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GitLab

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<h3>

Michael R. Crusoe pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/f45477d680fb90e67ec9249e70dbad79d2483de4">f45477d6</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-05-10T13:54:29+02:00</i>

</div>

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

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/adc5d4bf2614f5a88e621d96177739aff4691512">adc5d4bf</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-05-10T13:54:30+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1061</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/1ccf975047a65dcdfd87a335756e2500039316df">1ccf9750</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-05-10T13:54:31+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1061'

Update to upstream version '1061'

with Debian dir cbf4b2fe73fed25e728e720204a766e1ecd14b09</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/830a97da55db70d0389a90a825c4b2c4d654f5bb">830a97da</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-05-10T13:58:01+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release 1061-1 to unstable

</pre>

</li>

</ul>

<h4>4 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#57bf262130f956caf76c405086f0815caf4e0a89">

ChangeLog.txt

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#7cec908f40ab30058cc7553cf0463829623d0080">

src/tantan.cc

</a>

</li>

<li class="file-stats">

<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">

src/version.hh

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="57bf262130f956caf76c405086f0815caf4e0a89">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/23dffa5cdb44a6a0af9144d40e73ecdaf3d921c9...830a97da55db70d0389a90a825c4b2c4d654f5bb#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">2020-05-07  Martin C. Frith  <Martin C. Frith></span>

</pre>

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2

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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

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

</pre>

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

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

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">      [543d36d39ce3] [tip]</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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

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

</pre>

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1

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">2020-03-16  Martin C. Frith  <Martin C. Frith></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">      * src/split/cbrc_split_aligner.cc, src/split/cbrc_split_aligner.hh:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">     Reduce last-split memory & time usage a bit</span>

</pre>

</td>

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5

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">      [ca3f417edc01]<span class="idiff left right"> [tip]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">     [ca3f417edc01]</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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

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

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">     * src/split/cbrc_int_exponentiator.hh:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">     Make last-split a bit faster</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/23dffa5cdb44a6a0af9144d40e73ecdaf3d921c9...830a97da55db70d0389a90a825c4b2c4d654f5bb#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">last-align (1061-1) unstable; urgency=medium</span>

</pre>

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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">  * Team upload.</span>

</pre>

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4

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

</pre>

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5

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

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 10 May 2020 13:57:46 +0200</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">last-align (1060-5) unstable; urgency=medium</span>

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9

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

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

</pre>

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<br>

</li>

<li id="7cec908f40ab30058cc7553cf0463829623d0080">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/23dffa5cdb44a6a0af9144d40e73ecdaf3d921c9...830a97da55db70d0389a90a825c4b2c4d654f5bb#7cec908f40ab30058cc7553cf0463829623d0080"><strong>src/tantan.cc</strong></a>

<hr>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -274,6 +274,10 @@ struct Tantan {</td>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">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>

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

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxOffsetInTheSequence</span><span class="p">()</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">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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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC281" 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;">seqFurthestBack</span><span class="p">()</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">isNearSeqBeg</span><span class="p">()</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;">seqPtr</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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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp">  <span class="p">}</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -296,6 +300,50 @@ struct Tantan {</td>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">calcForwardTransitionAndEmissionProbs</span><span class="p">()</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC304" 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="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp">      <span class="n" style="color: #333;">calcForwardTransitionProbsWithGaps</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp">      <span class="n" style="color: #333;">calcEmissionProbs</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</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="LC311" 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>

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<pre style="margin: 0;">+<span id="LC312" 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="LC313" 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;">lrRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">likelihoodRatioMatrix</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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<pre style="margin: 0;">+<span id="LC314" 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>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">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;">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="LC317" 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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<pre style="margin: 0;">+<span id="LC318" 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 new old_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp">      <span class="n" style="color: #333;">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="p">(</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 class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lrRow</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="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="LC320" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC322" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">calcEmissionAndBackwardTransitionProbs</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="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">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="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp">      <span class="n" style="color: #333;">calcBackwardTransitionProbsWithGaps</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC332" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp">    <span class="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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">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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<pre style="margin: 0;">+<span id="LC335" 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;">lrRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">likelihoodRatioMatrix</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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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxOffsetInTheSequence</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"></span>

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<td class="diff-line-num new new_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">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;">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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<td class="diff-line-num new new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC339" 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 class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lrRow</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="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="LC340" 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="LC341" 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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<td class="diff-line-num new new_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC344" 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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<td class="diff-line-num new new_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">rescale</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC348" 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;">scale</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp">    <span class="n" style="color: #333;">multiplyAll</span><span class="p">(</span><span class="n" style="color: #333;">foregroundProbs</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -322,8 +370,7 @@ struct Tantan {</td>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp">    <span class="n" style="color: #333;">initializeForwardAlgorithm</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC372" 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;">seqEnd</span><span class="p">)</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;">calcForwardTransitionProbs</span><span class="p">();</span></span>

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<td class="diff-line-num old old_line" data-linenumber="326" style="width: 35px; color: rgba(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="LC326" class="line" lang="cpp">      <span class="n" style="color: #333;">calcEmissionProbs</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp">      <span class="n" style="color: #333;">calcForwardTransitionAndEmissionProbs</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp">      <span class="n" style="color: #333;">rescaleForward</span><span class="p">();</span></span>

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<td class="diff-line-num old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">letterProbs</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;">float</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">backgroundProb</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">letterProbs</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -343,8 +390,7 @@ struct Tantan {</td>

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// a sequence:</span></span>

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<td class="diff-line-num old_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">letterProbs</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="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;">float</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">nonRepeatProb</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp">      <span class="n" style="color: #333;">rescaleBackward</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cpp">      <span class="n" style="color: #333;">calcEmissionProbs</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cpp">      <span class="n" style="color: #333;">calcBackwardTransitionProbs</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp">      <span class="n" style="color: #333;">calcEmissionAndBackwardTransitionProbs</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">backwardTotal</span><span class="p">();</span></span>

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<a href="https://salsa.debian.org/med-team/last-align/-/compare/23dffa5cdb44a6a0af9144d40e73ecdaf3d921c9...830a97da55db70d0389a90a825c4b2c4d654f5bb#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;">"106<span class="idiff left right">0</span>"</span></span></pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"106<span class="idiff left right">1</span>"</span></span></pre>

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