropAligner::alignPssm(const uchar *seq,</td>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Score</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zScores</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxValue</span><span class="p">(</span><span class="n" style="color: #333;">x2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">z1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">z2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapUnalignedCost</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp">      <span class="n" style="color: #333;">updateBest1</span><span class="p">(</span><span class="n" style="color: #333;">bestEdgeScore</span><span class="p">,</span> <span class="n" style="color: #333;">bestEdgeAntidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">bestSeq1position</span><span class="p">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="83" 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="LC83" class="line" lang="cpp">             <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1<span class="idiff left right">beg</span></span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(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="LC81" class="line" lang="cpp">             <span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1<span class="idiff left">end</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">numCells</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp">    <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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDelimiter1</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="151" 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="149" 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">@@ -151,6 +149,7 @@ int GappedXdropAligner::alignPssm(const uchar *seq,</td>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp">    <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="153" 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">

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<td class="diff-line-num new_line" data-linenumber="151" 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">

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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><span class="n" style="color: #333;">x0</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INF</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" 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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<td class="diff-line-num old_line" data-linenumber="154" 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">

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1end</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp">      <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="156" 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">

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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp">      <span class="n" style="color: #333;">seq1queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">simdLen</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="165" 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="164" 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">@@ -165,10 +164,10 @@ int GappedXdropAligner::alignPssm(const uchar *seq,</td>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp">      <span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="166" 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">

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp">      <span class="n" style="color: #333;">isDelimiter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isDelimiter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="168" 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="LC168" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="169" style="width: 35px; color: rgba(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="167" style="width: 35px; color: rgba(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="LC167" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="169" style="width: 35px; color: rgba(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="168" style="width: 35px; color: rgba(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="LC168" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="169" 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">

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="170" 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">

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos</span><span class="p">;</span></span>

</pre>

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171

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq1end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="173" 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">

173

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp">  <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="174" 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">

174

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<td class="diff-line-num new_line" data-linenumber="173" 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">

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"></span>

</pre>

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</li>

<li id="4b7be8c3b80efc62977b307791d1a304c23e1fa4">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#4b7be8c3b80efc62977b307791d1a304c23e1fa4"><strong>src/LastalArguments.cc</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="382" 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="382" 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">@@ -382,7 +382,10 @@ LAST home page: http://last.cbrc.jp/\n\</td>

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382

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isTranslated</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">inputFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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383

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<td class="diff-line-num new_line" data-linenumber="383" 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">

383

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp">    <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"can't combine option -F with option -Q 5"</span> <span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="384" 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">

384

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<td class="diff-line-num new_line" data-linenumber="384" 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">

384

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="385" 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">

385

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<td class="diff-line-num new_line old" data-linenumber="385" 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="LC385" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isFrameshift</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(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="LC385" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">frameshiftCosts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">frameshiftCosts</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="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp">    <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"can't combine option -F > 0 with option -j > 3"</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

387

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

388

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isFrameshift</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">7</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="386" 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">

386

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<td class="diff-line-num new_line" data-linenumber="389" 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">

389

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp">    <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"can't combine option -F > 0 with option -j > 3"</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="387" 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">

387

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<td class="diff-line-num new_line" data-linenumber="390" 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">

390

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="388" 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">

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<td class="diff-line-num new_line" data-linenumber="391" 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">

391

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isFrameshift</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a"><strong>src/lastal.cc</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" 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="12" 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">@@ -12,15 +12,12 @@</td>

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<td class="diff-line-num old_line" data-linenumber="12" 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">

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 "GeneticCode.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" 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">

13

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<td class="diff-line-num new_line" data-linenumber="13" 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">

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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 "SubsetMinimizerFinder.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" 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">

14

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<td class="diff-line-num new_line" data-linenumber="14" 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">

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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 "SubsetSuffixArray.hh"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" 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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<td class="diff-line-num new_line old" data-linenumber="15" 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="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Centroid.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

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<td class="diff-line-num new_line" data-linenumber="15" 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">

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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 "AlignmentPot.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" 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">

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<td class="diff-line-num new_line" data-linenumber="16" 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">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Alignment.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" 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">

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<td class="diff-line-num new_line" data-linenumber="17" 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">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "SegmentPairPot.hh"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" 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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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "SegmentPair.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

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<td class="diff-line-num new_line" data-linenumber="18" 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">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ScoreMatrix.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" 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">

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<td class="diff-line-num new_line" data-linenumber="19" 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">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "TantanMasker.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" 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">

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<td class="diff-line-num new_line" data-linenumber="20" 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">

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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 "DiagonalTable.hh"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" 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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<td class="diff-line-num new_line old" data-linenumber="21" 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="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "GreedyXdropAligner.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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">

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<td class="diff-line-num new_line" data-linenumber="21" 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">

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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 "gaplessXdrop.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" 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">

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<td class="diff-line-num new_line" data-linenumber="22" 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">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "gaplessPssmXdrop.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" 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">

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<td class="diff-line-num new_line" data-linenumber="23" 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">

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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 "gaplessTwoQualityXdrop.hh"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" 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="25" 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">@@ -28,6 +25,9 @@</td>

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<td class="diff-line-num old_line" data-linenumber="28" 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">

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<td class="diff-line-num new_line" data-linenumber="25" 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">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "zio.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" 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">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "stringify.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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">

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<td class="diff-line-num new_line" data-linenumber="27" 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">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "threadUtil.hh"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(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="28" style="width: 35px; color: rgba(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="LC28" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(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="29" style="width: 35px; color: rgba(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="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(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="30" style="width: 35px; color: rgba(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="LC30" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iomanip>  // setw</span></span>

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<pre style="margin: 0;"> <span id="LC32" 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="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></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">@@ -45,21 +45,26 @@ static void warn( const char* programName, const char* s ){</td>

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<pre style="margin: 0;"> <span id="LC45" 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="LC46" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">LastAligner</span> <span class="p">{</span>  <span class="c1" style="color: #998; font-style: italic;">// data that changes between queries</span></span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp">  <span class="n" style="color: #333;">Centroid</span> <span class="n" style="color: #333;">centroid</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp">  <span class="n" style="color: #333;">GreedyXdropAligner</span> <span class="n" style="color: #333;">greedyAligner</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">  <span class="n" style="color: #333;">Aligners</span> <span class="n" style="color: #333;">engines</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">qualityPssm</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp">  <span class="n" style="color: #333;">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;">AlignmentText</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">textAlns</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">SubstitutionMatrices</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">scores</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">][</span><span class="n" style="color: #333;">scoreMatrixRowSize</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;">int</span> <span class="n" style="color: #333;">scoresMasked</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">][</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp">  <span class="n" style="color: #333;">mcf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SubstitutionMatrixStats</span> <span class="n" style="color: #333;">stats</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;">OneQualityScoreMatrix</span> <span class="n" style="color: #333;">oneQual</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="55" 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="LC59" class="line" lang="cpp">  <span class="n" style="color: #333;">OneQualityScoreMatrix</span> <span class="n" style="color: #333;">oneQualMasked</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

60

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55

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">  <span class="n" style="color: #333;">OneQualityExpMatrix</span> <span class="n" style="color: #333;">oneQualExp</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" 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">

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<td class="diff-line-num new_line" data-linenumber="56" 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">

56

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">  <span class="n" style="color: #333;">QualityPssmMaker</span> <span class="n" style="color: #333;">maker</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(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="57" style="width: 35px; color: rgba(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="LC57" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(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="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">scores</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">][</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ratiosMatrix</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">][</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(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="LC60" 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;">ratios</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp">  <span class="n" style="color: #333;">OneQualityScoreMatrix</span> <span class="n" style="color: #333;">oneQual</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp">  <span class="n" style="color: #333;">TwoQualityScoreMatrix</span> <span class="n" style="color: #333;">twoQual</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">scoresMasked</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">][</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ratiosMaskedMatrix</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">][</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC66" 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;">ratiosMasked</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp">  <span class="n" style="color: #333;">OneQualityScoreMatrix</span> <span class="n" style="color: #333;">oneQualMasked</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp">  <span class="n" style="color: #333;">TwoQualityScoreMatrix</span> <span class="n" style="color: #333;">twoQualMasked</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="p">};</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"></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>

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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">@@ -118,7 +123,9 @@ calculateSubstitutionScoreMatrixStatistics(const std::string &matrixName) {</td>

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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 class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="120" 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">

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<pre style="margin: 0;"> <span id="LC125" 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>

</pre>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp">      <span class="n" style="color: #333;">LOG</span><span class="p">(</span><span class="s" style="color: #d14;">"can't calculate probabilities"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(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="LC126" 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;">msg</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"can't calculate probabilities"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(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="LC127" 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 class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// xxx what if temperature is given?</span></span>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp">      <span class="n" style="color: #333;">LOG</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp">      <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="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC130" 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;">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="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">canonicalMatrixName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">canonicalName</span><span class="p">(</span><span class="n" style="color: #333;">matrixName</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="175" 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="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -175,9 +182,9 @@ void makeScoreMatrix( const std::string& matrixName,</td>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="177" 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">

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp">  <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC185" 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;">SubstitutionMatrixStats</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC186" 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>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp">    <span class="n" style="color: #333;">calculateSubstitutionScoreMatrixStatistics</span><span class="p">(</span><span class="n" style="color: #333;">matrixName</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="180" 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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<td class="diff-line-num new_line old" data-linenumber="188" 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="LC180" 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;">SubstitutionMatrixStats</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</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>

</pre>

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<pre style="margin: 0;"> <span id="LC188" 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;">stats</span><span class="p">.</span><span class="n" style="color: #333;">isBad</span><span class="p">())</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp">      <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">addAmbiguousScores</span><span class="p">(</span><span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">dna</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp">                               <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">ambiguousLetterOpt</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 unfold js-unfold old_line" data-linenumber="208" 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="215" 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">@@ -208,6 +215,20 @@ void makeScoreMatrix( const std::string& matrixName,</td>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp">    <span class="n" style="color: #333;">complementMatrix</span><span class="p">(</span><span class="n" style="color: #333;">fwdMatrices</span><span class="p">.</span><span class="n" style="color: #333;">scores</span><span class="p">,</span> <span class="n" style="color: #333;">revMatrices</span><span class="p">.</span><span class="n" style="color: #333;">scores</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp">    <span class="n" style="color: #333;">complementMatrix</span><span class="p">(</span><span class="n" style="color: #333;">fwdMatrices</span><span class="p">.</span><span class="n" style="color: #333;">scoresMasked</span><span class="p">,</span> <span class="n" style="color: #333;">revMatrices</span><span class="p">.</span><span class="n" style="color: #333;">scoresMasked</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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<pre style="margin: 0;">+<span id="LC219" 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;">stats</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">();</span></span>

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<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(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="LC220" 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;">scoreMatrixRowSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp">    <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;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fwdMatrices</span><span class="p">.</span><span class="n" style="color: #333;">ratiosMatrix</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="LC222" class="line" lang="cpp">    <span class="n" style="color: #333;">revMatrices</span><span class="p">.</span><span class="n" style="color: #333;">ratios</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;">revMatrices</span><span class="p">.</span><span class="n" style="color: #333;">ratiosMatrix</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="LC223" class="line" lang="cpp">    <span class="n" style="color: #333;">fwdMatrices</span><span class="p">.</span><span class="n" style="color: #333;">ratiosMasked</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;">fwdMatrices</span><span class="p">.</span><span class="n" style="color: #333;">ratiosMaskedMatrix</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="LC224" class="line" lang="cpp">    <span class="n" style="color: #333;">revMatrices</span><span class="p">.</span><span class="n" style="color: #333;">ratiosMasked</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;">revMatrices</span><span class="p">.</span><span class="n" style="color: #333;">ratiosMaskedMatrix</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="LC225" 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;">scoreMatrixRowSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp">      <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;">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;">exp</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;">fwdMatrices</span><span class="p">.</span><span class="n" style="color: #333;">scores</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="LC227" class="line" lang="cpp">      <span class="n" style="color: #333;">revMatrices</span><span class="p">.</span><span class="n" style="color: #333;">ratios</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;">exp</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;">revMatrices</span><span class="p">.</span><span class="n" style="color: #333;">scores</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="LC228" class="line" lang="cpp">      <span class="n" style="color: #333;">fwdMatrices</span><span class="p">.</span><span class="n" style="color: #333;">ratiosMasked</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;">exp</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;">fwdMatrices</span><span class="p">.</span><span class="n" style="color: #333;">scoresMasked</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp">      <span class="n" style="color: #333;">revMatrices</span><span class="p">.</span><span class="n" style="color: #333;">ratiosMasked</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;">exp</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;">revMatrices</span><span class="p">.</span><span class="n" style="color: #333;">scoresMasked</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="LC230" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="233" 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">

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">makeQualityScorers</span><span class="p">(</span><span class="n" style="color: #333;">SubstitutionMatrices</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isCheck</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="443" 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="464" 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">@@ -443,6 +464,7 @@ struct Dispatcher{</td>

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<td class="diff-line-num old_line" data-linenumber="443" 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">

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<td class="diff-line-num new_line" data-linenumber="464" 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">

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<pre style="margin: 0;"> <span id="LC464" 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;">j</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// the query quality data</span></span>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="465" 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">

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<pre style="margin: 0;"> <span id="LC465" 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;">p</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// the query PSSM</span></span>

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<td class="diff-line-num old_line" data-linenumber="445" 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">

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<td class="diff-line-num new_line" data-linenumber="466" 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">

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<pre style="margin: 0;"> <span id="LC466" 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;">m</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// the score matrix</span></span>

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<td class="diff-line-num new old_line" data-linenumber="446" style="width: 35px; color: rgba(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="467" style="width: 35px; color: rgba(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="LC467" 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;">r</span><span class="p">;</span>   <span class="c1" style="color: #998; font-style: italic;">// the substitution probability ratios</span></span>

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<td class="diff-line-num old_line" data-linenumber="446" 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">

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<td class="diff-line-num new_line" data-linenumber="468" 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">

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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;">TwoQualityScoreMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="447" 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">

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<td class="diff-line-num new_line" data-linenumber="469" 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">

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">d</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// the maximum score drop</span></span>

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<td class="diff-line-num old_line" data-linenumber="448" 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">

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">z</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="455" 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="477" 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">@@ -455,6 +477,7 @@ struct Dispatcher{</td>

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455

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<td class="diff-line-num new_line" data-linenumber="477" 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">

477

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="cpp">      <span class="n" style="color: #333;">j</span><span class="p">(</span> <span class="n" style="color: #333;">getQueryQual</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">)</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="456" 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">

456

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<td class="diff-line-num new_line" data-linenumber="478" 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">

478

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<pre style="margin: 0;"> <span id="LC478" class="line" lang="cpp">      <span class="n" style="color: #333;">p</span><span class="p">(</span> <span class="n" style="color: #333;">getQueryPssm</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="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="457" 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">

457

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<td class="diff-line-num new_line" data-linenumber="479" 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">

479

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="cpp">      <span class="n" style="color: #333;">m</span><span class="p">(</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">scoresMasked</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;">scores</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

480

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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp">      <span class="n" style="color: #333;">r</span><span class="p">(</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">ratiosMasked</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;">ratios</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="458" 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">

458

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<td class="diff-line-num new_line" data-linenumber="481" 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">

481

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="cpp">      <span class="n" style="color: #333;">t</span><span class="p">(</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">twoQualMasked</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;">twoQual</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="459" 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">

459

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<td class="diff-line-num new_line" data-linenumber="482" 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">

482

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="cpp">      <span class="n" style="color: #333;">d</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">==</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="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropGapless</span> <span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="460" 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">

460

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<td class="diff-line-num new_line" data-linenumber="483" 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">

483

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<pre style="margin: 0;"> <span id="LC483" class="line" lang="cpp">         <span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">==</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 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="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropFinal</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="719" 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="742" 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">@@ -719,9 +742,10 @@ void alignGapped( LastAligner& aligner,</td>

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<td class="diff-line-num old_line" data-linenumber="719" 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">

719

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<td class="diff-line-num new_line" data-linenumber="742" 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">

742

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<pre style="margin: 0;"> <span id="LC742" class="line" lang="cpp">    <span class="n" style="color: #333;">shrinkToLongestIdenticalRun</span><span class="p">(</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">seed</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="720" 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">

720

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<td class="diff-line-num new_line" data-linenumber="743" 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">

743

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<pre style="margin: 0;"> <span id="LC743" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="721" 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">

721

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<td class="diff-line-num new_line" data-linenumber="744" 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">

744

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<pre style="margin: 0;"> <span id="LC744" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// do gapped extension from each end of the seed:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="722" 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">

722

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<td class="diff-line-num new_line old" data-linenumber="745" 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="LC722" class="line" lang="cpp">    <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">centroid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">aligner</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">greedyAligner</span></span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

745

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC745" class="line" lang="cpp">    <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">engines</span></span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="723" 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">

723

</td>

<td class="diff-line-num new_line" data-linenumber="746" 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">

746

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<pre style="margin: 0;"> <span id="LC746" class="line" lang="cpp">            <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="724" 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">

724

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<td class="diff-line-num new_line old" data-linenumber="747" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC724" class="line" lang="cpp">            <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="725" style="width: 35px; color: rgba(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="747" style="width: 35px; color: rgba(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="LC747" class="line" lang="cpp">            <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="725" style="width: 35px; color: rgba(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="748" style="width: 35px; color: rgba(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="LC748" class="line" lang="cpp">            <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</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;">gapCosts</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="749" 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">

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<pre style="margin: 0;"> <span id="LC749" class="line" lang="cpp">            <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;">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="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="726" 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">

726

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<pre style="margin: 0;"> <span id="LC750" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gappedExtensionCount</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="727" 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">

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<td class="diff-line-num new_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">

751

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<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="753" 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="777" 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">@@ -753,7 +777,7 @@ void alignGapped( LastAligner& aligner,</td>

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<pre style="margin: 0;"> <span id="LC777" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">alignFinish</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlignmentPot</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="778" 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">

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<pre style="margin: 0;"> <span id="LC778" 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>

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<td class="diff-line-num new_line" data-linenumber="779" 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">

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<pre style="margin: 0;"> <span id="LC779" 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="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="756" 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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<td class="diff-line-num new_line old" data-linenumber="780" 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="LC756" class="line" lang="cpp">  <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">centroid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">centroid</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="757" style="width: 35px; color: rgba(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="780" style="width: 35px; color: rgba(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="LC780" class="line" lang="cpp">  <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">centroid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">engines</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">centroid</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="781" 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">

781

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<pre style="margin: 0;"> <span id="LC781" 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="k" style="font-weight: 600;">final</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>

</pre>

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<pre style="margin: 0;"> <span id="LC782" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryLen</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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="783" 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">

783

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<pre style="margin: 0;"> <span id="LC783" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</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;">isFrameshift</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">queryLen</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="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="786" 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="810" 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">@@ -786,9 +810,10 @@ void alignFinish( LastAligner& aligner, const AlignmentPot& gappedAlns,</td>

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<pre style="margin: 0;"> <span id="LC810" class="line" lang="cpp">      <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">probAln</span><span class="p">;</span></span>

</pre>

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787

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<td class="diff-line-num new_line" data-linenumber="811" 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">

811

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<pre style="margin: 0;"> <span id="LC811" class="line" lang="cpp">      <span class="n" style="color: #333;">AlignmentExtras</span> <span class="n" style="color: #333;">extras</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="788" 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">

788

</td>

<td class="diff-line-num new_line" data-linenumber="812" 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">

812

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<pre style="margin: 0;"> <span id="LC812" class="line" lang="cpp">      <span class="n" style="color: #333;">probAln</span><span class="p">.</span><span class="n" style="color: #333;">seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">seed</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="789" 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">

789

</td>

<td class="diff-line-num new_line old" data-linenumber="813" 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="LC789" class="line" lang="cpp">      <span class="n" style="color: #333;">probAln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">centroid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">aligner</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">greedyAligner</span></span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

813

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC813" class="line" lang="cpp">      <span class="n" style="color: #333;">probAln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">aligner</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">engines</span></span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="790" 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">

790

</td>

<td class="diff-line-num new_line" data-linenumber="814" 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">

814

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC814" class="line" lang="cpp">                  <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">globality</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="791" 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">

791

</td>

<td class="diff-line-num new_line old" data-linenumber="815" 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="LC791" class="line" lang="cpp">                  <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">,</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

815

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<pre style="margin: 0;">+<span id="LC815" class="line" lang="cpp">                  <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

816

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<pre style="margin: 0;">+<span id="LC816" class="line" lang="cpp">                  <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</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;">gapCosts</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="792" 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">

792

</td>

<td class="diff-line-num new_line" data-linenumber="817" 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">

817

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<pre style="margin: 0;"> <span id="LC817" class="line" lang="cpp">                  <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;">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="n" style="color: #333;">alph</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="793" 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">

793

</td>

<td class="diff-line-num new_line" data-linenumber="818" 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">

818

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<pre style="margin: 0;"> <span id="LC818" class="line" lang="cpp">                  <span class="n" style="color: #333;">extras</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="794" 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">

794

</td>

<td class="diff-line-num new_line" data-linenumber="819" 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">

819

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<pre style="margin: 0;"> <span id="LC819" class="line" lang="cpp">      <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INF</span> <span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1232" 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="1257" 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">@@ -1232,7 +1257,8 @@ void lastal( int argc, char** argv ){</td>

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<td class="diff-line-num old_line" data-linenumber="1232" 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">

1232

</td>

<td class="diff-line-num new_line" data-linenumber="1257" 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">

1257

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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>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1233" 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">

1233

</td>

<td class="diff-line-num new_line" data-linenumber="1258" 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">

1258

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1258" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1234" 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">

1234

</td>

<td class="diff-line-num new_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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1259" 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>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1235" 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">

1235

</td>

<td class="diff-line-num new_line old" data-linenumber="1260" 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">

</td>

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<pre style="margin: 0;">-<span id="LC1235" 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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1260

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<pre style="margin: 0;">+<span id="LC1260" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1261

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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="cpp">           <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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1236" 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">

1236

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<td class="diff-line-num new_line" data-linenumber="1262" 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">

1262

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<pre style="margin: 0;"> <span id="LC1262" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1237" 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">

1237

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<td class="diff-line-num new_line" data-linenumber="1263" 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">

1263

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<pre style="margin: 0;"> <span id="LC1263" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1238" 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">

1238

</td>

<td class="diff-line-num new_line" data-linenumber="1264" 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">

1264

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<pre style="margin: 0;"> <span id="LC1264" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isDna</span> <span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;">// allow user-defined alphabet</span></span>

</pre>

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<br>

</li>

<li id="58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2"><strong>src/makefile</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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="33" 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">@@ -33,11 +33,11 @@ ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o                       \</td>

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<td class="diff-line-num old_line" data-linenumber="33" 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">

33

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<td class="diff-line-num new_line" data-linenumber="33" 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">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make">dna_words_finder.o fileMap.o tantan.o LastalArguments.o                   <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="34" 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">

34

</td>

<td class="diff-line-num new_line" data-linenumber="34" 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">

34

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make">GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o     <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="35" 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">

35

</td>

<td class="diff-line-num new_line" data-linenumber="35" 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">

35

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make">GappedXdropAligner2qual.o GappedXdropAligner3frame.o                      <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="36" 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">

36

</td>

<td class="diff-line-num new_line old" data-linenumber="36" 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">

</td>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="make">GappedXdropAlignerFrame.o mcf_<span class="idiff left right">gap_costs.o GeneticCode.o    </span>           <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="37" 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">

37

</td>

<td class="diff-line-num new_line old" data-linenumber="36" 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">

</td>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="make"><span class="idiff left right">GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o </span>   <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="38" 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">

38

</td>

<td class="diff-line-num new_line old" data-linenumber="36" 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">

</td>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="make"><span class="idiff left right">QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o  </span>   <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="39" 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">

39

</td>

<td class="diff-line-num new_line old" data-linenumber="36" 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">

</td>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="make">gapless<span class="idiff left right">PssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg</span>.o             <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="40" 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">

40

</td>

<td class="diff-line-num new_line old" data-linenumber="36" 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="LC40" class="line" lang="make">mcf_substitution_matrix_stats.o <span class="nv" style="color: #008080;">$(alpObj)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make">GappedXdropAlignerFrame.o mcf_<span class="idiff left right">frameshift_xdrop_aligner.o</span>              <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC37" class="line" lang="make"><span class="idiff left right">mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o</span>      <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC38" class="line" lang="make"><span class="idiff left right">OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o</span>    <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

39

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="make">gapless<span class="idiff left right">Xdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop</span>.o            <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="make"><span class="idiff left right">cbrc_linalg.o </span>mcf_substitution_matrix_stats.o <span class="nv" style="color: #008080;">$(alpObj)</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="make"></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="make"><span class="nv" style="color: #008080;">alignObj4</span> <span class="o" style="font-weight: 600;">=</span> Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o       <span class="se" style="color: #d14;">\</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make">DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o <span class="se" style="color: #d14;">\</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CXX)</span> <span class="nt" style="color: #000080;">-MM</span> alp/<span class="k" style="font-weight: 600;">*</span>.cpp | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s|.*:|alp/&|'</span> <span class="o" style="font-weight: 600;">>></span> m</span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CXX)</span> <span class="nt" style="color: #000080;">-MM</span> <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nb" style="color: #0086b3;">split</span>/<span class="k" style="font-weight: 600;">*</span>.cc | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s|.*:|split/&|'</span> | <span class="nv" style="color: #008080;">$(fix8)</span> <span class="o" style="font-weight: 600;">>></span> m</span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mv </span>m makefile</span>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="make"><span class="nl">Alignment.o Alignment.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Alignment.cc Alignment.hh ScoreMatrixRow.hh SegmentPair.hh </span>\</span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_gap_costs.hh Alphabet.hh Centroid.hh GappedXdropAligner.hh </span>\</span>

</pre>

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_reverse_queue.hh mcf_simd.hh </span>\</span>

</pre>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh GeneticCode.hh </span>\</span>

</pre>

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GreedyXdropAligner.hh TwoQualityScoreMatrix.hh</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="152" 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="LC152" class="line" lang="make"><span class="nl">AlignmentPot.o AlignmentPot.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">AlignmentPot.cc AlignmentPot.hh Alignment.hh </span>\</span>

</pre>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> ScoreMatrixRow.hh SegmentPair.hh mcf_gap_costs.hh</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="make"><span class="nl">AlignmentWrite.o AlignmentWrite.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">AlignmentWrite.cc Alignment.hh ScoreMatrixRow.hh </span>\</span>

</pre>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> SegmentPair.hh mcf_gap_costs.hh GeneticCode.hh LastEvaluer.hh </span>\</span>

</pre>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> alp/sls_alignment_evaluer.hpp alp/sls_pvalues.hpp alp/sls_basic.hpp </span>\</span>

</pre>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> alp/sls_falp_alignment_evaluer.hpp alp/sls_fsa1_pvalues.hpp </span>\</span>

</pre>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC158" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> MultiSequence.hh VectorOrMmap.hh Mmap.hh fileMap.hh stringify.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

159

</td>

<td class="diff-line-num new_line old" data-linenumber="147" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC159" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> Alphabet.hh</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

147

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC147" class="line" lang="make"><span class="nl">Alignment.o Alignment.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Alignment.cc Alignment.hh Centroid.hh GappedXdropAligner.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

148

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC148" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_reverse_queue.hh mcf_gap_costs.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

149

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC149" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_simd.hh ScoreMatrixRow.hh SegmentPair.hh OneQualityScoreMatrix.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

150

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC150" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_substitution_matrix_stats.hh GreedyXdropAligner.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC151" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_frameshift_xdrop_aligner.hh Alphabet.hh GeneticCode.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

152

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC152" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> TwoQualityScoreMatrix.hh</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

153

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC153" class="line" lang="make"><span class="nl">AlignmentPot.o AlignmentPot.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">AlignmentPot.cc AlignmentPot.hh Alignment.hh Centroid.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

154

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC154" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_reverse_queue.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

155

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC155" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_gap_costs.hh mcf_simd.hh ScoreMatrixRow.hh SegmentPair.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

156

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC156" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

157

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC157" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GreedyXdropAligner.hh mcf_frameshift_xdrop_aligner.hh</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

158

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC158" class="line" lang="make"><span class="nl">AlignmentWrite.o AlignmentWrite.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">AlignmentWrite.cc Alignment.hh Centroid.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

159

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC159" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_reverse_queue.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

160

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC160" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_gap_costs.hh mcf_simd.hh ScoreMatrixRow.hh SegmentPair.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

161

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC161" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

162

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC162" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GreedyXdropAligner.hh mcf_frameshift_xdrop_aligner.hh GeneticCode.hh </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

163

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC163" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> LastEvaluer.hh alp/sls_alignment_evaluer.hpp alp/sls_pvalues.hpp </span>\</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

164

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC164" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> alp/sls_basic.hpp alp/sls_falp_alignment_evaluer.hpp </span>\</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> alp/sls_fsa1_pvalues.hpp MultiSequence.hh VectorOrMmap.hh Mmap.hh </span>\</span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> fileMap.hh stringify.hh Alphabet.hh</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="160" 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">

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="make"><span class="nl">Alphabet.o Alphabet.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Alphabet.cc Alphabet.hh</span></span>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="make"><span class="nl">Centroid.o Centroid.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Centroid.cc Centroid.hh GappedXdropAligner.hh </span>\</span>

</pre>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_reverse_queue.hh mcf_gap_costs.hh </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">@@ -251,11 +258,12 @@ lastal.o lastal.o8: lastal.cc last.hh Alphabet.hh CyclicSubsetSeed.hh \</td>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_substitution_matrix_stats.hh TwoQualityScoreMatrix.hh LastEvaluer.hh </span>\</span>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> alp/sls_alignment_evaluer.hpp alp/sls_pvalues.hpp alp/sls_basic.hpp </span>\</span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> alp/sls_falp_alignment_evaluer.hpp alp/sls_fsa1_pvalues.hpp </span>\</span>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GeneticCode.hh SubsetMinimizerFinder.hh SubsetSuffixArray.hh Centroid.hh </span>\</span>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_reverse_queue.hh </span>\</span>

</pre>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_gap_costs.hh mcf_simd.hh SegmentPair.hh AlignmentPot.hh Alignment.hh </span>\</span>

</pre>

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> SegmentPairPot.hh ScoreMatrix.hh TantanMasker.hh tantan.hh </span>\</span>

</pre>

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> DiagonalTable.hh GreedyXdropAligner.hh gaplessXdrop.hh </span>\</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> GeneticCode.hh SubsetMinimizerFinder.hh SubsetSuffixArray.hh </span>\</span>

</pre>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> AlignmentPot.hh Alignment.hh Centroid.hh GappedXdropAligner.hh </span>\</span>

</pre>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_contiguous_queue.hh mcf_reverse_queue.hh mcf_gap_costs.hh </span>\</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(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="LC264" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_simd.hh SegmentPair.hh GreedyXdropAligner.hh </span>\</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_frameshift_xdrop_aligner.hh SegmentPairPot.hh ScoreMatrix.hh </span>\</span>

</pre>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> TantanMasker.hh tantan.hh DiagonalTable.hh gaplessXdrop.hh </span>\</span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> gaplessPssmXdrop.hh gaplessTwoQualityXdrop.hh zio.hh mcf_zstream.hh </span>\</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> threadUtil.hh version.hh</span></span>

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<td class="diff-line-num old_line" data-linenumber="261" 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">

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<td class="diff-line-num new_line" data-linenumber="269" 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">

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="make"><span class="nl">lastdb.o lastdb.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">lastdb.cc last.hh Alphabet.hh CyclicSubsetSeed.hh </span>\</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="263" 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="271" 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">@@ -263,6 +271,8 @@ lastdb.o lastdb.o8: lastdb.cc last.hh Alphabet.hh CyclicSubsetSeed.hh \</td>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> stringify.hh SequenceFormat.hh dna_words_finder.hh qualityScoreUtil.hh </span>\</span>

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<td class="diff-line-num old_line" data-linenumber="264" 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">

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> LastdbArguments.hh SubsetSuffixArray.hh TantanMasker.hh tantan.hh zio.hh </span>\</span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_zstream.hh threadUtil.hh version.hh</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(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="LC274" class="line" lang="make"><span class="nl">mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">mcf_frameshift_xdrop_aligner.cc </span>\</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(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="LC275" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_frameshift_xdrop_aligner.hh mcf_gap_costs.hh</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="276" 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">

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="make"><span class="nl">mcf_gap_costs.o mcf_gap_costs.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">mcf_gap_costs.cc mcf_gap_costs.hh</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="267" 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">

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<td class="diff-line-num new_line" data-linenumber="277" 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">

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="make"><span class="nl">mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.o8</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">mcf_substitution_matrix_stats.cc </span>\</span>

</pre>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> mcf_substitution_matrix_stats.hh LambdaCalculator.hh cbrc_linalg.hh</span></span>

</pre>

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<br>

</li>

<li id="b8658dba55bc28b741dfef5e4ea001b2623bdb9e">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#b8658dba55bc28b741dfef5e4ea001b2623bdb9e"><strong>src/mcf_frameshift_xdrop_aligner.cc</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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="cpp"><span class="c1" style="color: #998; font-style: italic;">// Author: Martin C. Frith 2020</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// SPDX-License-Identifier: GPL-3.0-or-later</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="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">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "mcf_frameshift_xdrop_aligner.hh"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="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">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <assert.h></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"></span>

</pre>

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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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#include <iostream>  // for debugging</span></span>

</pre>

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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="cpp"></span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">mcf</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="cpp"></span>

</pre>

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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="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;">forward</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(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="LC15" 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;">frame1</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frame2</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp">                                  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isRightwardExtension</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(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="LC18" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="19" style="width: 35px; color: rgba(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="LC19" 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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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(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="LC20" 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="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(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="LC21" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isRightwardExtension</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(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="LC22" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">protein</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">frame0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">frame1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">frame2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(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="LC23" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp">  <span class="n" style="color: #333;">proteinPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">protein</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(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="LC25" 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;">frame0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(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="LC26" 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;">frame1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="27" style="width: 35px; color: rgba(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="LC27" 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;">frame2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isRightwardExtension</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(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="LC29" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(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="LC30" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(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="LC31" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="32" style="width: 35px; color: rgba(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="LC32" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(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="LC33" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(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="LC34" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(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="LC35" 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>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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;">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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(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="LC39" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

40

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<pre style="margin: 0;">+<span id="LC40" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(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="LC41" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">proteinEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(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="LC43" 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;">padSize</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;">// xxx or 0 ?</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(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="LC44" 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;">diagPos6</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(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="LC45" 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;">horiPos5</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(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="LC46" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos4</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos3</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;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(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="LC48" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertPos1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(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="LC49" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisPos</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos1</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// xxx or + padSize ?</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(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="LC50" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumOfProbRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">logSumOfProbRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="55" style="width: 35px; color: rgba(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="LC55" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xdropShape</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="n" style="color: #333;">xdropShape</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;">thisPos</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

56

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="57" style="width: 35px; color: rgba(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="LC57" class="line" lang="cpp">  <span class="n" style="color: #333;">resizeFwdProbsIfSmaller</span><span class="p">(</span><span class="n" style="color: #333;">thisPos</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">behindProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">protein</span><span class="p">][</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frame0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp">  <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">behindProb</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;">// XXX might fail?</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(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="LC60" class="line" lang="cpp">  <span class="n" style="color: #333;">xFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">padSize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">behindProb</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// xxx or padSize ?</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(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="LC61" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">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;">proteinPtr</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" 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>

</pre>

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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;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp">    <span class="n" style="color: #333;">resizeFwdProbsIfSmaller</span><span class="p">(</span><span class="n" style="color: #333;">thisPos</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="n" style="color: #333;">numCells</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" 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;">padSize</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>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp">      <span class="n" style="color: #333;">xFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp">      <span class="n" style="color: #333;">yFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">      <span class="n" style="color: #333;">zFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" 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;">padSize</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">    <span class="n" style="color: #333;">Prob</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;">xFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp">    <span class="n" style="color: #333;">Prob</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;">yFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">    <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Z0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(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="LC77" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">X1</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="n" style="color: #333;">vertPos1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="78" style="width: 35px; color: rgba(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="LC78" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">X2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">vertPos2</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">horiPos3</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">horiPos3</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(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="LC81" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">X4</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="n" style="color: #333;">horiPos4</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(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="LC82" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">X5</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="n" style="color: #333;">horiPos5</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(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="LC83" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">X6</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="n" style="color: #333;">diagPos6</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="85" style="width: 35px; color: rgba(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="LC85" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumOfProbRatios</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">probDropLimit</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

86

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDelimiter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

88

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(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="LC89" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(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="LC90" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(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="LC91" 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;">X6</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;">substitutionProbs</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">X5</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;">delProb1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">X4</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;">delProb2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Y3</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;">delProb3</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">X1</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;">insProb1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">X2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insProb2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Z3</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;">insProb3</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC94" 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;">y</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;">z</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insOpenProb</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(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="LC95" class="line" lang="cpp">      <span class="n" style="color: #333;">X0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" 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;">b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC97" 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;">b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp">      <span class="n" style="color: #333;">sumOfProbRatios</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC99" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isDelimiter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">substitutionProbs</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="mi" style="color: #099;">0</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp">    <span class="n" style="color: #333;">diagPos6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos5</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp">    <span class="n" style="color: #333;">horiPos5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos4</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(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="LC106" class="line" lang="cpp">    <span class="n" style="color: #333;">horiPos4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos3</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp">    <span class="n" style="color: #333;">horiPos3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp">    <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp">    <span class="n" style="color: #333;">vertPos1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="110" style="width: 35px; color: rgba(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="LC110" class="line" lang="cpp">    <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="111" style="width: 35px; color: rgba(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="LC111" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">xdropShape</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;">a2</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;">xdropShape</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp">    <span class="n" style="color: #333;">xdropShape</span><span class="p">[</span><span class="n" style="color: #333;">a2</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;">proteinEnd</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp">    <span class="n" style="color: #333;">xdropShape</span><span class="p">[</span><span class="n" style="color: #333;">a2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isOkBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">X0</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minProb</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isDelimiter2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isOkEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">X0</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minProb</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isDelimiter1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

122

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

123

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isOkEnd</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">runOfEdges</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

124

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">runOfEdges</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

125

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<pre style="margin: 0;">+<span id="LC125" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

126

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<pre style="margin: 0;">+<span id="LC126" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

127

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">proteinEnd</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

128

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp">  <span class="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

129

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

130

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

131

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

132

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isOkBeg</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

133

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp">      <span class="n" style="color: #333;">runOfDrops</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

134

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

135

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">runOfDrops</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

136

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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<pre style="margin: 0;">+<span id="LC137" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

138

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<pre style="margin: 0;">+<span id="LC138" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

139

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp">  <span class="n" style="color: #333;">proteinPtr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(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="LC140" 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>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC141" 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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<pre style="margin: 0;">+<span id="LC142" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(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="LC143" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos6</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos5</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos3</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">vertPos2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">vertPos1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(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="LC144" class="line" lang="cpp">  <span class="n" style="color: #333;">runOfDrops</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"></span>

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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">rescaleStep</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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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp">      <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">sumOfProbRatios</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="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC150" 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;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sumOfProbRatios</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfRescales</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">rescaleStep</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rescales</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;">numOfRescales</span><span class="p">)</span> <span class="n" style="color: #333;">rescales</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">numOfRescales</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp">      <span class="n" style="color: #333;">rescales</span><span class="p">[</span><span class="n" style="color: #333;">numOfRescales</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;">scale</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp">      <span class="n" style="color: #333;">rescaleFwdProbs</span><span class="p">(</span><span class="n" style="color: #333;">begInProbs</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;">thisPos</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(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="LC155" class="line" lang="cpp">      <span class="n" style="color: #333;">logSumOfProbRatios</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;">sumOfProbRatios</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp">      <span class="n" style="color: #333;">sumOfProbRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp">  <span class="n" style="color: #333;">numOfAntidiagonals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(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="LC161" class="line" lang="cpp">  <span class="n" style="color: #333;">rescaledSumOfProbRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumOfProbRatios</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(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="LC162" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">logSumOfProbRatios</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;">sumOfProbRatios</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(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="LC163" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(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="LC164" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(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="LC165" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">FrameshiftXdropAligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isRightwardExtension</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(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="LC166" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="167" style="width: 35px; color: rgba(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="LC167" 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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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(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="LC168" 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;">isRightwardExtension</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(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="LC169" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC170" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(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="LC171" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(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="LC172" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC173" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC174" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

175

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

176

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp">  <span class="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

177

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

178

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

179

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">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;">padSize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

180

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<pre style="margin: 0;">+<span id="LC180" 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;">diagPos6</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

181

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<pre style="margin: 0;">+<span id="LC181" 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;">horiPos5</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

182

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos4</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

183

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos3</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;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertPos1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisPos</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfAntidiagonals</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

187

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="188" style="width: 35px; color: rgba(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="LC188" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scaledUnit</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;">rescaledSumOfProbRatios</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="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="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp">  <span class="n" style="color: #333;">resizeBckProbsIfSmaller</span><span class="p">(</span><span class="n" style="color: #333;">begInProbs</span><span class="p">(</span><span class="n" style="color: #333;">numOfAntidiagonals</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC192" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC194" 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;">proteinPtr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(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="LC195" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(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="LC196" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfCellsInAntidiagonal</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(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="LC199" 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;">padSize</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>

</pre>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp">      <span class="n" style="color: #333;">xBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp">      <span class="n" style="color: #333;">yBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp">      <span class="n" style="color: #333;">zBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</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;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC204" 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;">padSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp">    <span class="n" style="color: #333;">Prob</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;">xBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp">    <span class="n" style="color: #333;">Prob</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;">yBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp">    <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Z0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">vertPos1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">vertPos2</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">Prob</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">horiPos3</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">Prob</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">horiPos3</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Y4</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">horiPos4</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Y5</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">horiPos5</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">X6</span> <span class="o" style="font-weight: 600;">=</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;">diagPos6</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC216" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC217" 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;">X6</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(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="LC218" 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;">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;">delProb1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="219" style="width: 35px; color: rgba(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="LC219" 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;">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;">delProb2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(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="LC220" 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="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;">delProb3</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="221" style="width: 35px; color: rgba(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="LC221" 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="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;">insProb1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="222" style="width: 35px; color: rgba(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="LC222" 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="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;">insProb2</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC223" 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="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;">insProb3</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC224" 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="n" style="color: #333;">scaledUnit</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp">      <span class="n" style="color: #333;">X0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">substitutionProbs</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="226" style="width: 35px; color: rgba(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="LC226" 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;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC227" 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;">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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="228" style="width: 35px; color: rgba(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="LC228" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC229" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp">    <span class="n" style="color: #333;">diagPos6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos5</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp">    <span class="n" style="color: #333;">horiPos5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos4</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp">    <span class="n" style="color: #333;">horiPos4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos3</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="235" style="width: 35px; color: rgba(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="LC235" class="line" lang="cpp">    <span class="n" style="color: #333;">horiPos3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp">    <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp">    <span class="n" style="color: #333;">vertPos1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">    <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</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;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">endInProtein</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;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">endInProtein</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(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="LC243" class="line" lang="cpp">      <span class="n" style="color: #333;">proteinPtr</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="244" style="width: 35px; color: rgba(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="LC244" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC245" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC246" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos6</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos5</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos3</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">vertPos2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">vertPos1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(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="LC251" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">rescaleStep</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(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="LC252" class="line" lang="cpp">  <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfAntidiagonals</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC253" 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="n" style="color: #333;">rescales</span><span class="p">[</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">rescaleStep</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">begInProbs</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="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">begInProbs</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(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="LC255" class="line" lang="cpp">      <span class="n" style="color: #333;">rescaleBckProbs</span><span class="p">(</span><span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">thisPos</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp">      <span class="n" style="color: #333;">scaledUnit</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp">  <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">begInProbs</span><span class="p">(</span><span class="n" style="color: #333;">numOfAntidiagonals</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">FrameshiftXdropAligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isRightwardExtension</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC264" 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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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp">                             <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionCounts</span><span class="p">,</span></span>

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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC266" 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;">transitionCounts</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC267" 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;">isRightwardExtension</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="LC268" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC269" 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;">padSize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC270" 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;">diagPos6</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC271" 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;">horiPos5</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos4</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos3</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;">1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertPos1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisPos</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfAntidiagonals</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;">size_t</span> <span class="n" style="color: #333;">totalNumOfCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">begInProbs</span><span class="p">(</span><span class="n" style="color: #333;">numOfAntidiagonals</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">proteinEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endInProtein</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;">1</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isRightwardExtension</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp">    <span class="n" style="color: #333;">proteinPtr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">proteinEnd</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC282" 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="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">)</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="p">(</span><span class="n" style="color: #333;">proteinEnd</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="LC283" 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="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">proteinEnd</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="LC284" 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="p">(</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="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">proteinEnd</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="LC285" 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="LC286" class="line" lang="cpp">    <span class="n" style="color: #333;">proteinPtr</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">proteinEnd</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC287" 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="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">)</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="p">(</span><span class="n" style="color: #333;">proteinEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC288" 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="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">proteinEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC289" 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="p">(</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="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">proteinEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">del1</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;">del2</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;">del3</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;">delNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ins1</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;">ins2</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;">ins3</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;">insNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC295" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC297" 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;">proteinPtr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC298" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC299" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfCellsInAntidiagonal</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</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;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">vertPos1</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">vertPos2</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">horiPos3</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">horiPos3</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Y4</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">horiPos4</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Y5</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yBckProbs</span><span class="p">[</span><span class="n" style="color: #333;">horiPos5</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">X6</span> <span class="o" style="font-weight: 600;">=</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;">diagPos6</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fX0</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="n" style="color: #333;">totalNumOfCells</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+</span> <span class="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>

</pre>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fY0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">yFwdProbs</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;">thisPos</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>

</pre>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Prob</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fZ0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">zFwdProbs</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;">thisPos</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="LC314" class="line" lang="cpp"></span>

</pre>

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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;">d1</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;">d2</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;">d3</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;">dNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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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;">i1</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;">i2</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;">i3</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;">iNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC318" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(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="LC319" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">X6</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;">fX0</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="320" style="width: 35px; color: rgba(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="LC320" class="line" lang="cpp">      <span class="n" style="color: #333;">substitutionCounts</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 class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">matchProb</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="321" style="width: 35px; color: rgba(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="LC321" class="line" lang="cpp">      <span class="n" style="color: #333;">transitionCounts</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;">matchProb</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp">      <span class="n" style="color: #333;">d1</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;">fX0</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>

</pre>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp">      <span class="n" style="color: #333;">d2</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;">fX0</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="324" style="width: 35px; color: rgba(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="LC324" class="line" lang="cpp">      <span class="n" style="color: #333;">d3</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">Y3</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;">fX0</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>

</pre>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp">      <span class="n" style="color: #333;">dNext</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">Y3</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;">fY0</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="326" style="width: 35px; color: rgba(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="LC326" class="line" lang="cpp">      <span class="n" style="color: #333;">i1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">Z1</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;">fX0</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>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp">      <span class="n" style="color: #333;">i2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">Z2</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;">fX0</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>

</pre>

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp">      <span class="n" style="color: #333;">i3</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">Z3</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;">fX0</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="329" style="width: 35px; color: rgba(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="LC329" class="line" lang="cpp">      <span class="n" style="color: #333;">iNext</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">Z3</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;">fZ0</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(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="LC330" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC331" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="333" style="width: 35px; color: rgba(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="LC333" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="334" style="width: 35px; color: rgba(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="LC334" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">mod</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">rescaleStep</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="335" style="width: 35px; color: rgba(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="LC335" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mod</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">rescaleStep</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">6</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="336" style="width: 35px; color: rgba(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="LC336" class="line" lang="cpp">  <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mod</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rescaleStep</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfAntidiagonals</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="337" style="width: 35px; color: rgba(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="LC337" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mul</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;">rescales</span><span class="p">[</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">rescaleStep</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="338" style="width: 35px; color: rgba(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="LC338" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mod</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rescaleStep</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;">i1</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">mul</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

339

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mod</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rescaleStep</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;">i2</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">mul</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="340" style="width: 35px; color: rgba(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="LC340" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mod</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rescaleStep</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="341" style="width: 35px; color: rgba(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="LC341" class="line" lang="cpp">  <span class="n" style="color: #333;">i3</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">mul</span><span class="p">;</span> <span class="n" style="color: #333;">iNext</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">mul</span><span class="p">;</span> <span class="n" style="color: #333;">d3</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">mul</span><span class="p">;</span> <span class="n" style="color: #333;">dNext</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">mul</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="342" style="width: 35px; color: rgba(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="LC342" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="343" style="width: 35px; color: rgba(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="LC343" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mod</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rescaleStep</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="n" style="color: #333;">d2</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">mul</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="344" style="width: 35px; color: rgba(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="LC344" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mod</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rescaleStep</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">mul</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="345" style="width: 35px; color: rgba(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="LC345" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="346" style="width: 35px; color: rgba(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="LC346" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp">    <span class="n" style="color: #333;">ins1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i1</span><span class="p">;</span> <span class="n" style="color: #333;">ins2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i2</span><span class="p">;</span> <span class="n" style="color: #333;">ins3</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i3</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;">iNext</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="348" style="width: 35px; color: rgba(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="LC348" class="line" lang="cpp">    <span class="n" style="color: #333;">del1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">d1</span><span class="p">;</span> <span class="n" style="color: #333;">del2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">d2</span><span class="p">;</span> <span class="n" style="color: #333;">del3</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">d3</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;">dNext</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="349" style="width: 35px; color: rgba(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="LC349" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="350" style="width: 35px; color: rgba(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="LC350" class="line" lang="cpp">    <span class="n" style="color: #333;">diagPos6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos5</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

351

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp">    <span class="n" style="color: #333;">horiPos5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos4</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="352" style="width: 35px; color: rgba(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="LC352" class="line" lang="cpp">    <span class="n" style="color: #333;">horiPos4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos3</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="353" style="width: 35px; color: rgba(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="LC353" class="line" lang="cpp">    <span class="n" style="color: #333;">horiPos3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="354" style="width: 35px; color: rgba(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="LC354" class="line" lang="cpp">    <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="355" style="width: 35px; color: rgba(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="LC355" class="line" lang="cpp">    <span class="n" style="color: #333;">vertPos1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="356" style="width: 35px; color: rgba(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="LC356" class="line" lang="cpp">    <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

357

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="358" style="width: 35px; color: rgba(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="LC358" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</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;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="359" style="width: 35px; color: rgba(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="LC359" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="360" style="width: 35px; color: rgba(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="LC360" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">endInProtein</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;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">endInProtein</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="361" style="width: 35px; color: rgba(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="LC361" class="line" lang="cpp">      <span class="n" style="color: #333;">proteinPtr</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="362" style="width: 35px; color: rgba(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="LC362" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="363" style="width: 35px; color: rgba(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="LC363" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="364" style="width: 35px; color: rgba(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="LC364" 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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="365" style="width: 35px; color: rgba(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="LC365" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos6</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos5</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos3</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">vertPos2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">vertPos1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

366

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="367" style="width: 35px; color: rgba(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="LC367" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="368" style="width: 35px; color: rgba(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="LC368" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="369" style="width: 35px; color: rgba(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="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="370" style="width: 35px; color: rgba(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="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="371" style="width: 35px; color: rgba(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="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>

</pre>

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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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="373" style="width: 35px; color: rgba(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="LC373" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="374" style="width: 35px; color: rgba(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="LC374" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="375" style="width: 35px; color: rgba(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="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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="378" style="width: 35px; color: rgba(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="LC378" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"><span class="p">}</span></span></pre>

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</table>

<br>

</li>

<li id="7b7b86f617ae717ef44a71c27b54fe7b613973d1">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#7b7b86f617ae717ef44a71c27b54fe7b613973d1"><strong>src/mcf_frameshift_xdrop_aligner.hh</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Author: Martin C. Frith 2020</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// SPDX-License-Identifier: GPL-3.0-or-later</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef FRAMESHIFT_XDROP_ALIGNER_HH</span></span>

</pre>

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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">

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;">#define FRAMESHIFT_XDROP_ALIGNER_HH</span></span>

</pre>

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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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="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">

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 "mcf_gap_costs.hh"</span></span>

</pre>

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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">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="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">

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 <stddef.h></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="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">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="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">

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 <vector></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="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="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">mcf</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="15" style="width: 35px; color: rgba(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="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">const_dbl_ptr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</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;">dbl_ptr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="17" style="width: 35px; color: rgba(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="LC17" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(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="LC18" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FrameshiftXdropAligner</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(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="LC19" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">uchar</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(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="LC20" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">typedef</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;">const_uchar_ptr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(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="LC21" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Prob</span><span class="p">;</span></span>

</pre>

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22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">padSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">rescaleStep</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">32</span> <span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="nl">public:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(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="LC27" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">forward</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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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;">frame0</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;">// translated DNA,  0 frame</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frame1</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;">// translated DNA, +1 frame</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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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;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frame2</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;">// translated DNA, +2 frame</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isRightwardExtension</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(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="LC32" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(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="LC33" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="34" style="width: 35px; color: rgba(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="LC34" 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="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(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="LC36" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isRightwardExtension</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(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="LC37" 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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

39

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">count</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isRightwardExtension</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="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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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionCounts</span><span class="p">,</span></span>

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(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="LC43" 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;">transitionCounts</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(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="LC44" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">proteinCoordinate</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">dnaCoordinate</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="LC46" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proteinCoordinate</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="n" style="color: #333;">dnaCoordinate</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</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="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">numOfAntidiagonals</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">*</span> <span class="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;">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;">xdropShape</span><span class="p">[</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">+</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;">xdropShape</span><span class="p">[</span><span class="n" style="color: #333;">a</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;">proteinCoordinate</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</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;">xdropShape</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">]</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="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">xdropShape</span><span class="p">[</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</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;">b</span> <span class="o" style="font-weight: 600;">=</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="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="LC52" class="line" lang="cpp">    <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;">xdropShape</span><span class="p">[</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">+</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;">xdropShape</span><span class="p">[</span><span class="n" style="color: #333;">b</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;">proteinCoordinate</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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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;">totalNumOfCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropShape</span><span class="p">[</span><span class="n" style="color: #333;">numOfAntidiagonals</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="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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

55

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

56

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(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="LC57" class="line" lang="cpp"><span class="nl">private:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

58

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp">  <span class="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

59

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp">  <span class="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="60" style="width: 35px; color: rgba(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="LC60" 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;">zFwdProbs</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(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="LC61" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(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="LC62" 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;">xBckProbs</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" 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;">yBckProbs</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">zBckProbs</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">xdropShape</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" 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;">rescales</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="69" style="width: 35px; color: rgba(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="LC69" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="70" style="width: 35px; color: rgba(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="LC70" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rescaledSumOfProbRatios</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(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="LC71" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(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="LC72" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfAntidiagonals</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">proteinPtr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<pre style="margin: 0;">+<span id="LC75" 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="mi" style="color: #099;">3</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(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="LC77" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">begInProbs</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="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(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="LC78" class="line" lang="cpp">  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">xdropShape</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;">2</span><span class="p">];</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">endInProtein</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="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(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="LC81" class="line" lang="cpp">  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">xdropShape</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;">2</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(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="LC82" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(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="LC83" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numOfCellsInAntidiagonal</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="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp">  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">begInProbs</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;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">begInProbs</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(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="LC85" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">resizeFwdProbsIfSmaller</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xFwdProbs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC88" 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;">size</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(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="LC89" class="line" lang="cpp">      <span class="n" style="color: #333;">yFwdProbs</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

90

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp">      <span class="n" style="color: #333;">zFwdProbs</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

91

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

92

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

93

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

94

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">resizeBckProbsIfSmaller</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

95

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xBckProbs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

96

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp">      <span class="n" style="color: #333;">xBckProbs</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(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="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp">      <span class="n" style="color: #333;">yBckProbs</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp">      <span class="n" style="color: #333;">zBckProbs</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

99

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

100

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">rescaleFwdProbs</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">end</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="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">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;">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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp">      <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;">scale</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp">      <span class="n" style="color: #333;">yFwdProbs</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;">scale</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(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="LC106" class="line" lang="cpp">      <span class="n" style="color: #333;">zFwdProbs</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;">scale</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

109

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(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="LC110" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">rescaleBckProbs</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">end</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="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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<pre style="margin: 0;">+<span id="LC111" 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;">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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp">      <span class="n" style="color: #333;">xBckProbs</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;">scale</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp">      <span class="n" style="color: #333;">yBckProbs</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;">scale</span><span class="p">;</span></span>

</pre>

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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;">zBckProbs</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;">scale</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"><span class="p">};</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>

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<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#8266f3ec3e8e19e5efa1a2f239f8ba579e89eb00"><strong>src/mcf_gap_costs.cc</strong></a>

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<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" 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">@@ -5,6 +5,7 @@</td>

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5

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<td class="diff-line-num new_line" data-linenumber="5" 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">

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 <stdexcept></span></span>

</pre>

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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 <assert.h></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line" data-linenumber="7" 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">

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 <limits.h></span></span>

</pre>

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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 <math.h></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stddef.h>  // size_t</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="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;">err</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;">s</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="26" 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="27" 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">@@ -26,12 +27,23 @@ static void assignGapCostPieces(const std::vector<int> &openCosts,</td>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp">  <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">pieces</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">assignProbs</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;">GapCosts</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ProbPiece</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">probPieces</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;">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;">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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">costPieces</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp">                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</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="n" style="color: #333;">probPieces</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">costPieces</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="LC34" 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;">costPieces</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp">    <span class="n" style="color: #333;">probPieces</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">openProb</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;">costPieces</span><span class="p">[</span><span class="n" style="color: #333;">i</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="LC36" class="line" lang="cpp">    <span class="n" style="color: #333;">probPieces</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">growProb</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;">costPieces</span><span class="p">[</span><span class="n" style="color: #333;">i</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="LC37" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(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="LC39" class="line" lang="cpp"></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">assign</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="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">delOpenCosts</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="30" 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">

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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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">delGrowCosts</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="31" 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">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">insOpenCosts</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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">insGrowCosts</span><span class="p">,</span></span>

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<td class="diff-line-num new_line" data-linenumber="44" 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">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">frameshiftCosts</span><span class="p">,</span></span>

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<td class="diff-line-num new_line old" data-linenumber="45" 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="LC34" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unalignedPairCost</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unalignedPairCost</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp">  <span class="n" style="color: #333;">assignGapCostPieces</span><span class="p">(</span><span class="n" style="color: #333;">delOpenCosts</span><span class="p">,</span> <span class="n" style="color: #333;">delGrowCosts</span><span class="p">,</span> <span class="n" style="color: #333;">delPieces</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp">  <span class="n" style="color: #333;">assignGapCostPieces</span><span class="p">(</span><span class="n" style="color: #333;">insOpenCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insGrowCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insPieces</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unalignedPairCost</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" 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="56" 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">@@ -44,6 +56,9 @@ void GapCosts::assign(const std::vector<int> &delOpenCosts,</td>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">         <span class="n" style="color: #333;">pairCost</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">delPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growCost</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growCost</span> <span class="o" style="font-weight: 600;">+</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp">         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">delPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openCost</span><span class="p">,</span> <span class="n" style="color: #333;">insPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openCost</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp">  <span class="n" style="color: #333;">assignProbs</span><span class="p">(</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">,</span> <span class="n" style="color: #333;">delPieces</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="LC60" class="line" lang="cpp">  <span class="n" style="color: #333;">assignProbs</span><span class="p">(</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">,</span> <span class="n" style="color: #333;">insPieces</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="LC61" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">frameshiftCosts</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp">    <span class="n" style="color: #333;">frameshiftCost</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="LC64" 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;">frameshiftCosts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span 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">@@ -57,6 +72,13 @@ void GapCosts::assign(const std::vector<int> &delOpenCosts,</td>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp">    <span class="n" style="color: #333;">insScore2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growCost</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">frameshiftCosts</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="LC73" class="line" lang="cpp">    <span class="n" style="color: #333;">insScore3</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="p">(</span><span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growCost</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp">    <span class="n" style="color: #333;">frameshiftCost</span> <span class="o" style="font-weight: 600;">=</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="LC75" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">    <span class="n" style="color: #333;">delProb1</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="n" style="color: #333;">delScore1</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp">    <span class="n" style="color: #333;">delProb2</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="n" style="color: #333;">delScore2</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp">    <span class="n" style="color: #333;">delProb3</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="n" style="color: #333;">delScore3</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;">insProb1</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="n" style="color: #333;">insScore1</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp">    <span class="n" style="color: #333;">insProb2</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="n" style="color: #333;">insScore2</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp">    <span class="n" style="color: #333;">insProb3</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="n" style="color: #333;">insScore3</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="84" 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">

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"></span>

</pre>

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<br>

</li>

<li id="f4c2aa5ffe5ddbfe5093d67a91ae22b61c035703">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#f4c2aa5ffe5ddbfe5093d67a91ae22b61c035703"><strong>src/mcf_gap_costs.hh</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" 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="27" 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">@@ -27,6 +27,11 @@ struct GapCosts {</td>

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<td class="diff-line-num old_line" data-linenumber="27" 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">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">growCost</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp">  <span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(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="30" style="width: 35px; color: rgba(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="LC30" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">ProbPiece</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(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="31" style="width: 35px; color: rgba(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="LC31" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(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="LC32" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(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="33" style="width: 35px; color: rgba(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="LC33" class="line" lang="cpp">  <span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(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="34" style="width: 35px; color: rgba(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="LC34" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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">

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<td class="diff-line-num new_line" data-linenumber="35" 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">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Piece</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">delPieces</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" 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">

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<td class="diff-line-num new_line" data-linenumber="36" 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">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Piece</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">insPieces</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" 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">

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<td class="diff-line-num new_line" data-linenumber="37" 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">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pairCost</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" 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="48" 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">@@ -43,6 +48,16 @@ struct GapCosts {</td>

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<td class="diff-line-num old_line" data-linenumber="43" 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">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" 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">

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<td class="diff-line-num new_line" data-linenumber="49" 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">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isAffine</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="45" 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">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="46" style="width: 35px; color: rgba(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="LC51" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// these are for calculating alignment probabilities:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp">  <span class="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;">ProbPiece</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">delProbPieces</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="46" style="width: 35px; color: rgba(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="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ProbPiece</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">insProbPieces</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delProb1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delProb2</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;">double</span> <span class="n" style="color: #333;">delProb3</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;">double</span> <span class="n" style="color: #333;">insProb1</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;">double</span> <span class="n" style="color: #333;">insProb2</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insProb3</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Assign piecewise linear open and grow costs, and one pairCost.</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// If unalignedPairCost <= 0, assign non-generalized costs.</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Throw a runtime_error if any growCost is <= 0.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" 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">@@ -56,7 +71,8 @@ struct GapCosts {</td>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">insOpenCosts</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">insGrowCosts</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">frameshiftCosts</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unalignedPairCost</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unalignedPairCost</span><span class="p">,</span></span>

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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp">         <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// probability ratio  =  exp(scale * score)</span></span>

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60

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<td class="diff-line-num new_line" data-linenumber="76" 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">

76

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" 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">

61

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<td class="diff-line-num new_line" data-linenumber="77" 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">

77

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// The cost of a "gap" consisting of unaligned letters in the query</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" 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">

62

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<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

78

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// and/or reference sequence</span></span>

</pre>

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<li id="69737f84c540417aafef4e696f66adcc9f92fa66">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/d6f8dcc9f61aa96a2437138eab65296dd5363455...5c0d82d459d98ffaac17546c38e70b2500d73072#69737f84c540417aafef4e696f66adcc9f92fa66"><strong>src/version.hh</strong></a>

<hr>

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<td class="diff-line-num old old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"11<span class="idiff left right">33</span>"</span></span></pre>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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">

1

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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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