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<h3>

Sascha Steinbiss pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049">1063526e</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2018-12-22T20:36:53Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 22</pre>

</li>

</ul>

<h4>13 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#57bf262130f956caf76c405086f0815caf4e0a89">

ChangeLog.txt

</a>

</li>

<li class="file-stats">

<a href="#73ff05a9f629bff633fa7a0499495556f0f1a07f">

README.html

</a>

</li>

<li class="file-stats">

<a href="#fda3484edf8db0684440157ce0b110d784d42704">

README.txt

</a>

</li>

<li class="file-stats">

<a href="#8475d4d49b41be53a257bfb9040629db473a883f">

src/mcf_tantan_options.cc

</a>

</li>

<li class="file-stats">

<a href="#f47bc0f64f7f84a6b297f01be0f207e098844969">

src/mcf_tantan_options.hh

</a>

</li>

<li class="file-stats">

<a href="#7cec908f40ab30058cc7553cf0463829623d0080">

src/tantan.cc

</a>

</li>

<li class="file-stats">

<a href="#08d18a28f9f43426ba0305df09ef35871d021752">

src/tantan_app.cc

</a>

</li>

<li class="file-stats">

<a href="#cb87d4448c885fb7b36ecf5f9502a1c7535cd121">

<span class="new-file">

+

src/tantan_repeat_finder.cc

</span>

</a>

</li>

<li class="file-stats">

<a href="#6ffe7697fa2b7a52ab8b6f315ee31523c85ae5c1">

<span class="new-file">

+

src/tantan_repeat_finder.hh

</span>

</a>

</li>

<li class="file-stats">

<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">

src/version.hh

</a>

</li>

<li class="file-stats">

<a href="#b9eb9f70cb43642f308d5a3f3f451d95a5984a96">

<span class="new-file">

+

test/hard.fa

</span>

</a>

</li>

<li class="file-stats">

<a href="#dda902050115a2b1759155bb4f11361a446208e0">

test/tantan_test.out

</a>

</li>

<li class="file-stats">

<a href="#905a9d4bc9e20118254b08495f8411e1fb0cc07d">

test/tantan_test.sh

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="57bf262130f956caf76c405086f0815caf4e0a89">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2018-12-19  Martin C. Frith  <Martin C. Frith></span>

</pre>

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

2

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

</pre>

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3

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

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">      Make it faster</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">      [3523060bcfb9] [tip]</span>

</pre>

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6

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

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">      * src/tantan_repeat_finder.cc, src/tantan_repeat_finder.hh:</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">      Make -f4 a bit faster</span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">      [1fccdf6e21be]</span>

</pre>

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10

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

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">     * README.txt, src/mcf_tantan_options.cc, src/mcf_tantan_options.hh,</span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">     src/tantan_app.cc, src/tantan_repeat_finder.cc,</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">     src/tantan_repeat_finder.hh, test/hard.fa, test/tantan_test.out,</span>

</pre>

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14

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

</pre>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">     Add option to find straightforward tandem repeats</span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">     [1bae60144712]</span>

</pre>

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17

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

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">     * README.txt, src/mcf_tantan_options.cc, src/tantan.cc,</span>

</pre>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">     src/tantan_app.cc:</span>

</pre>

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20

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

</pre>

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21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">     [fc1ca32a72aa]</span>

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22

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

</pre>

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1

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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">

23

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">2018-12-10  Martin C. Frith  <Martin C. Frith></span>

</pre>

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2

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24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>

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3

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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">

25

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">     * README.txt, src/mcf_tantan_options.cc, src/mcf_tantan_options.hh,</span>

</pre>

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4

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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">

26

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">     src/tantan_app.cc, test/tantan_test.out, test/tantan_test.sh:</span>

</pre>

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5

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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">

27

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">     Add match score, mismatch cost options</span>

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6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">      [2383404c795a]<span class="idiff left right"> [tip]</span></span>

</pre>

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28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">     [2383404c795a]</span>

</pre>

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7

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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">

29

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>

</pre>

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8

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">     * src/tantan.cc:</span>

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9

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">     Refactor</span>

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</li>

<li id="73ff05a9f629bff633fa7a0499495556f0f1a07f">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#73ff05a9f629bff633fa7a0499495556f0f1a07f"><strong>README.html</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); 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="451" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -451,7 +451,7 @@ repeats, so it's easy to lift the masking after determining homology.</p></td>

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451

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>preserve uppercase/lowercase in non-masked regions<span class="nt" style="color: navy;"></td></tr></span></span>

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452

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<td class="diff-line-num new_line" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

452

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

453

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<td class="diff-line-num new_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

453

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-m<span class="nt" style="color: navy;"></span></kbd></td></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="454" 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">

454

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<td class="diff-line-num new_line old" data-linenumber="454" 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="LC454" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>file for letter<span class="idiff left right"> pair scores (scoring matrix)</span><span class="nt" style="color: navy;"></td></tr></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>file for letter<span class="idiff left right">-pair score matrix</span><span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-r<span class="nt" style="color: navy;"></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>probability of a repeat starting per position<span class="nt" style="color: navy;"></td></tr></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">@@ -480,9 +480,12 @@ repeats, so it's easy to lift the masking after determining homology.</p></td>

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-s<span class="nt" style="color: navy;"></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>minimum repeat probability for masking<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-n<span class="nt" style="color: navy;"></span></kbd></td></span></span>

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<pre style="margin: 0;">+<span id="LC484" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>minimum copy number, affects -f4 only<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-f<span class="nt" style="color: navy;"></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>output type: 0=masked sequence, 1=repeat probabilities,</span>

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<pre style="margin: 0;">-<span id="LC485" class="line" lang="html">2=repeat counts, 3=BED<span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;">+<span id="LC488" class="line" lang="html">2=repeat counts, 3=BED<span class="idiff left right">, 4=tandem repeats</span><span class="nt" style="color: navy;"></td></tr></span></span>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC490" class="line" lang="html"><span class="nt" style="color: navy;"><kbd><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>-h<span class="nt" style="color: navy;"></span></span>, <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: navy;">></span>--help<span class="nt" style="color: navy;"></span></kbd></td></span></span>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="html"><span class="nt" style="color: navy;"><td></span>show help message, then exit<span class="nt" style="color: navy;"></td></tr></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">@@ -512,6 +515,29 @@ TGCTAGCAA ttaggcttaggtcagtgc TTAGGCTTAGGTCAGTGC AACGTA</td>

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

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<pre style="margin: 0;"> <span id="LC516" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>(My thanks to Junko Tsuji and Paul Horton for finding these issues.)<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;">+<span id="LC518" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"finding-straightforward-tandem-repeats"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC519" class="line" lang="html"><span class="nt" style="color: navy;"><h1></span>Finding straightforward tandem repeats<span class="nt" style="color: navy;"></h1></span></span>

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<pre style="margin: 0;">+<span id="LC520" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Option -f4 runs tantan in a different mode, where it finds</span>

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<pre style="margin: 0;">+<span id="LC521" class="line" lang="html">straightforward tandem repeats only.  (Technically, it uses a Viterbi</span>

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<pre style="margin: 0;">+<span id="LC522" class="line" lang="html">algorithm instead of a Forward-Backward algorithm.)  This is <span class="nt" style="color: navy;"><em></span>not<span class="nt" style="color: navy;"></em></span></span>

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<pre style="margin: 0;">+<span id="LC523" class="line" lang="html">recommended for avoiding false homologs!  But it might be useful for</span>

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<pre style="margin: 0;">+<span id="LC524" class="line" lang="html">studying tandem repeats.  The output looks like this:<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC525" class="line" lang="html"><span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC526" class="line" lang="html">mySeq   14765   14780   6       2.5     GTCATG  GTCATG,GTCATG,GTC</span>

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<pre style="margin: 0;">+<span id="LC527" class="line" lang="html">mySeq   632362  632377  2       6       GC      GC,GC,GC,GCt,GCT,GCT</span>

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<pre style="margin: 0;">+<span id="LC528" class="line" lang="html">mySeq   1278353 1278369 3       6.5     TCA     TCA,TCA,TCA,TC-,TC,TC,T</span>

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<pre style="margin: 0;">+<span id="LC529" class="line" lang="html">mySeq   3616084 3616100 3       5.33333 TGG     TGA,TGA,TGG,TGG,TGG,T</span>

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<pre style="margin: 0;">+<span id="LC530" class="line" lang="html"><span class="nt" style="color: navy;"></pre></span></span>

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<pre style="margin: 0;">+<span id="LC531" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The first 3 columns show the start and end coordinates of the</span>

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<pre style="margin: 0;">+<span id="LC532" class="line" lang="html">repetitive region, in <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://genome.ucsc.edu/FAQ/FAQformat.html#format1"</span><span class="nt" style="color: navy;">></span>BED<span class="nt" style="color: navy;"></a></span> format.  Column</span>

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="html">4 shows the length of the repeating unit (which might vary due to</span>

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534

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="html">insertions and deletions, so this column shows the most common</span>

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535

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<pre style="margin: 0;">+<span id="LC535" class="line" lang="html">length).  Column 5 shows the number of repeat units.  Column 6 shows</span>

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536

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<pre style="margin: 0;">+<span id="LC536" class="line" lang="html">the repeating unit (which again might vary, so this is just a</span>

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537

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

<pre style="margin: 0;">+<span id="LC537" class="line" lang="html">representative).  Column 7 shows the whole repeat: lowercase letters</span>

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538

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<pre style="margin: 0;">+<span id="LC538" class="line" lang="html">are insertions relative to the previous repeat unit, and dashes are</span>

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539

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<pre style="margin: 0;">+<span id="LC539" class="line" lang="html">deletions relative to the previous repeat unit.<span class="nt" style="color: navy;"></p></span></span>

</pre>

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540

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<pre style="margin: 0;">+<span id="LC540" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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541

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"miscellaneous"</span><span class="nt" style="color: navy;">></span></span>

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542

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="html"><span class="nt" style="color: navy;"><h1></span>Miscellaneous<span class="nt" style="color: navy;"></h1></span></span>

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>tantan is distributed under the GNU General Public License, either</span>

</pre>

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<br>

</li>

<li id="fda3484edf8db0684440157ce0b110d784d42704">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#fda3484edf8db0684440157ce0b110d784d42704"><strong>README.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 unfold js-unfold old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -136,7 +136,7 @@ Options</td>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">-p  interpret the sequences as proteins</span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext">-x  letter to use for masking, instead of lowercase</span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext">-c  preserve uppercase/lowercase in non-masked regions</span>

</pre>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext">-m  file for letter<span class="idiff left right"> pair scores (scoring matrix)</span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">-m  file for letter<span class="idiff left right">-pair score matrix</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">-r  probability of a repeat starting per position</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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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext">-e  probability of a repeat ending per position</span>

</pre>

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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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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext">-w  maximum tandem repeat period to consider</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">@@ -146,8 +146,9 @@ Options</td>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext">-a  gap existence cost</span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext">-b  gap extension cost</span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext">-s  minimum repeat probability for masking</span>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">-n  minimum copy number, affects -f4 only</span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext">-f  output type: 0=masked sequence, 1=repeat probabilities,</span>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext">                 2=repeat counts, 3=BED</span>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">                 2=repeat counts, 3=BED<span class="idiff left right">, 4=tandem repeats</span></span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext">-h, --help  show help message, then exit</span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext">--version   show version information, then exit</span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="plaintext">(My thanks to Junko Tsuji and Paul Horton for finding these issues.)</span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">Finding straightforward tandem repeats</span>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">--------------------------------------</span>

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">Option -f4 runs tantan in a different mode, where it finds</span>

</pre>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">straightforward tandem repeats only.  (Technically, it uses a Viterbi</span>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">algorithm instead of a Forward-Backward algorithm.)  This is *not*</span>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">recommended for avoiding false homologs!  But it might be useful for</span>

</pre>

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183

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">studying tandem repeats.  The output looks like this::</span>

</pre>

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184

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">  mySeq   14765   14780   6       2.5     GTCATG  GTCATG,GTCATG,GTC</span>

</pre>

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186

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">  mySeq   632362  632377  2       6       GC      GC,GC,GC,GCt,GCT,GCT</span>

</pre>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">  mySeq   1278353 1278369 3       6.5     TCA     TCA,TCA,TCA,TC-,TC,TC,T</span>

</pre>

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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">

188

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">  mySeq   3616084 3616100 3       5.33333 TGG     TGA,TGA,TGG,TGG,TGG,T</span>

</pre>

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189

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"></span>

</pre>

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190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">The first 3 columns show the start and end coordinates of the</span>

</pre>

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191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">repetitive region, in `BED</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">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"><https://genome.ucsc.edu/FAQ/FAQformat.html#format1>`_ format.  Column</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">4 shows the length of the repeating unit (which might vary due to</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">

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">insertions and deletions, so this column shows the most common</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="plaintext">length).  Column 5 shows the number of repeat units.  Column 6 shows</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">

196

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">the repeating unit (which again might vary, so this is just a</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">representative).  Column 7 shows the whole repeat: lowercase letters</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">are insertions relative to the previous repeat unit, and dashes are</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="plaintext">deletions relative to the previous repeat unit.</span>

</pre>

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200

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"></span>

</pre>

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175

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="plaintext">Miscellaneous</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); 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="plaintext">-------------</span>

</pre>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="plaintext"></span>

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<li id="8475d4d49b41be53a257bfb9040629db473a883f">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#8475d4d49b41be53a257bfb9040629db473a883f"><strong>src/mcf_tantan_options.cc</strong></a>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,7 +36,7 @@ static int myGetopt(int argc, char **argv, const char *optstring,</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span><span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">>></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">TantanOptions</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="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC37" 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="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num old_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 class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

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

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

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<pre style="margin: 0;">-<span id="LC39" 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="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;"><span class="idiff left right">3</span></span><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 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="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;"><span class="idiff left right">4</span></span><span class="p">)</span></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="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">setstate</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;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">failbit</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp">    <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TantanOptions</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="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,6 +57,7 @@ TantanOptions::TantanOptions() :</td>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp">    <span class="n" style="color: #333;">gapExistenceCost</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="LC58" class="line" lang="cpp">    <span class="n" style="color: #333;">gapExtensionCost</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="c1" style="color: #998; font-style: italic;">// means: no gaps</span></span>

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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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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp">    <span class="n" style="color: #333;">minMaskProb</span><span class="p">(</span><span class="mf" style="color: #099;">0.5</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;">minCopyNumber</span><span class="p">(</span><span class="mf" style="color: #099;">2.0</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp">    <span class="n" style="color: #333;">outputType</span><span class="p">(</span><span class="n" style="color: #333;">maskOut</span><span class="p">),</span></span>

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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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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp">    <span class="n" style="color: #333;">indexOfFirstNonOptionArgument</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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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -69,7 +70,7 @@ Options (default settings):\n\</td>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="s" style="color: #d14;"> -p  interpret the sequences as proteins</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="s" style="color: #d14;"> -x  letter to use for masking, instead of lowercase</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"><span class="s" style="color: #d14;"> -c  preserve uppercase/lowercase in non-masked regions</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"><span class="s" style="color: #d14;"> -m  file for letter<span class="idiff left right"> pair scores (+1/-1, but -p selects BLOSUM62)</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"><span class="s" style="color: #d14;"> -m  file for letter<span class="idiff left right">-pair score matrix</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"><span class="s" style="color: #d14;"> -r  probability of a repeat starting per position ("</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">repeatProb</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"><span class="s" style="color: #d14;"> -e  probability of a repeat ending per position ("</span></span>

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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -77,15 +78,17 @@ Options (default settings):\n\</td>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"><span class="s" style="color: #d14;"> -w  maximum tandem repeat period to consider (100, but -p selects 50)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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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="s" style="color: #d14;"> -d  probability decay per period ("</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">repeatOffsetProbDecay</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"><span class="s" style="color: #d14;"> -i  match score (<span class="idiff left right">1, but -p selects BLOSUM62</span>)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"><span class="s" style="color: #d14;"> -j  mismatch cost (<span class="idiff left right">1, but -p selects BLOSUM62</span>)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"><span class="s" style="color: #d14;"> -i  match score (<span class="idiff left right">BLOSUM62 if -p, else 2 if -f4, else 1</span>)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"><span class="s" style="color: #d14;"> -j  mismatch cost (<span class="idiff left right">BLOSUM62 if -p, else 7 if -f4, else 1</span>)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="s" style="color: #d14;"> -a  gap existence cost ("</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">gapExistenceCost</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"><span class="s" style="color: #d14;"> -b  gap extension cost (<span class="idiff left right">infinite: no gaps</span>)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"><span class="s" style="color: #d14;"> -b  gap extension cost (<span class="idiff left right">7 if -f4, else infinity</span>)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="s" style="color: #d14;"> -s  minimum repeat probability for masking ("</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">minMaskProb</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"><span class="s" style="color: #d14;"> -n  minimum copy number, affects -f4 only ("</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">minCopyNumber</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"><span class="s" style="color: #d14;"> -f  output type: 0=masked sequence, 1=repeat probabilities,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"><span class="s" style="color: #d14;">                  2=repeat counts, 3=BED ("</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="s" style="color: #d14;">                  2=repeat counts, 3=BED<span class="idiff left right">, 4=tandem repeats</span> ("</span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">outputType</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC93" class="line" lang="cpp"><span class="s" style="color: #d14;"> -h, --help  show help message, then exit</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC94" class="line" lang="cpp"><span class="s" style="color: #d14;"> --version   show version information, then exit</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); 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="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,12 +96,13 @@ Options (default settings):\n\</td>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"><span class="s" style="color: #d14;">Report bugs to: tantan@cbrc.jp</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"><span class="s" style="color: #d14;">Home page: http://www.cbrc.jp/tantan/</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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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<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="c1" style="color: #998; font-style: italic;">// -k for transition cost?</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"></span>

</pre>

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97

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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

101

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"tantan "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

102

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "version.hh"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num 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">

103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp">      <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

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<td class="diff-line-num new_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">

104

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" 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">

101

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<td class="diff-line-num new_line old" data-linenumber="105" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC101" 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;">optstring</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"px:cm:r:e:w:d:i:j:a:b:s:f:h"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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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<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="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;">optstring</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"px:cm:r:e:w:d:i:j:a:b:s:<span class="idiff left right">n:</span>f:h"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

102

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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

106

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"></span>

</pre>

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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="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">

107

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

<pre style="margin: 0;"> <span id="LC107" 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="p">;</span></span>

</pre>

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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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<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">

108

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

<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">while</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;">myGetopt</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">optstring</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -158,6 +162,9 @@ Home page: http://www.cbrc.jp/tantan/\n\</td>

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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">

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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="n" style="color: #333;">unstringify</span><span class="p">(</span><span class="n" style="color: #333;">minMaskProb</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span><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">

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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="c1" style="color: #998; font-style: italic;">// don't bother checking for stupid values?</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="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="cpp">        <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="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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<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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_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">

</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">

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

<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp">  <span class="n" style="color: #333;">unstringify</span><span class="p">(</span><span class="n" style="color: #333;">minCopyNumber</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_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">

</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">

167

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

<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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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">

161

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

<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num 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">

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

<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp">        <span class="n" style="color: #333;">unstringify</span><span class="p">(</span><span class="n" style="color: #333;">outputType</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span><span class="p">);</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="LC170" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -168,11 +175,18 @@ Home page: http://www.cbrc.jp/tantan/\n\</td>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp">    <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="LC176" class="line" lang="cpp">  <span class="p">}</span></span>

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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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<td class="diff-line-num new_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="LC177" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_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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<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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gapExtensionCost</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="n" style="color: #333;">repOut</span><span class="p">)</span> <span class="n" style="color: #333;">gapExtensionCost</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 new old_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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<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">

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); 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="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gapExtensionCost</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;">gapExistenceCost</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gapExtensionCost</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_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="cpp">    <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"gap existence + extension cost is too low"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maxCycleLength</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;">maxCycleLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">isProtein</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">50</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">100</span><span class="p">);</span></span>

</pre>

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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="cpp"></span>

</pre>

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<td class="diff-line-num new old_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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<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;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isProtein</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">matchScore</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mismatchCost</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="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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<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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">matchScore</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;">matchScore</span>   <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">repOut</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 new old_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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<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">

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mismatchCost</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;">mismatchCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">repOut</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 old_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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<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="p">}</span></span>

</pre>

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<td class="diff-line-num new old_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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<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>

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<td class="diff-line-num old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC190" class="line" lang="cpp">  <span class="n" style="color: #333;">indexOfFirstNonOptionArgument</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optind</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"></span>

</pre>

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<li id="f47bc0f64f7f84a6b297f01be0f207e098844969">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#f47bc0f64f7f84a6b297f01be0f207e098844969"><strong>src/mcf_tantan_options.hh</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,7 +23,8 @@ struct TantanOptions {</td>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapExistenceCost</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapExtensionCost</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minMaskProb</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">OutputType</span> <span class="p">{</span> <span class="n" style="color: #333;">maskOut</span><span class="p">,</span> <span class="n" style="color: #333;">probOut</span><span class="p">,</span> <span class="n" style="color: #333;">countOut</span><span class="p">,</span> <span class="n" style="color: #333;">bedOut</span> <span class="p">}</span> <span class="n" style="color: #333;">outputType</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minCopyNumber</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">OutputType</span> <span class="p">{</span> <span class="n" style="color: #333;">maskOut</span><span class="p">,</span> <span class="n" style="color: #333;">probOut</span><span class="p">,</span> <span class="n" style="color: #333;">countOut</span><span class="p">,</span> <span class="n" style="color: #333;">bedOut</span><span class="p">,</span> <span class="n" style="color: #333;">repOut</span> <span class="p">}</span> <span class="n" style="color: #333;">outputType</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">indexOfFirstNonOptionArgument</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="p">};</span></span>

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</li>

<li id="7cec908f40ab30058cc7553cf0463829623d0080">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#7cec908f40ab30058cc7553cf0463829623d0080"><strong>src/tantan.cc</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,10 +20,10 @@ void multiplyAll(std::vector<double> &v, double factor) {</td>

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

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

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">firstRepeatOffsetProb</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probMult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">probMult</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;">probMult</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">probMult</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;">probMult</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">probMult</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="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;">pow</span><span class="p">(</span><span class="n" style="color: #333;">probMult</span><span class="p">,</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">));</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp">  <span class="k" style="font-weight: 600;"><span class="idiff left right">else</span></span></span>

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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">

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<td class="diff-line-num new_line old" 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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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp">  <span class="idiff left right">  </span><span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">;</span></span>

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<td class="diff-line-num new old_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="LC25" class="line" lang="cpp">  <span class="p"><span class="idiff left right">}</span></span></span>

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<td class="diff-line-num new old_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="LC26" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">;</span></span>

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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="p">}</span></span>

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

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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 class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">checkForwardAndBackwardTotals</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">fTot</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">bTot</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="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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,6 +64,7 @@ struct Tantan {</td>

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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="LC64" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b2fLast</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// background state to last foreground state</span></span>

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<td class="diff-line-num old_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">

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

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<td class="diff-line-num old_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">

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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="n" style="color: #333;">backgroundProb</span><span class="p">;</span></span>

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<td class="diff-line-num new old_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;">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;">b2fProbs</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// background state to each foreground state</span></span>

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<td class="diff-line-num old_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">

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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;">foregroundProbs</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;">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;">insertionProbs</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_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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<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">

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,9 +111,16 @@ struct Tantan {</td>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp">    <span class="n" style="color: #333;">b2fFirst</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">repeatProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">firstRepeatOffsetProb</span><span class="p">(</span><span class="n" style="color: #333;">b2fDecay</span><span class="p">,</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp">    <span class="n" style="color: #333;">b2fLast</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">repeatProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">firstRepeatOffsetProb</span><span class="p">(</span><span class="n" style="color: #333;">b2fGrowth</span><span class="p">,</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">);</span></span>

</pre>

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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="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="LC114" class="line" lang="cpp">    <span class="n" style="color: #333;">b2fProbs</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">maxRepeatOffset</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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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp">    <span class="n" style="color: #333;">foregroundProbs</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp">    <span class="n" style="color: #333;">insertionProbs</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">maxRepeatOffset</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="LC117" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b2fFirst</span><span class="p">;</span></span>

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<td class="diff-line-num new old_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="LC119" 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;">maxRepeatOffset</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="LC120" class="line" lang="cpp">      <span class="n" style="color: #333;">b2fProbs</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;">p</span><span class="p">;</span></span>

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<td class="diff-line-num new old_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="LC121" class="line" lang="cpp">      <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">b2fDecay</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp">    <span class="p">}</span></span>

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

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp">    <span class="n" style="color: #333;">scaleFactors</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">((</span><span class="n" style="color: #333;">seqEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seqBeg</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scaleStepSize</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); 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="219" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -211,20 +219,17 @@ struct Tantan {</td>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">calcForwardTransitionProbs</span><span class="p">()</span> <span class="p">{</span></span>

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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;">endGapProb</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="n" style="color: #333;">calcForwardTransitionProbsWithGaps</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="214" 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="LC214" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left">fromBackground</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">backgroundProb</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">b2fLast</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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="LC222" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left">b</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">backgroundProb</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_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">

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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;">fromForeground</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="216" 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="224" 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="LC216" 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;">foregroundPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">END</span><span class="p">(</span><span class="n" style="color: #333;">foregroundProbs</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num 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">

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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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundBeg</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;">foregroundProbs</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC225" class="line" lang="cpp"></span>

</pre>

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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="226" 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;">while</span> <span class="p">(</span><span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">foregroundBeg</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="220" 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="226" 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="LC220" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">foregroundPtr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="221" 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="226" 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="LC221" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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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<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="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;">maxRepeatOffset</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="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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<td class="diff-line-num new new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC227" 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;">foregroundBeg</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_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); 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="228" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC228" class="line" lang="cpp">      <span class="n" style="color: #333;">fromForeground</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="223" 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="229" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fromBackground</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f2f0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="224" 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="229" 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="LC224" class="line" lang="cpp">      <span class="n" style="color: #333;">fromBackground</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">b2fGrowth</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">foregroundBeg</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;">b2fProbs</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;">f</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f2f0</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>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp">    <span class="n" style="color: #333;">backgroundProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b<span class="idiff left right">ackgroundProb</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b2b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fromForeground</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f2b</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp">    <span class="n" style="color: #333;">backgroundProb</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;">b2b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fromForeground</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f2b</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">calcBackwardTransitionProbs</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">@@ -232,18 +237,15 @@ struct Tantan {</td>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">toBackground</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f2b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">backgroundProb</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">toForeground</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="LC235" 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;">foregroundPtr</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;">foregroundProbs</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC236" 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;">foregroundEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">END</span><span class="p">(</span><span class="n" style="color: #333;">foregroundProbs</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC240" 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;">foregroundBeg</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;">foregroundProbs</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC241" 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;">while</span> <span class="p">(</span><span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">foregroundEnd</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="cpp">      <span class="n" style="color: #333;">toForeground</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">b2fGrowth</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC240" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp">      <span class="n" style="color: #333;">toForeground</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toBackground</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f2f0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">foregroundPtr</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">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;">maxRepeatOffset</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="LC243" 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;">foregroundBeg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

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<td class="diff-line-num new old_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;">toForeground</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">b2fProbs</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;">f</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp">      <span class="n" style="color: #333;">foregroundBeg</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;">toBackground</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f2f0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp">    <span class="n" style="color: #333;">backgroundProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b2b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">backgroundProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left">b2fLast</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">toForeground</span><span class="p">;</span></span>

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<td class="diff-line-num new old_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="LC248" class="line" lang="cpp">    <span class="n" style="color: #333;">backgroundProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b2b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">backgroundProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toForeground</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">addEndCounts</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">forwardProb</span><span class="p">,</span></span>

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<br>

</li>

<li id="08d18a28f9f43426ba0305df09ef35871d021752">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#08d18a28f9f43426ba0305df09ef35871d021752"><strong>src/tantan_app.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">@@ -9,17 +9,18 @@</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 "mcf_tantan_options.hh"</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 "mcf_util.hh"</span></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">

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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">

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

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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 "LambdaCalculator.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">

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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 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 <algorithm>  // copy, fill_n</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="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 <cassert></span></span>

</pre>

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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 <cmath></span></span>

</pre>

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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="cp" style="color: #999; font-weight: 600;">#include <cstring>  // strchr</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="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 <cstdlib>  // EXIT_SUCCESS, EXIT_FAILURE</span></span>

</pre>

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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 <exception>  // exception</span></span>

</pre>

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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 <fstream></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="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 <iostream></span></span>

</pre>

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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 <new>  // bad_alloc</span></span>

</pre>

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<td class="diff-line-num new old_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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<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="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>

</pre>

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<td class="diff-line-num old_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="LC24" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define BEG(v) ((v).empty() ? 0 : &(v).front())</span></span>

</pre>

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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;">#define END(v) ((v).empty() ? 0 : &(v).back() + 1)</span></span>

</pre>

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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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,7 +34,7 @@ bool isDubiousDna(const uchar *beg, const uchar *end) {</td>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">badLetters</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="LC35" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// just check the first 100 letters</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="p">{</span></span>

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

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<pre style="margin: 0;">-<span id="LC36" 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;">st<span class="idiff left">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">st</span>rchr</span><span class="p">(</span><span class="s" style="color: #d14;">"AaCcGgTtNnUu"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">beg</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC37" 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;">strchr</span><span class="p">(</span><span class="s" style="color: #d14;">"AaCcGgTtNnUu"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">beg</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">badLetters</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">badLetters</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<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="p">}</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,6 +46,7 @@ bool isDubiousDna(const uchar *beg, const uchar *end) {</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="n" style="color: #333;">TantanOptions</span> <span class="n" style="color: #333;">options</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;">Alphabet</span> <span class="n" style="color: #333;">alphabet</span><span class="p">;</span></span>

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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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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="n" style="color: #333;">tantan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RepeatFinder</span> <span class="n" style="color: #333;">repeatFinder</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">scoreMatrixSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">64</span> <span class="p">};</span></span>

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<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;">int</span> <span class="n" style="color: #333;">fastMatrix</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixSize</span><span class="p">][</span><span class="n" style="color: #333;">scoreMatrixSize</span><span class="p">];</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -76,16 +78,14 @@ void initScoresAndProbabilities() {</td>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">scoreMatrixFileName</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp">    <span class="n" style="color: #333;">unfilify</span><span class="p">(</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">scoreMatrixFileName</span><span class="p">);</span></span>

</pre>

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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">

80

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<pre style="margin: 0;"> <span id="LC80" 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;">options</span><span class="p">.</span><span class="n" style="color: #333;">isProtein</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="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">

79

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<td class="diff-line-num new_line old" data-linenumber="81" 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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</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="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">

80

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<td class="diff-line-num new_line old" data-linenumber="81" 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;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">initMatchMismatch</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span><span class="p">,</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="81" 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">

81

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<td class="diff-line-num new_line old" data-linenumber="81" 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC81" 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;">options</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</span><span class="p">,</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="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">

</td>

<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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</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="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">

</td>

<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">

82

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

<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp">      <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">initMatchMismatch</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span><span class="p">,</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</span><span class="p">,</span></span>

</pre>

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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">

82

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<td class="diff-line-num 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">

83

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

<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp">                               <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">protein</span><span class="p">);</span></span>

</pre>

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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">

83

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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">

84

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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;">else</span> <span class="p">{</span></span>

</pre>

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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">

84

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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">

85

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp">      <span class="n" style="color: #333;">unstringify</span><span class="p">(</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">ScoreMatrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">blosum62</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">

85

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

86

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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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="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">  <span class="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 old old_line" 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">

87

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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">

</td>

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

<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp">    <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">initMatchMismatch</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span></span>

</pre>

</td>

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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">

88

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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="LC88" class="line" lang="cpp">                             <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</span><span class="p">,</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="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">

</td>

<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;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">initMatchMismatch</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">matchScore</span><span class="p">,</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">mismatchCost</span><span class="p">,</span></span>

</pre>

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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">

89

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

<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">                             <span class="s" style="color: #d14;">"ACGTU"</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// allow for RNA</span></span>

</pre>

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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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<td class="diff-line-num new_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="LC90" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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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">

91

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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">

91

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

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

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -101,7 +101,9 @@ void initScoresAndProbabilities() {</td>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC102" 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;">scoreMatrixSize</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="LC103" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">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;">scoreMatrixSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="104" 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="LC104" class="line" lang="cpp">      <span class="n" style="color: #333;">probMatrix</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">matrixLambda</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fastMatrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="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="LC104" 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;">matrixLambda</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fastMatrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

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<td class="diff-line-num new old_line" data-linenumber="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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<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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">repOut</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp">      <span class="n" style="color: #333;">probMatrix</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;">x</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,6 +118,10 @@ void initScoresAndProbabilities() {</td>

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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">

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// XXX check if firstGapProb is too high</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"></span>

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<td class="diff-line-num new old_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="LC121" class="line" lang="cpp">  <span class="n" style="color: #333;">repeatFinder</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">maxCycleLength</span><span class="p">,</span> <span class="n" style="color: #333;">probMatrixPointers</span><span class="p">,</span></span>

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<td class="diff-line-num new old_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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<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">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp">              <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">repeatProb</span><span class="p">,</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">repeatEndProb</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp">              <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">repeatOffsetProbDecay</span><span class="p">,</span> <span class="n" style="color: #333;">firstGapProb</span><span class="p">,</span> <span class="n" style="color: #333;">otherGapProb</span><span class="p">);</span></span>

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

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">//std::cerr << "lambda: " << matrixLambda << "\n";</span></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">//std::cerr << "firstGapProb: " << firstGapProb << "\n";</span></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">//std::cerr << "otherGapProb: " << otherGapProb << "\n";</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -157,6 +163,138 @@ void writeBed(const float *probBeg, const float *probEnd,</td>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maskBeg</span><span class="p">)</span> <span class="n" style="color: #333;">writeBedLine</span><span class="p">(</span><span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">probBeg</span><span class="p">,</span> <span class="n" style="color: #333;">maskBeg</span><span class="p">,</span> <span class="n" style="color: #333;">probEnd</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">storeSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp">  <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp">    <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</span><span class="p">.</span><span class="n" style="color: #333;">numbersToLetters</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp">  <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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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">RepeatUnit</span> <span class="p">{</span></span>

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

</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

178

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">less</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">RepeatUnit</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;">RepeatUnit</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">len</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;">len</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;">len</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;">len</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">c</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="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;">beg</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;">beg</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

184

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

185

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">mainLen</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RepeatUnit</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">repUnits</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

186

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestLen</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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 class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bestCount</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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;">size_t</span> <span class="n" style="color: #333;">count</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC189" 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;">repUnits</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 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">

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<pre style="margin: 0;">+<span id="LC190" 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;">repUnits</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">repUnits</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 class="n" style="color: #333;">len</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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 class="n" style="color: #333;">count</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

193

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

<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;">count</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestCount</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

195

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp">      <span class="n" style="color: #333;">bestCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

196

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp">      <span class="n" style="color: #333;">bestLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">repUnits</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

197

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

198

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

199

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestLen</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

200

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

201

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="LC202" 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="nf" style="color: #900; font-weight: 600;">mainBeg</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RepeatUnit</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">repUnits</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="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;">bestBeg</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bestCount</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">count</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="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;">repUnits</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">repUnits</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">len</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 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="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

208

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">repUnits</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 class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">repUnits</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

209

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp">      <span class="n" style="color: #333;">count</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="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="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

210

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

211

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">count</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

212

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bestCount</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 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="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

213

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestCount</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">repUnits</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">bestBeg</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="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="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="n" style="color: #333;">bestCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

215

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp">      <span class="n" style="color: #333;">bestBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">repUnits</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

216

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

217

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestBeg</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeRepeat</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FastaSequence</span> <span class="o" style="font-weight: 600;">&</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="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;">repBeg</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;">repEnd</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

223

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">repText</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;">RepeatUnit</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">repUnits</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">commaPos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">finalOffset</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">repText</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">repText</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="sc" style="color: #d14;">','</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">copyNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">repeatCount</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">repEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">commaPos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">finalOffset</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">copyNumber</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">minCopyNumber</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="LC228" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp">  <span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">repUnits</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">repUnits</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">less</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mainLen</span><span class="p">(</span><span class="n" style="color: #333;">repUnits</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mainBeg</span><span class="p">(</span><span class="n" style="color: #333;">repUnits</span><span class="p">,</span> <span class="n" style="color: #333;">bestLen</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"></span>

</pre>

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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;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BEG</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC234" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">firstWord</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">title</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span></span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp">      <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">repBeg</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">beg</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">repEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">beg</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp">      <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bestLen</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">copyNumber</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC237" 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;">bestLen</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="LC238" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</span><span class="p">.</span><span class="n" style="color: #333;">numbersToLetters</span><span class="p">[</span><span class="n" style="color: #333;">bestBeg</span><span class="p">[</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="LC239" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC241" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC242" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">repText</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 new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">findRepeatsInOneSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FastaSequence</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BEG</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC247" 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;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">END</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">sequence</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>

</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 class="n" style="color: #333;">repeatFinder</span><span class="p">.</span><span class="n" style="color: #333;">calcBestPathScore</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"></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="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;">RepeatUnit</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">repUnits</span><span class="p">;</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">repText</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="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;">repBeg</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="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;">commaPos</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</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">

256

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

257

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqPtr</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;">seqPtr</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;">seqPtr</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

258

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newState</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">repeatFinder</span><span class="p">.</span><span class="n" style="color: #333;">nextState</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

259

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">newState</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

261

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="n" style="color: #333;">writeRepeat</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">repBeg</span><span class="p">,</span> <span class="n" style="color: #333;">seqPtr</span><span class="p">,</span> <span class="n" style="color: #333;">repText</span><span class="p">,</span> <span class="n" style="color: #333;">repUnits</span><span class="p">,</span> <span class="n" style="color: #333;">commaPos</span><span class="p">,</span> <span class="n" style="color: #333;">state</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

263

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="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;">newState</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">maxCycleLength</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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="n" style="color: #333;">repUnits</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp">  <span class="n" style="color: #333;">repBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqPtr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">newState</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp">  <span class="n" style="color: #333;">storeSequence</span><span class="p">(</span><span class="n" style="color: #333;">repBeg</span><span class="p">,</span> <span class="n" style="color: #333;">seqPtr</span><span class="p">,</span> <span class="n" style="color: #333;">repText</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp">  <span class="n" style="color: #333;">commaPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">repBeg</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC270" 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;">state</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">maxCycleLength</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">state</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;">newState</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="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqPtr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">commaPos</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="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

273

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp">      <span class="n" style="color: #333;">repText</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

274

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp">      <span class="n" style="color: #333;">commaPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqPtr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

275

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

276

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp">    <span class="n" style="color: #333;">repText</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="sc" style="color: #d14;">'-'</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

277

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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 class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

279

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp">      <span class="n" style="color: #333;">RepeatUnit</span> <span class="n" style="color: #333;">unit</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">seqPtr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">newState</span><span class="p">,</span> <span class="n" style="color: #333;">newState</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

280

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">      <span class="n" style="color: #333;">repUnits</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">unit</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqPtr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">commaPos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">newState</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="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp">  <span class="n" style="color: #333;">repText</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp">  <span class="n" style="color: #333;">commaPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqPtr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp">      <span class="n" style="color: #333;">repText</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</span><span class="p">.</span><span class="n" style="color: #333;">numbersToLetters</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqPtr</span><span class="p">]));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC286" 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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp">      <span class="n" style="color: #333;">repText</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tolower</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</span><span class="p">.</span><span class="n" style="color: #333;">numbersToLetters</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqPtr</span><span class="p">]));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp">    <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newState</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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;">state</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="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="LC294" class="line" lang="cpp">    <span class="n" style="color: #333;">writeRepeat</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">repBeg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">repText</span><span class="p">,</span> <span class="n" style="color: #333;">repUnits</span><span class="p">,</span> <span class="n" style="color: #333;">commaPos</span><span class="p">,</span> <span class="n" style="color: #333;">state</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processOneSequence</span><span class="p">(</span><span class="n" style="color: #333;">FastaSequence</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">output</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp">  <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">beg</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;">f</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp">  <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">END</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -181,6 +319,8 @@ void processOneSequence(FastaSequence &f, std::ostream &output) {</td>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp">                             <span class="n" style="color: #333;">BEG</span><span class="p">(</span><span class="n" style="color: #333;">transitionCounts</span><span class="p">));</span></span>

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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;">sequenceLength</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;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

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<td class="diff-line-num old_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="LC321" class="line" lang="cpp">    <span class="n" style="color: #333;">transitionTotal</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sequenceLength</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="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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<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="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;">options</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">repOut</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="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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<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="n" style="color: #333;">findRepeatsInOneSequence</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="LC324" 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="LC325" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">probabilities</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">beg</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">probBeg</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;">probabilities</span><span class="p">);</span></span>

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<br>

</li>

<li id="cb87d4448c885fb7b36ecf5f9502a1c7535cd121">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#cb87d4448c885fb7b36ecf5f9502a1c7535cd121"><strong>src/tantan_repeat_finder.cc</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2018 Martin C. Frith</span></span>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tantan_repeat_finder.hh"</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"></span>

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

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

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>

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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>

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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;">namespace</span> <span class="n" style="color: #333;">tantan</span> <span class="p">{</span></span>

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

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">max3</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="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;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">),</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>

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

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

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"></span>

</pre>

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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="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">myLog</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</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="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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">HUGE_VAL</span><span class="p">;</span></span>

</pre>

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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="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">

20

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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 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;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">firstRepeatOffsetProb</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probMult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxRepeatOffset</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">probMult</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;">probMult</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="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="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">probMult</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">probMult</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">));</span></span>

</pre>

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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="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">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">maxRepeatOffset</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="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="p">}</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>

</pre>

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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="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numOfDpScoresPerLetter</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">endGapScore</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="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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">endGapScore</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">HUGE_VAL</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="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="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">maxRepeatOffset</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">INT_MAX</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>

</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;">return</span> <span class="n" style="color: #333;">maxRepeatOffset</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="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="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp">  <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">maxRepeatOffset</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">INT_MAX</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">maxRepeatOffset</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="LC35" class="line" lang="cpp"><span class="p">}</span></span>

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

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">minStoredPositions</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// We will do a dynamic programming algorithm along the sequence.</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// To save memory, we will keep only some DP values, and recalculate</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// the others later.  We keep the values in an array x of size s.</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// We will store DP initial values in x[0].  We will put</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// the DP values after the first s-1 sequence positions in x[1],</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// the DP values after the next s-2 positions in x[2],</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// the DP values after the next s-3 positions in x[3], etc.</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// This function returns the minimum possible value of s.</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;">unsigned</span> <span class="n" style="color: #333;">t</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="LC47" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">beg</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">    <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">    <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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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">  <span class="p">}</span></span>

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

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">t</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="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="p">}</span></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="cpp"></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">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">RepeatFinder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxRepeatOffset</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">

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp">                   <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_double_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionMatrix</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="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">

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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;">repeatProb</span><span class="p">,</span></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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatEndProb</span><span class="p">,</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">

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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;">repeatOffsetProbDecay</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">firstGapProb</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="n" style="color: #333;">otherGapProb</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="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;">assert</span><span class="p">(</span><span class="n" style="color: #333;">maxRepeatOffset</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="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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxRepeatOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxRepeatOffset</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;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">substitutionMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionMatrix</span><span class="p">;</span></span>

</pre>

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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>

</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="n" style="color: #333;">b2b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myLog</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">repeatProb</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="n" style="color: #333;">f2b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myLog</span><span class="p">(</span><span class="n" style="color: #333;">repeatEndProb</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="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;">g2g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myLog</span><span class="p">(</span><span class="n" style="color: #333;">otherGapProb</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;">oneGapScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myLog</span><span class="p">(</span><span class="n" style="color: #333;">firstGapProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">otherGapProb</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;">endGapScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myLog</span><span class="p">(</span><span class="n" style="color: #333;">firstGapProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">maxRepeatOffset</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="LC70" class="line" lang="cpp">  <span class="n" style="color: #333;">f2f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myLog</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">repeatEndProb</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;">f2f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myLog</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">repeatEndProb</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">firstGapProb</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">  <span class="n" style="color: #333;">f2f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myLog</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">repeatEndProb</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">firstGapProb</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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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" 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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">repeatOffsetProbDecay</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;">b2fGrowth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myLog</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">  <span class="n" style="color: #333;">b2fLast</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myLog</span><span class="p">(</span><span class="n" style="color: #333;">repeatProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">firstRepeatOffsetProb</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp">  <span class="n" style="color: #333;">dpScoresPerLetter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfDpScoresPerLetter</span><span class="p">(</span><span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">,</span> <span class="n" style="color: #333;">endGapScore</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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">RepeatFinder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initializeBackwardScores</span><span class="p">()</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp">  <span class="n" style="color: #333;">scoresPtr</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;">b2b</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fill_n</span><span class="p">(</span><span class="n" style="color: #333;">scoresPtr</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;">maxRepeatOffset</span><span class="p">,</span> <span class="n" style="color: #333;">f2b</span><span class="p">);</span></span>

</pre>

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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;">endGapScore</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">HUGE_VAL</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 class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fill_n</span><span class="p">(</span><span class="n" style="color: #333;">scoresPtr</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;">maxRepeatOffset</span><span class="p">,</span> <span class="n" style="color: #333;">maxRepeatOffset</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;">HUGE_VAL</span><span class="p">);</span></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="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">

87

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"><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>

</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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">RepeatFinder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">calcBackwardTransitionScoresWithGaps</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">toBackground</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f2b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoresPtr</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 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresPtr</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="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;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</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;">toForeground</span> <span class="o" style="font-weight: 600;">=</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 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>

</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">insertionPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresPtr</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;">maxRepeatOffset</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">insertionPtr</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max3</span><span class="p">(</span><span class="n" style="color: #333;">toBackground</span><span class="p">,</span> <span class="n" style="color: #333;">f2f1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span><span class="p">,</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="LC98" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endGapScore</span> <span class="o" style="font-weight: 600;">+</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 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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">foregroundPtr</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">  <span class="n" style="color: #333;">toForeground</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">b2fGrowth</span><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">

101

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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">

102

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">maxRepeatOffset</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">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp">    <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</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;">toForeground</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;">toForeground</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 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;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">insertionPtr</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="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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max3</span><span class="p">(</span><span class="n" style="color: #333;">toBackground</span><span class="p">,</span> <span class="n" style="color: #333;">f2f2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">oneGapScore_f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oneGapScore</span> <span class="o" style="font-weight: 600;">+</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 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">insertionPtr</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;">oneGapScore_f</span><span class="p">,</span> <span class="n" style="color: #333;">g2g</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="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

109

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp">    <span class="n" style="color: #333;">d</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;">oneGapScore_f</span><span class="p">,</span> <span class="n" style="color: #333;">g2g</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span><span class="p">);</span></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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">foregroundPtr</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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">insertionPtr</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">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp">    <span class="n" style="color: #333;">toForeground</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">b2fGrowth</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">

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

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

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp">  <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</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;">toForeground</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;">toForeground</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="LC117" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max3</span><span class="p">(</span><span class="n" style="color: #333;">toBackground</span><span class="p">,</span> <span class="n" style="color: #333;">f2f1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><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 class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">insertionPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endGapScore</span> <span class="o" style="font-weight: 600;">+</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 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>

</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 class="n" style="color: #333;">scoresPtr</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;">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;">b2b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoresPtr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">b2fLast</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toForeground</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="p">}</span></span>

</pre>

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122

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">RepeatFinder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">calcBackwardTransitionScores</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">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">endGapScore</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">HUGE_VAL</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">calcBackwardTransitionScoresWithGaps</span><span class="p">();</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"></span>

</pre>

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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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">toBackground</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f2b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoresPtr</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 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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">toForeground</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">HUGE_VAL</span><span class="p">;</span></span>

</pre>

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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="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresPtr</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="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">

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<pre style="margin: 0;">+<span id="LC129" 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;">foregroundEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">;</span></span>

</pre>

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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>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">foregroundPtr</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">foregroundEnd</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="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="n" style="color: #333;">toForeground</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">b2fGrowth</span><span class="p">;</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp">    <span class="n" style="color: #333;">toForeground</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;">toForeground</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 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;">foregroundPtr</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;">toBackground</span><span class="p">,</span> <span class="n" style="color: #333;">f2f0</span> <span class="o" style="font-weight: 600;">+</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 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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">foregroundPtr</span><span class="p">;</span></span>

</pre>

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<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="p">}</span></span>

</pre>

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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>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp">  <span class="n" style="color: #333;">scoresPtr</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;">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;">b2b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoresPtr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">b2fLast</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">toForeground</span><span class="p">);</span></span>

</pre>

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<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">

140

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

141

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">RepeatFinder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">calcEmissionScores</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="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="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;">matrixRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionMatrix</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqPtr</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">oldScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dpScoresPerLetter</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">maxOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxOffsetInTheSequence</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC146" 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="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="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>

</pre>

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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="n" style="color: #333;">scoresPtr</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;">oldScores</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 new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

149

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"></span>

</pre>

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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="k" style="font-weight: 600;">for</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;">maxOffset</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="LC151" class="line" lang="cpp">    <span class="n" style="color: #333;">scoresPtr</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;">oldScores</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;">matrixRow</span><span class="p">[</span><span class="n" style="color: #333;">seqPtr</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="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="p">}</span></span>

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"></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="k" style="font-weight: 600;">for</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;">maxRepeatOffset</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="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;">scoresPtr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">HUGE_VAL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">oldScores</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;">scoresPtr</span><span class="p">,</span> <span class="n" style="color: #333;">scoresPtr</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="LC159" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"></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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">RepeatFinder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">makeCheckpoint</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="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="n" style="color: #333;">checkpoint</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">dpScoresPerLetter</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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dpScoresPerLetter</span><span class="p">,</span> <span class="n" style="color: #333;">scoresPtr</span><span class="p">,</span> <span class="n" style="color: #333;">checkpoint</span><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 class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">checkpoint</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dpScoresPerLetter</span><span class="p">;</span></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="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoresEnd</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">RepeatFinder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">redoCheckpoint</span><span class="p">()</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp">  <span class="n" style="color: #333;">seqPtr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">scoresEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">scoresPtr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">dpScoresPerLetter</span><span class="p">;</span></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;">while</span> <span class="p">(</span><span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoresEnd</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="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="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">seqPtr</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="n" style="color: #333;">calcScoresForOneSequencePosition</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="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">dpScoresPerLetter</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="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp">  <span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">dpScoresPerLetter</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">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp">  <span class="n" style="color: #333;">checkpoint</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">dpScoresPerLetter</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">RepeatFinder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">calcBestPathScore</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;">seqBeg</span><span class="p">,</span></span>

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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">

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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;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqEnd</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="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">

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqBeg</span><span class="p">;</span></span>

</pre>

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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="cpp">  <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqEnd</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">numOfStoredPositions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minStoredPositions</span><span class="p">(</span><span class="n" style="color: #333;">seqBeg</span><span class="p">,</span> <span class="n" style="color: #333;">seqEnd</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">numOfScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numOfStoredPositions</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dpScoresPerLetter</span><span class="p">;</span></span>

</pre>

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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="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">numOfStoredPositions</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="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 class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">numOfScores</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="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="n" style="color: #333;">dpScores</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">numOfScores</span><span class="p">);</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp">  <span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dpScores</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 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">

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp">  <span class="n" style="color: #333;">scoresEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numOfScores</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp">  <span class="n" style="color: #333;">checkpoint</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresPtr</span><span class="p">;</span></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="n" style="color: #333;">seqPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqEnd</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

193

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"></span>

</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="n" style="color: #333;">initializeBackwardScores</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>

</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;">while</span> <span class="p">(</span><span class="n" style="color: #333;">seqPtr</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seqBeg</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="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">seqPtr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp">    <span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">dpScoresPerLetter</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">scoresEnd</span><span class="p">)</span> <span class="n" style="color: #333;">makeCheckpoint</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="n" style="color: #333;">calcScoresForOneSequencePosition</span><span class="p">();</span></span>

</pre>

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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="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"></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="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">scoresPtr</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="LC205" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">RepeatFinder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">offsetWithMaxScore</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrixRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionMatrix</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqPtr</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxOffsetInTheSequence</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestOffset</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="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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">toForeground</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">HUGE_VAL</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxOffset</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="LC214" class="line" lang="cpp">    <span class="n" style="color: #333;">toForeground</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">b2fGrowth</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreWithEmission</span><span class="p">(</span><span class="n" style="color: #333;">matrixRow</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="LC216" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">toForeground</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp">      <span class="n" style="color: #333;">toForeground</span> <span class="o" style="font-weight: 600;">=</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="LC218" class="line" lang="cpp">      <span class="n" style="color: #333;">bestOffset</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="LC219" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestOffset</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>

</pre>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">RepeatFinder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">deletionWithMaxScore</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrixRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionMatrix</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqPtr</span><span class="p">];</span></span>

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<td class="diff-line-num new new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestOffset</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="LC228" 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;">scoreWithEmission</span><span class="p">(</span><span class="n" style="color: #333;">matrixRow</span><span class="p">,</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="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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endGapScore</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC231" 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;">2</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;">state</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="LC232" class="line" lang="cpp">    <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">g2g</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;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreWithEmission</span><span class="p">(</span><span class="n" style="color: #333;">matrixRow</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="LC234" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">oneGapScore</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp">      <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oneGapScore</span> <span class="o" style="font-weight: 600;">+</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="LC236" class="line" lang="cpp">      <span class="n" style="color: #333;">bestOffset</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="LC237" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">  <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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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestOffset</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"></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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">RepeatFinder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">nextState</span><span class="p">()</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresPtr</span><span class="p">[</span><span class="n" style="color: #333;">state</span><span class="p">];</span></span>

</pre>

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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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">checkpoint</span><span class="p">)</span> <span class="n" style="color: #333;">redoCheckpoint</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp">  <span class="n" style="color: #333;">scoresPtr</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">dpScoresPerLetter</span><span class="p">;</span></span>

</pre>

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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>

</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">b2b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoresPtr</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;">maxScore</span><span class="p">)</span> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offsetWithMaxScore</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC250" 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;">state</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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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;">f2b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoresPtr</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;">maxScore</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="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;">state</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="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="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;">endGapScore</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">HUGE_VAL</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="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;">double</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreWithEmission</span><span class="p">(</span><span class="n" style="color: #333;">substitutionMatrix</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqPtr</span><span class="p">],</span> <span class="n" style="color: #333;">state</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f2f1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxScore</span><span class="p">)</span> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">;</span></span>

</pre>

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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="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;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">maxRepeatOffset</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="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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f2f1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxScore</span><span class="p">)</span> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deletionWithMaxScore</span><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 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;">f2f2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxScore</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="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scoresPtr</span><span class="p">[</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">maxScore</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="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;">state</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">;</span></span>

</pre>

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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 class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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

263

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">    <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deletionWithMaxScore</span><span class="p">();</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="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="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="p">}</span></span>

</pre>

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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="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="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC267" 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="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">state</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="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">dpScoresPerLetter</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">g2g</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoresPtr</span><span class="p">[</span><span class="n" style="color: #333;">state</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxScore</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="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp">      <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">maxRepeatOffset</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="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp">    <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="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

272

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

<pre style="margin: 0;">+<span id="LC272" 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="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seqPtr</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">state</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="6ffe7697fa2b7a52ab8b6f315ee31523c85ae5c1">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#6ffe7697fa2b7a52ab8b6f315ee31523c85ae5c1"><strong>src/tantan_repeat_finder.hh</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2018 Martin C. Frith</span></span>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This class finds tandem repeats in a sequence, using a Viterbi</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// algorithm.</span></span>

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

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// The input parameters are as in tantan.hh, with one difference: the</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// substitutionMatrix should be a *log* likelihood ratio matrix:</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// substitutionMatrix[x][y] = lambda * scoringMatrix[x][y].</span></span>

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

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Usage: first call init.  Then call calcBestPathScore, which runs</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// the Viterbi algorithm backwards from the end to the start of the</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// sequence.  Finally, call nextState once per sequence letter, to get</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// the "state" of each letter from start to end.</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="c1" style="color: #998; font-style: italic;">// state = 0: non-repeat.</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// 0 < state <= maxRepeatOffset: tandem repeat with period = state.</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// maxRepeatOffset < state < 2*maxRepeatOffset: insertion in repeat.</span></span>

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

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef TANTAN_REPEAT_FINDER_HH</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define TANTAN_REPEAT_FINDER_HH</span></span>

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

</pre>

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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 <vector></span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">tantan</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">uchar</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC27" 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_double_ptr</span><span class="p">;</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="k" style="font-weight: 600;">public</span><span class="o" style="font-weight: 600;">:</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp">       <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_double_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionMatrix</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp">       <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatProb</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp">       <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatEndProb</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp">       <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatOffsetProbDecay</span><span class="p">,</span></span>

</pre>

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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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">firstGapProb</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">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp">       <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">otherGapProb</span><span class="p">);</span></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">

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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 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;">double</span> <span class="n" style="color: #333;">calcBestPathScore</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;">seqBeg</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;">seqEnd</span><span class="p">);</span></span>

</pre>

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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="cpp"></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;">nextState</span><span class="p">();</span></span>

</pre>

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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>

</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="cpp"><span class="k" style="font-weight: 600;">private</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="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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_double_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionMatrix</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"></span>

</pre>

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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;">b2b</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">f2b</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">g2g</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">oneGapScore</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">endGapScore</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">f2f0</span><span class="p">;</span></span>

</pre>

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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;">f2f1</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;">double</span> <span class="n" style="color: #333;">f2f2</span><span class="p">;</span></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">

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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;">b2fGrowth</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b2fLast</span><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">

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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxRepeatOffset</span><span class="p">;</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">

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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;">dpScoresPerLetter</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>

</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;">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;">dpScores</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 class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scoresPtr</span><span class="p">;</span></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="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scoresEnd</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">checkpoint</span><span class="p">;</span></span>

</pre>

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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>

</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="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;">seqBeg</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="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;">seqEnd</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="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;">seqPtr</span><span class="p">;</span></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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">state</span><span class="p">;</span></span>

</pre>

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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 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;">void</span> <span class="n" style="color: #333;">initializeBackwardScores</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 class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">calcBackwardTransitionScoresWithGaps</span><span class="p">();</span></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;">void</span> <span class="n" style="color: #333;">calcBackwardTransitionScores</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">

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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;">calcEmissionScores</span><span class="p">();</span></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">

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">makeCheckpoint</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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">redoCheckpoint</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 class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offsetWithMaxScore</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="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;">int</span> <span class="n" style="color: #333;">deletionWithMaxScore</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="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>

</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 class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isNearSeqBeg</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="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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seqPtr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seqBeg</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxRepeatOffset</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="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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<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;">maxOffsetInTheSequence</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="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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">isNearSeqBeg</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">seqPtr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seqBeg</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">maxRepeatOffset</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 class="p">}</span></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>

</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreWithEmission</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matrixRow</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset</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 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="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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">scoresPtr</span><span class="p">[</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;">matrixRow</span><span class="p">[</span><span class="n" style="color: #333;">seqPtr</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">offset</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="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>

</pre>

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91

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">calcScoresForOneSequencePosition</span><span class="p">()</span> <span class="p">{</span></span>

</pre>

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92

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp">    <span class="n" style="color: #333;">calcEmissionScores</span><span class="p">();</span></span>

</pre>

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93

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp">    <span class="n" style="color: #333;">calcBackwardTransitionScores</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">

94

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

<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp">  <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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"><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>

</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">

97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"></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="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>

</td>

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<br>

</li>

<li id="69737f84c540417aafef4e696f66adcc9f92fa66">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#69737f84c540417aafef4e696f66adcc9f92fa66"><strong>src/version.hh</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"<span class="idiff left right">18</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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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"<span class="idiff left right">22</span>"</span></span></pre>

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<br>

</li>

<li id="b9eb9f70cb43642f308d5a3f3f451d95a5984a96">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#b9eb9f70cb43642f308d5a3f3f451d95a5984a96"><strong>test/hard.fa</strong></a>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>hard</span>

</pre>

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2

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

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">atcatatcatatcatatcatatcat</span></pre>

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</li>

<li id="dda902050115a2b1759155bb4f11361a446208e0">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#dda902050115a2b1759155bb4f11361a446208e0"><strong>test/tantan_test.out</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1489" style="width: 35px; color: rgba(0,0,0,0.3); 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="1489" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1489,3 +1489,27 @@ GTGGTCCACATATACAATGGAATATTACTCAGCTATCAGAAAGAA</td>

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<pre style="margin: 0;"> <span id="LC1489" class="line" lang="plaintext">IIIIIIIIIIIIIIIIDIII2BDHIIHCF=/-6A1921*/1-*-7</span>

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1490

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<pre style="margin: 0;"> <span id="LC1490" class="line" lang="plaintext"></span>

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1491

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<pre style="margin: 0;"> <span id="LC1491" class="line" lang="plaintext">205</span>

</pre>

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1492

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<pre style="margin: 0;">+<span id="LC1492" class="line" lang="plaintext"></span>

</pre>

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1493

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<pre style="margin: 0;">+<span id="LC1493" class="line" lang="plaintext">SRR019778.4        6       27      7       3       TTGTGTG TGTGTAT,TGTGTGT,TGTGTGT</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="1492" style="width: 35px; color: rgba(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="1494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1494

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<pre style="margin: 0;">+<span id="LC1494" class="line" lang="plaintext">SRR019778.4        28      45      2       12      GT      GT,GT,GT,GT,GT,-T,T,T,T,T,T,T</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="1492" style="width: 35px; color: rgba(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="1495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1495

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<pre style="margin: 0;">+<span id="LC1495" class="line" lang="plaintext">SRR019778.42       3       44      4       11      TGTG    TGTG,TGTG,TGTG,TGTG,TGTG,TGTG,TGTT,TGTT,T-TT,TTT,TTT</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="1492" style="width: 35px; color: rgba(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="1496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1496

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<pre style="margin: 0;">+<span id="LC1496" class="line" lang="plaintext">SRR019778.45       9       37      8       3.33333 GTGTGTGG        GTGTGTGG,GTGTGTGT,GTtGTGTGT,GTT</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="1492" style="width: 35px; color: rgba(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="1497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1497

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<pre style="margin: 0;">+<span id="LC1497" class="line" lang="plaintext">SRR019778.50       0       21      7       3       GTGTGTT GTGTGTT,GTGTGTT,GAGTGTT</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="1492" style="width: 35px; color: rgba(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="1498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1498

</td>

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

<pre style="margin: 0;">+<span id="LC1498" class="line" lang="plaintext">SRR019778.50       22      33      2       5.5     TG      TG,TG,TG,TG,TG,T</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="1492" style="width: 35px; color: rgba(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="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1499

</td>

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<pre style="margin: 0;">+<span id="LC1499" class="line" lang="plaintext">SRR019778.64       30      44      3       4.66667 GAG     GAG,GAG,GAG,GAG,GA</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="1492" style="width: 35px; color: rgba(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="1500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1500

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<pre style="margin: 0;">+<span id="LC1500" class="line" lang="plaintext">SRR019778.65       2       13      2       5.5     TG      TG,TG,TG,TG,TG,T</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="1492" style="width: 35px; color: rgba(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="1501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1501

</td>

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

<pre style="margin: 0;">+<span id="LC1501" class="line" lang="plaintext">SRR019778.65       4       37      16      2.0625  TGTGTGTGTTTTCTGT        TGTGTGTGTTTTCTGT,TGTGTGTGTTTTTTGT,T</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="1492" style="width: 35px; color: rgba(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="1502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1502

</td>

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<pre style="margin: 0;">+<span id="LC1502" class="line" lang="plaintext">SRR019778.78       9       31      10      2.2     TGCCTTACTA      TGCCTTACTA,TGCCTTACTA,TG</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="1492" style="width: 35px; color: rgba(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="1503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1503

</td>

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

<pre style="margin: 0;">+<span id="LC1503" class="line" lang="plaintext">SRR019778.95       2       18      4       4       TGAT    TGAT,TGAT,TGAT,TGAT</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="1492" style="width: 35px; color: rgba(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="1504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1504

</td>

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

<pre style="margin: 0;">+<span id="LC1504" class="line" lang="plaintext">SRR019778.95       22      45      4       5.75    ATAG    ATAG,ATAG,ATAG,ATAG,ATAG,ATA</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="1492" style="width: 35px; color: rgba(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="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1505

</td>

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

<pre style="margin: 0;">+<span id="LC1505" 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="1492" style="width: 35px; color: rgba(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="1506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1506

</td>

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

<pre style="margin: 0;">+<span id="LC1506" class="line" lang="plaintext">hard       0       14      3       4.66667 CAT     CAT,CAT,CAT,CAT,CA</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="1492" style="width: 35px; color: rgba(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="1507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1507

</td>

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

<pre style="margin: 0;">+<span id="LC1507" class="line" lang="plaintext">hard       10      40      5       6       ATCAT   ATCAT,ATCAT,ATCAT,ATCAT,ATCAT,ATCAT</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="1492" style="width: 35px; color: rgba(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="1508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1508

</td>

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

<pre style="margin: 0;">+<span id="LC1508" 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="1492" style="width: 35px; color: rgba(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="1509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1509

</td>

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<pre style="margin: 0;">+<span id="LC1509" class="line" lang="plaintext">chrM       207     220     4       3.25    TTAA    TTAA,TTAA,TTAA,T</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="1492" style="width: 35px; color: rgba(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="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1510

</td>

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<pre style="margin: 0;">+<span id="LC1510" class="line" lang="plaintext">chrM       515     526     2       5.5     CA      CA,CA,CA,CA,CA,C</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="1492" style="width: 35px; color: rgba(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="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1511

</td>

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<pre style="margin: 0;">+<span id="LC1511" class="line" lang="plaintext">chrM       5305    5326    12      1.75    CCACCATCATAG    CCACCATCATAG,CCACCATCA</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="1492" style="width: 35px; color: rgba(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="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1512

</td>

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

<pre style="margin: 0;">+<span id="LC1512" class="line" lang="plaintext">chrM       8271    8290    9       2.11111 ACCCCCTCT       ACCCCCTCT,ACCCCCTCT,A</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="1492" style="width: 35px; color: rgba(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="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1513

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<pre style="margin: 0;">+<span id="LC1513" class="line" lang="plaintext">chrM       13647   13691   30      1.48276 CCCCACCCTTACTAACATTAACGAAAATAA  CCCCACCCTTACTAACATTAACGAAAATAA,CCCCACCCT-ACTAA</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1514

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<pre style="margin: 0;">+<span id="LC1514" class="line" lang="plaintext">chrM       15829   15844   6       2.5     AATCCT  AATCCT,AATCCT,AAT</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1492" style="width: 35px; color: rgba(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="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1515

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<pre style="margin: 0;">+<span id="LC1515" class="line" lang="plaintext">chrM       16183   16195   1       12      C       C,C,C,C,C,C,C,C,C,C,C,C</span></pre>

</td>

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</table>

<br>

</li>

<li id="905a9d4bc9e20118254b08495f8411e1fb0cc07d">

<a href="https://salsa.debian.org/med-team/tantan/commit/1063526ec91bd472dd347b5a39d44052ce6f3049#905a9d4bc9e20118254b08495f8411e1fb0cc07d"><strong>test/tantan_test.sh</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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,5 +29,11 @@ countLowercaseLetters () {</td>

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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">

29

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">    </span>tantan panda.fastq</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">

30

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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">

30

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

<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">echo</span></span>

</pre>

</td>

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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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">    </span>tantan <span class="nt" style="color: navy;">-i2</span> <span class="nt" style="color: navy;">-j3</span> hg19_chrM.fa | countLowercaseLetters</span>

</pre>

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<td class="diff-line-num new old_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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<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="shell">    <span class="nb" style="color: #0086b3;">echo</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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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<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="shell"><span class="nb" style="color: #0086b3;">    </span>tantan <span class="nt" style="color: navy;">-f4</span> panda.fastq</span>

</pre>

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<td class="diff-line-num new old_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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<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">

34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">echo</span></span>

</pre>

</td>

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

<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">    </span>tantan <span class="nt" style="color: navy;">-f4</span> <span class="nt" style="color: navy;">-b12</span> hard.fa</span>

</pre>

</td>

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

<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">echo</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">    </span>tantan <span class="nt" style="color: navy;">-f4</span> <span class="nt" style="color: navy;">-n1</span> hg19_chrM.fa</span>

</pre>

</td>

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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="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">

38

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

<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span> 2>&1 |</span>

</pre>

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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="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">

39

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell">diff <span class="nt" style="color: navy;">-u</span> tantan_test.out -</span></pre>

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