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GitLab

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<h3>

Andreas Tille pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/bali-phy/-/commit/5bda12c4b37ac8bf5d36f6353d442d1006487000">5bda12c4</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-08-30T17:50:03+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Fix watchfile to detect new versions on github

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bali-phy/-/commit/60599e45231d39a47fb4932e98f888290bc93689">60599e45</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-08-30T17:50:12+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.6.1+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bali-phy/-/commit/4cab409bc7bb23b0ea9da881c30d8cfca2322386">4cab409b</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-08-30T17:50:12+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/bali-phy/-/commit/70b804b0257498e8fba64f8dbfcef6f774591678">70b804b0</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-08-30T17:50:16+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.6.1+dfsg'

Update to upstream version '3.6.1+dfsg'

with Debian dir c1dfff0685aeab157692fb4c7fbba49a75a4cbcd</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bali-phy/-/commit/da12c0a8b79417573924b8f8a25217267e8316ad">da12c0a8</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-08-30T17:50:16+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bali-phy/-/commit/1ba75016cc8bccefc3f77d06493646b3f8c907a8">1ba75016</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-08-30T17:50:26+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove constraints unnecessary since buster

* Build-Depends: Drop versioned constraint on meson.

Changes-By: deb-scrub-obsolete</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bali-phy/-/commit/9cc015b75d097fe2400f47cd6232d4e150f6a950">9cc015b7</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-08-30T18:00:40+02:00</i>

</div>

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

</pre>

</li>

</ul>

<h4>30 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#0c345f0bb5b5a2d4b9c71a79c2119620aebbd7fa">

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+

.vscode/c_cpp_properties.json

</span>

</a>

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<li class="file-stats">

<a href="#f14cb12fa7462cdba1e6e6e4b499bce722fe22ba">

<span class="new-file">

+

.vscode/launch.json

</span>

</a>

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<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

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<li class="file-stats">

<a href="#e57eced52cc4e1b54cb6922500ddb4ad14539b41">

bindings/models/m2a.json

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<li class="file-stats">

<a href="#b1142a3db339624daf65038100ac9e04aa617512">

bindings/models/m2a_test.json

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<li class="file-stats">

<a href="#d105655f71cdea40ccc4e87ff293dbbb49126fbd">

bindings/models/m3_test.json

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<li class="file-stats">

<a href="#7e958c69b7c0ca0bd8b7ec21f95d9400ab0279fa">

bindings/models/m8.json

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<li class="file-stats">

<a href="#3fcb59523017b1c9ca7a6be17417062a0a746bb1">

bindings/models/m8a.json

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<a href="#16d20574f50bb71e5ab4fd284565451b5ac4b0dc">

bindings/models/m8a_test.json

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<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

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<li class="file-stats">

<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">

debian/watch

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<li class="file-stats">

<a href="#e26903080922fed937b6d35e65a8428fb2361d62">

doc/README.itex.xml

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<li class="file-stats">

<a href="#3e2daa08aea898322cb10bfdfae471974db4f198">

haskell/Probability/Distribution/Mixture.hs

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<li class="file-stats">

<a href="#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">

meson.build

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<a href="#fd745eb42b76be12f9ba032d71f67c2001677e3b">

src/alignment/load.H

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<a href="#f9c02f01207d5d200fc0360acaea4b488f711119">

src/alignment/load.cc

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<a href="#865ca7a790386f7472962bf795f41805aaea8cc2">

src/bali-phy/A-T-model.cc

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<a href="#2179cd1191f1302041c0cd85304a3b27ece2d66c">

src/bali-phy/bali-phy.cc

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<a href="#238e374095867defed8cf9bfefbd51d3028da46b">

src/builtins/PopGen.cc

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<a href="#0a7e2430f68ad463d640bc16eec3fbd5401c0878">

src/computation/expression/expression_ref.H

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<li class="file-stats">

<a href="#cf54d7ede176936d89260818c8d70ee19d32cbe9">

src/computation/optimization/float-out.cc

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<a href="#cd6d57441fe89247b6e6a9e74d810778209c4f42">

src/dp/alignment-sums.H

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<a href="#535235710e10492b72a1f4ed649df7d4a5736803">

src/math/exponential.cc

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<a href="#f784e669c8f7b7c916e62bab68d5fc49d8247850">

src/math/logprod.H

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<li class="file-stats">

<a href="#b56bfbbf69bb94c0e10814775ed402a5732685f0">

src/probability/choose.cc

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<a href="#074bf1d6d3874f73c6d0fc2b177af772a6934be8">

src/sequence/sequence-format.H

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<li class="file-stats">

<a href="#2b49d788b7727bf59b6addf9630d6185b61b3a73">

src/sequence/sequence-format.cc

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<a href="#d40956e0ef89c695ee758deaa21c1d0a996c2cbc">

src/tools/pickout.cc

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<li class="file-stats">

<a href="#b7018a0aaa166740c68039b579041123634699f3">

src/util/include/util/math/log-double.H

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</ul>

<h4>Changes:</h4>

<li id="0c345f0bb5b5a2d4b9c71a79c2119620aebbd7fa">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#0c345f0bb5b5a2d4b9c71a79c2119620aebbd7fa"><strong>.vscode/c_cpp_properties.json</strong></a>

<hr>

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<td class="new_line diff-line-num new" 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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="json"><span class="p">{</span></span>

</pre>

</td>

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"configurations"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span></span>

</pre>

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</td>

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

3

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"includePath"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span></span>

</pre>

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

5

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;">                </span><span class="s2" style="color: #d14;">"${workspaceFolder}/**"</span></span>

</pre>

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

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="p">],</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"defines"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[],</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"cStandard"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"c17"</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"cppStandard"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"c++17"</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"compileCommands"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"${workspaceFolder}/builddir/compile_commands.json"</span></span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">}</span></span>

</pre>

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

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="p">],</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">4</span></span>

</pre>

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14

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

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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>

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<br>

</li>

<li id="f14cb12fa7462cdba1e6e6e4b499bce722fe22ba">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#f14cb12fa7462cdba1e6e6e4b499bce722fe22ba"><strong>.vscode/launch.json</strong></a>

<hr>

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

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="json"><span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">    </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Use</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">IntelliSense</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">to</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">learn</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">about</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">possible</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">attributes.</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">    </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">Hover</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">to</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">view</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">descriptions</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">of</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">existing</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">attributes.</span></span>

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<td class="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">    </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">For</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">more</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">information</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">visit:</span><span class="w" style="color: #bbb;"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">https://go.microsoft.com/fwlink/?linkid=</span><span class="mi" style="color: #099;">830387</span></span>

</pre>

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

5

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0.2.0"</span><span class="p">,</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"configurations"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"(gdb) Launch"</span><span class="p">,</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"cppdbg"</span><span class="p">,</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"request"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"launch"</span><span class="p">,</span></span>

</pre>

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

</td>

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"program"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"${workspaceFolder}/builddir/src/bali-phy/bali-phy"</span><span class="p">,</span></span>

</pre>

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

</td>

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

12

</td>

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"args"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"${workspaceFolder}/examples/sequences/5S-rRNA/5d-muscle.fasta"</span><span class="p">,</span><span class="s2" style="color: #d14;">"--iter=10"</span><span class="p">,</span><span class="s2" style="color: #d14;">"--package-path=${workspaceFolder}/builddir/src/builtins:${workspaceFolder}"</span><span class="p">],</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"stopAtEntry"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">false</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

14

</td>

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

<pre style="margin: 0;">+<span id="LC14" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"cwd"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"${workspaceFolder}/run/"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

</td>

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

15

</td>

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

<pre style="margin: 0;">+<span id="LC15" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"environment"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[],</span></span>

</pre>

</td>

</tr>

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

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC16" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"externalConsole"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">false</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC17" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"MIMode"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"gdb"</span><span class="p">,</span></span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC18" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"setupCommands"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC19" class="line" lang="json"><span class="w" style="color: #bbb;">                </span><span class="p">{</span></span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC20" class="line" lang="json"><span class="w" style="color: #bbb;">                    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Enable pretty-printing for gdb"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

21

</td>

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

<pre style="margin: 0;">+<span id="LC21" class="line" lang="json"><span class="w" style="color: #bbb;">                    </span><span class="nl">"text"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"-enable-pretty-printing"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

22

</td>

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

<pre style="margin: 0;">+<span id="LC22" class="line" lang="json"><span class="w" style="color: #bbb;">                    </span><span class="nl">"ignoreFailures"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">true</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

23

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

<pre style="margin: 0;">+<span id="LC23" class="line" lang="json"><span class="w" style="color: #bbb;">                </span><span class="p">}</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

24

</td>

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

<pre style="margin: 0;">+<span id="LC24" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="p">]</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">}</span></span>

</pre>

</td>

</tr>

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

</td>

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

26

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

<pre style="margin: 0;">+<span id="LC26" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="p">]</span></span>

</pre>

</td>

</tr>

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

27

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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="LC27" class="line" lang="json"><span class="p">}</span></span></pre>

</td>

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

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

<td class="new_line diff-line-num" style="width: 35px; color: rgba(0,0,0,0.3); 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">\ No newline at end of file</td>

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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -4,19 +4,7 @@</td>

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4

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</td>

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;">Install</span></span>

</pre>

</td>

</tr>

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

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

5

</td>

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

5

</td>

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;">-------</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" 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

</td>

<td class="new_line diff-line-num" 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

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown">Please visit the <span class="p">[</span><span class="nv" style="color: #008080;">releases page</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.bali-phy.org/download.php</span><span class="p">)</span> to download official binaries.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown">You can also install via homebrew on a Mac, and using <span class="sb" style="color: #d14;">`apt-get`</span> on recent version of Debian or Ubuntu.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;">Documentation</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;">------------</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">http://bali-phy.org/</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bali-phy.org/</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Manual</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bali-phy.org/README.xhtml</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Tutorial</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bali-phy.org/Tutorial3.html</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Developer's Guide</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bali-phy.org/developer.html</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num 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">

18

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

</td>

<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown">The Manual describes <span class="p">[</span><span class="nv" style="color: #008080;">how to install</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bali-phy.org/README.xhtml#installation</span><span class="p">)</span> bali-phy in detail.  Simplified instructions are below.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">If you just want to install bali-phy, please visit the <span class="p">[</span><span class="nv" style="color: #008080;">release page</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.bali-phy.org/download.php</span><span class="p">)</span>.  If you want to compile BAli-phy from source, the quick start instructions are below.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

</td>

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

8

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

</td>

<td class="new_line diff-line-num" 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

</td>

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;">Compiling</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" 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">

22

</td>

<td class="new_line diff-line-num" 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

</td>

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

<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;">---------</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,26 +14,20 @@ You will need a C++ compiler that understands C++17.</td>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="markdown"><span class="p"> *</span> clang 8 (or higher) works</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<td class="new_line diff-line-num" 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">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="p"> *</span> XCode 11 (or higher) works</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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">

16

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown">You will also need to install</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

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<td class="new_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="p"> *</span> cairo graphics library (optional, but required to build the <span class="sb" style="color: #d14;">`draw-tree`</span> program)</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

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<td class="new_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

32

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<td class="new_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown">You will also need</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

33

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<td class="new_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"><span class="p"> *</span> python3</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

34

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<td class="new_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="p"> *</span> ninja</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

35

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<td class="new_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="p"> *</span> meson >= 0.53</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

36

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<td class="new_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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

<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;">Install Prerequisites</span></span>

</pre>

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

18

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

<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;">---------------------</span></span>

</pre>

</td>

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

<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown">On Ubuntu, you can use apt-get:</span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

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<td class="new_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">sudo </span>apt-get <span class="nb" style="color: #0086b3;">install </span>g++ libcairo2-dev <span class="idiff left">ninja-build pyth</span>on<span class="idiff right">3</span></span>

</pre>

</td>

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

</td>

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

21

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

<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">sudo </span>apt-get <span class="nb" style="color: #0086b3;">install </span>g++ libcairo2-dev <span class="idiff left right">mes</span>on</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

</td>

<td class="new_line diff-line-num" 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">

22

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

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

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

42

</td>

<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown">You also need to install meson.  First try:</span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

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

23

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

<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" 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">

</td>

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

24

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

<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown">On Mac (or Linux, actually) you can use homebrew:</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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

<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

44

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

<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"><span class="nb" style="color: #0086b3;"><span class="idiff left">sudo </span></span><span class="idiff right">apt-get</span> <span class="nb" style="color: #0086b3;">install </span>meson</span>

</pre>

</td>

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

</td>

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

26

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

<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="idiff left">brew</span> <span class="nb" style="color: #0086b3;">install </span><span class="idiff right">cairo </span>meson</span>

</pre>

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<td class="old_line diff-line-num" 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">

45

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<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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

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

</pre>

</td>

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<td class="old_line diff-line-num" 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">

46

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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

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<td class="new_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown">If the version of meson is not at least 0.<span class="idiff left right">49</span>, then you need to install</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

48

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<td class="new_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown">meson through pip:</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

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

<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">If the version of meson is not at least 0.<span class="idiff left right">53</span>, then you need to install</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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

<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown">meson through <span class="idiff left">the python package manager "</span>pip<span class="idiff right">"</span>:</span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

</td>

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

<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

</td>

<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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</td>

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

<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown">python3 <span class="nt" style="color: #000080;">-m</span> venv meson</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

51

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">source </span>meson/bin/activate</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,7 +39,7 @@ Build BAli-Phy</td>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown">git clone https://github.com/bredelings/BAli-Phy.git</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown">cd BAli-Phy</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(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="new_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown">meson build --prefix=$HOME/Applications/bali-phy<span class="idiff left right"> --buildtype=release</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

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

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

<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">meson build --prefix=$HOME/Applications/bali-phy</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown">ninja -C build install</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown">ninja -C build test</span>

</pre>

</td>

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,3 +61,12 @@ If you installed in `$HOME/Applications/bali-phy/` as recommended above, then fi</td>

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<td class="old_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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<td class="new_line diff-line-num" 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="LC61" class="line" lang="markdown">| ~/Applications/bali-phy/share/doc/bali-phy/                    | Documentation.          |</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="markdown"><span class="gh" style="color: #800080; font-weight: 600;">Further Documentation</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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="markdown"><span class="gh" style="color: #800080; font-weight: 600;">---------------------</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="markdown"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">http://bali-phy.org/</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bali-phy.org/</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Manual</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bali-phy.org/README.xhtml</span><span class="p">)</span></span>

</pre>

</td>

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

69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Tutorial</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bali-phy.org/Tutorial4.html</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="markdown"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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="markdown">The Manual describes <span class="p">[</span><span class="nv" style="color: #008080;">how to install</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bali-phy.org/README.xhtml#installation</span><span class="p">)</span> bali-phy in greater detail.</span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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="markdown"></span></pre>

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<br>

</li>

<li id="e57eced52cc4e1b54cb6922500ddb4ad14539b41">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#e57eced52cc4e1b54cb6922500ddb4ad14539b41"><strong>bindings/models/m2a.json</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="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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +21,7 @@</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"p0"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Double"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~uniform[0,1]"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

24

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<td class="new_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(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="LC24" class="line" lang="json"><span class="w" style="color: #bbb;">       </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The fraction of conserved sites among non-positively selected sites<span class="idiff left right">.</span>"</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">       </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The fraction of conserved sites among non-positively selected sites"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">},</span></span>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

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<td class="old_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"posP"</span><span class="p">,</span></span>

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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 @@</td>

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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The dN</span><span class="se" style="color: #d14;">\/</span><span class="s2" style="color: #d14;">dS value for positively selected sites"</span></span>

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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="p">],</span></span>

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<td class="old_line diff-line-num 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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<td class="new_line diff-line-num 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="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"description"</span><span class="p">:</span><span class="s2" style="color: #d14;">"A mixture of conserved, neutral, and positively-selected sites.  The conserved sites dN/dS=omega0 and the positively-selected sites have dN/dS=posW.  In this parameterization of the M2a model, p0 is the probability of being conserved conditional on not being positively selected.</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">The M2a model modifies the M2 model to avoid forcing the conserved dN/dS to 0."</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"description"</span><span class="p">:</span><span class="s2" style="color: #d14;">"A mixture of conserved, neutral, and positively-selected sites.  The conserved sites <span class="idiff left right">have </span>dN/dS=omega0 and the positively-selected sites have dN/dS=posW.  In this parameterization of the M2a model, p0 is the probability of being conserved conditional on not being positively selected.</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">The M2a model modifies the M2 model to avoid forcing the conserved dN/dS to 0."</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"citation"</span><span class="p">:{</span><span class="nl">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"article"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="json"><span class="w" style="color: #bbb;">           </span><span class="nl">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="json"><span class="w" style="color: #bbb;">           </span><span class="nl">"year"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2004"</span><span class="p">,</span></span>

</pre>

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<br>

</li>

<li id="b1142a3db339624daf65038100ac9e04aa617512">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#b1142a3db339624daf65038100ac9e04aa617512"><strong>bindings/models/m2a_test.json</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,5 +58,6 @@</td>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="json"><span class="w" style="color: #bbb;">                           </span><span class="nl">"id"</span><span class="p">:</span><span class="s2" style="color: #d14;">"10.1534/genetics.104.031153 "</span><span class="p">}]</span></span>

</pre>

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<td class="old_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">          </span><span class="p">},</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"examples"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"function[w,gy94[omega=w,pi=f1x4]]+m2a_test"</span><span class="p">,</span><span class="s2" style="color: #d14;">"function[w,mg94[omega=w]]+m2a_test"</span><span class="p">,</span><span class="s2" style="color: #d14;">"function[w,fMutSel0[omega=w]]+m2a_test"</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"see"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"m1a"</span><span class="p">,</span><span class="s2" style="color: #d14;">"m2a"</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"extract"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"all"</span></span>

</pre>

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

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<br>

</li>

<li id="d105655f71cdea40ccc4e87ff293dbbb49126fbd">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#d105655f71cdea40ccc4e87ff293dbbb49126fbd"><strong>bindings/models/m3_test.json</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,7 +39,7 @@</td>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"posSelection"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Int"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~bernoulli[0.5]"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(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="new_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The model selector: 1 if positive selection, 0 if not<span class="idiff left right">.</span>"</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The model selector: 1 if positive selection, 0 if not"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">},</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"n"</span><span class="p">,</span></span>

</pre>

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<br>

</li>

<li id="7e958c69b7c0ca0bd8b7ec21f95d9400ab0279fa">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#7e958c69b7c0ca0bd8b7ec21f95d9400ab0279fa"><strong>bindings/models/m8.json</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,7 +33,7 @@</td>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"posP"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Double"</span><span class="p">,</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~beta[1,10]"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

36

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;"><span class="idiff left">  </span>    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The fraction of <span class="idiff right">neutral</span> sites"</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;"><span class="idiff left">        </span>    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The fraction of <span class="idiff right">positively selected</span> sites"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">},</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"posW"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,7 +42,8 @@</td>

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<td class="old_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The dN</span><span class="se" style="color: #d14;">\/</span><span class="s2" style="color: #d14;">dS value for positively selected sites"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"A site-heterogeneous model with a discrete Beta distribution on dN/dS values, plus a category of positively-selected sites.  See the m7 model for the definition of mu and gamma."</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"see"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"m7"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"m8a"</span><span class="p">,</span><span class="s2" style="color: #d14;">"m8a_test"</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC46" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The m8 model is an m7 model with an additional category of positively-selected sites.  The additional category of sites has proportion=posP and dN/dS=posW."</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"citation"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="nl">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"article"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC48" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"year"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2000"</span><span class="p">,</span></span>

</pre>

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</table>

<br>

</li>

<li id="3fcb59523017b1c9ca7a6be17417062a0a746bb1">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#3fcb59523017b1c9ca7a6be17417062a0a746bb1"><strong>bindings/models/m8a.json</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,10 +33,11 @@</td>

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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"posP"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Double"</span><span class="p">,</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~beta[1,10]"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

36

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;"><span class="idiff left right">    </span>    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The fraction of neutral sites"</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;"><span class="idiff left">        </span>    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The fraction of <span class="idiff">*</span>neutral<span class="idiff right">*</span> sites"</span></span>

</pre>

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37

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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC38" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="p">],</span></span>

</pre>

</td>

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<td class="old_line diff-line-num 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">

39

</td>

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

<pre style="margin: 0;">-<span id="LC39" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"A site-heterogeneous model with a discrete Beta distribution on dN/dS values, plus a category of neutral sites.  See the m7 model for the definition of mu and gamma."</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

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

39

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

<pre style="margin: 0;">+<span id="LC39" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The m8a model is an m7 model with an additional category of neutral sites. The additional category of sites has proportion posP.</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">The m8a model is also equivalent to m8[posW=1].  That is, you get m8a by constraining posW to 1 in the m8 model.  Therefore, the m8a model is nested within the m8 model.</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">The m8a model was created as an improved null hypothesis for use in a likelihood ratio test.  (See m8a_test)"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"see"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"m7"</span><span class="p">,</span><span class="s2" style="color: #d14;">"m8"</span><span class="p">,</span><span class="s2" style="color: #d14;">"m8a_test"</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

40

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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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

<pre style="margin: 0;"> <span id="LC41" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"citation"</span><span class="p">:{</span><span class="nl">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"article"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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

<pre style="margin: 0;"> <span id="LC42" class="line" lang="json"><span class="w" style="color: #bbb;">           </span><span class="nl">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Pervasive Adaptive Evolution in Mammalian Fertilization Proteins"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="json"><span class="w" style="color: #bbb;">           </span><span class="nl">"year"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2003"</span><span class="p">,</span></span>

</pre>

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</table>

<br>

</li>

<li id="16d20574f50bb71e5ab4fd284565451b5ac4b0dc">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#16d20574f50bb71e5ab4fd284565451b5ac4b0dc"><strong>bindings/models/m8a_test.json</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="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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

1

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="json"><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"m8a_test"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

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

3

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Bayesian version of the M8a test for positive selection"</span><span class="p">,</span></span>

</pre>

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

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"synonyms"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"M8a_Test"</span><span class="p">],</span></span>

</pre>

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

5

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"result_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"MixtureModel[Codons[a]]"</span><span class="p">,</span></span>

</pre>

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

5

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

6

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"call"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"SModel.m8a_test[@mu,@gamma,@n,@posP,@posW,@posSelection,@submodel]"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +9,8 @@</td>

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

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"n"</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Int"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"4"</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"4"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="json"><span class="w" style="color: #bbb;">       </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The number of bins for discretizing the Beta distribution"</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">        </span><span class="p">},</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"submodel"</span><span class="p">,</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,28 +21,44 @@</td>

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<td class="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

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<td class="old_line diff-line-num" 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="LC22" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"mu"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Double"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~uniform[0,1]"</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~uniform[0,1]"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="json"><span class="w" style="color: #bbb;">       </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The mean of the Beta distribution"</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">        </span><span class="p">},</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"gamma"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Double"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(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="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC27" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~beta[1,10]"</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~beta[1,10]"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

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

31

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

<pre style="margin: 0;">+<span id="LC31" class="line" lang="json"><span class="w" style="color: #bbb;">       </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The fraction of possible Beta variance given mu"</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" 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">

28

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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC32" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">},</span></span>

</pre>

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

<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"posP"</span><span class="p">,</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Double"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(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="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC32" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~beta[1,10]"</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~beta[1,10]"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC37" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The fraction of positively-selected or neutral sites"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC38" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">},</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC39" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

</pre>

</td>

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

35

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

<pre style="margin: 0;"> <span id="LC40" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"posW"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

36

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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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

<pre style="margin: 0;"> <span id="LC41" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Double"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num 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">

37

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<td class="new_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC37" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~log_gamma[4,0.25]"</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

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

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

<pre style="margin: 0;">+<span id="LC42" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~log_gamma[4,0.25]"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

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

43

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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="LC43" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The dN</span><span class="se" style="color: #d14;">\/</span><span class="s2" style="color: #d14;">dS value for positively-selected or neutral sites"</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC44" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">},</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC45" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"posSelection"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"arg_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Int"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~bernoulli[0.5]"</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"default_value"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"~bernoulli[0.5]"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"The model indicator -- H0 or H1"</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="json"><span class="w" style="color: #bbb;">        </span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="p">],</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"This is a Bayesian version of the M8a test for positive selection. The original M8a test is a likelihood-ratio test. The Bayesian version of the test chooses a prior with 50% mass on the null hypothesis H0 and 50% on the alternative hypothesis H1:</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">   H0: no positive selection</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">   H1: some positive selection.</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">When posSelection = 0, the value of posW is ignored and dN/dS=1. When posSelection = 1, the value of posW is used and dN/dS=posW. The posterior probability of posSelection gives the posterior probability of H1.  The Bayes Factor is given by Pr(posSelection=1)/Pr(posSelection=0).</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">The M8a test (Swanson et al, 2003) has null and alternative hypotheses given by:</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">   H0: m8[posW=1] = m8a</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">   H1: m8</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">This is an improvement over the test originally proposed by Yang (2000):</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">   H0: m8[posP=1] = m7</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">   H1: m8</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">In the originally proposed likelihood-ratio test, a mixture of conserved and neutral sites would not fit the null hypothesis (m7), leading to the erroneous inference of positive selection. In the M8a test, the null hypothesis (m8a) has been improved to handle both neutral and conserved sites, so that positive selection is not incorrectly inferred."</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"see"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"m7"</span><span class="p">,</span><span class="s2" style="color: #d14;">"m8a"</span><span class="p">,</span><span class="s2" style="color: #d14;">"m8a"</span><span class="p">],</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"citation"</span><span class="p">:{</span><span class="nl">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"article"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="json"><span class="w" style="color: #bbb;">           </span><span class="nl">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Pervasive Adaptive Evolution in Mammalian Fertilization Proteins"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="json"><span class="w" style="color: #bbb;">           </span><span class="nl">"year"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2003"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="json"><span class="w" style="color: #bbb;">           </span><span class="nl">"author"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[{</span><span class="nl">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Swanson, Willie J."</span><span class="p">},</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="json"><span class="w" style="color: #bbb;">                      </span><span class="p">{</span><span class="nl">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Nielsen, Rasmus"</span><span class="p">},</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="json"><span class="w" style="color: #bbb;">                      </span><span class="p">{</span><span class="nl">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Yang, Qiaofeng"</span><span class="p">}],</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="json"><span class="w" style="color: #bbb;">           </span><span class="nl">"journal"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="nl">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Molecular Biology and Evolution"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="nl">"volume"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"20"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="nl">"number"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"1"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="nl">"pages"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"18--20"</span><span class="p">},</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="json"><span class="w" style="color: #bbb;">           </span><span class="nl">"identifier"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[{</span><span class="nl">"type"</span><span class="p">:</span><span class="s2" style="color: #d14;">"doi"</span><span class="p">,</span><span class="nl">"id"</span><span class="p">:</span><span class="s2" style="color: #d14;">"10.1093/oxfordjournals.molbev.a004233"</span><span class="p">}]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="json"><span class="w" style="color: #bbb;">          </span><span class="p">},</span></span>

</pre>

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45

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"extract"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"all"</span></span>

</pre>

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46

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="json"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bali-phy (3.6.1+dfsg-1) unstable; urgency=medium</span>

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

3

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

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * New upstream version</span>

</pre>

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<td class="old_line diff-line-num new" 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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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Standards-Version: 4.6.0 (routine-update)</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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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Mon, 30 Aug 2021 17:50:26 +0200</span>

</pre>

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8

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

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">bali-phy (3.6.0+dfsg-1.1) UNRELEASED; urgency=medium</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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">  * Non-maintainer upload.</span>

</pre>

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

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">  * Fix watchfile to detect new versions on github (routine-update)</span>

</pre>

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13

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Mon, 30 Aug 2021 17:50:03 +0200</span>

</pre>

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15

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

</pre>

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1

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16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">bali-phy (3.6.0+dfsg-1) unstable; urgency=medium</span>

</pre>

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2

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

</pre>

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3

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<td class="new_line diff-line-num" 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="plaintext">  [ Benjamin Redelings ]</span>

</pre>

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</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Uploaders: Benjamin Redelings <benjamin.redelings@gmail.com></td>

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

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>

</pre>

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5

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

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

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<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">               meson<span class="idiff left right"> (>=0.53)</span>,</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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">               libcairo2-dev,</span>

</pre>

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

9

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<td class="new_line diff-line-num" 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">               libeigen3-dev,</span>

</pre>

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

10

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<td class="new_line diff-line-num" 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">               nlohmann-json3-dev,</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@ Build-Depends: debhelper-compat (= 13),</td>

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<td class="old_line diff-line-num" 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">

16

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<td class="new_line diff-line-num" 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">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">               libboost-filesystem-dev,</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">               libboost-chrono-dev,</span>

</pre>

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<td class="old_line diff-line-num" 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">

18

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<td class="new_line diff-line-num" 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">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">               librange-v3-dev</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

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<td class="new_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bali-phy</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bali-phy.git</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" 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">

22

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<td class="new_line diff-line-num" 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">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Homepage: http://www.bali-phy.org</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>

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

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">  https://github.com/bredelings/BAli-Phy/<span class="idiff left right">releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@</span></span></pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  https://github.com/bredelings/BAli-Phy/<span class="idiff left right">tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz</span></span></pre>

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<br>

</li>

<li id="e26903080922fed937b6d35e65a8428fb2361d62">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#e26903080922fed937b6d35e65a8428fb2361d62"><strong>doc/README.itex.xml</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">@@ -106,7 +106,7 @@ C:\cygwin64\home\<emphasis>username</emphasis>\Applications\</td>

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

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="xml">    <span class="nt" style="color: #000080;"><section><info><title></span>Install on Mac OS X<span class="nt" style="color: #000080;"></title></info></span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="xml">    <span class="nt" style="color: #000080;"><section><info><title></span>Install BAli-Phy using homebrew (recommended) <span class="nt" style="color: #000080;"></title></info></span></span>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>First install the <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"https://developer.apple.com/xcode/"</span><span class="nt" style="color: #000080;">></span>XCode<span class="nt" style="color: #000080;"></link></span> (version <span class="idiff left right">6</span> or higher) command line tools:</span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>First install the <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"https://developer.apple.com/xcode/"</span><span class="nt" style="color: #000080;">></span>XCode<span class="nt" style="color: #000080;"></link></span> (version <span class="idiff left right">11</span> or higher) command line tools:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="xml">    <span class="nt" style="color: #000080;"><screen><prompt></span>%<span class="nt" style="color: #000080;"></prompt></span> <span class="nt" style="color: #000080;"><userinput></span>xcode-select --install<span class="nt" style="color: #000080;"></userinput></screen></span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="xml">    Then install <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://brew.sh/"</span><span class="nt" style="color: #000080;">></span>homebrew<span class="nt" style="color: #000080;"></link></span> and use homebrew to compile and install <span class="nt" style="color: #000080;"><command></span>bali-phy<span class="nt" style="color: #000080;"></command></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">@@ -1148,7 +1148,7 @@ The majority consensus tree is usually not fully resolved, so we recommend using</td>

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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="xml">      <span class="nt" style="color: #000080;"><info><title></span>Frequencies<span class="nt" style="color: #000080;"></title></info></span></span>

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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Frequencies are estimated by default.  Frequencies can be fixed by setting the <span class="nt" style="color: #000080;"><userinput></span>pi<span class="nt" style="color: #000080;"></userinput></span> parameter to a constant value, if the model allows unequal frequencies.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Constant frequencies are specified as a list of pairs that associates each letter with its frequency:<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC1151" class="line" lang="xml">      <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>gtr[pi=List[<span class="idiff left">Pair</span>["A",0.1],<span class="idiff">Pair</span>["C",0.2],<span class="idiff">Pair</span>["T",0.3],<span class="idiff right">Pair</span>["G",0.4]]<span class="nt" style="color: #000080;"></programlisting></span></span>

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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="xml">      <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>gtr[pi=List[<span class="idiff left">Tuple</span>["A",0.1],<span class="idiff">Tuple</span>["C",0.2],<span class="idiff">Tuple</span>["T",0.3],<span class="idiff right">Tuple</span>["G",0.4]]<span class="nt" style="color: #000080;"></programlisting></span></span>

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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Frequencies can also be specified using functions:<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1153" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC1154" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); 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="1283" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1283,10 +1283,10 @@ The majority consensus tree is usually not fully resolved, so we recommend using</td>

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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="xml">      <span class="nt" style="color: #000080;"><info><title></span>Frequencies<span class="nt" style="color: #000080;"></title></info></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Frequencies are estimated by default.  Frequencies can be fixed by setting the <span class="nt" style="color: #000080;"><userinput></span>pi<span class="nt" style="color: #000080;"></userinput></span> parameter to a constant value, if the model allows unequal frequencies.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Constant frequencies are specified as a list of pairs that associates each letter with its frequency:<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC1286" class="line" lang="xml">      <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>wag+f[pi=List[<span class="idiff left">Pair</span>["A",0.047],<span class="idiff right">Pair</span>["R",0.19],...]]<span class="nt" style="color: #000080;"></programlisting></span></span>

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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="xml">      <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>wag+f[pi=List[<span class="idiff left">Tuple</span>["A",0.047],<span class="idiff right">Tuple</span>["R",0.19],...]]<span class="nt" style="color: #000080;"></programlisting></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1287" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Frequencies can also be specified using functions:<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1288" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC1289" class="line" lang="xml"> <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>wag+f[pi=Frequencies.uniform]<span class="idiff left right">]</span><span class="nt" style="color: #000080;"></programlisting></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="xml"> <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>wag+f[pi=Frequencies.uniform]<span class="nt" style="color: #000080;"></programlisting></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="xml">      <span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="xml"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="xml">      <span class="nt" style="color: #000080;"><informaltable></span></span>

</pre>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1421" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1421,9 +1421,9 @@ The majority consensus tree is usually not fully resolved, so we recommend using</td>

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<pre style="margin: 0;"> <span id="LC1421" class="line" lang="xml">      <span class="nt" style="color: #000080;"><info><title></span>Frequencies<span class="nt" style="color: #000080;"></title></info></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1422" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Frequencies are estimated by default.  Frequencies can be fixed by setting the <span class="nt" style="color: #000080;"><userinput></span>pi<span class="nt" style="color: #000080;"></userinput></span> parameter to a constant value, if the model allows unequal frequencies.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1423" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Constant frequencies are specified as a list of pairs that associates each letter with its frequency.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC1424" class="line" lang="xml">      <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>hky85[pi=List[<span class="idiff left">Pair</span>["A",0.1],<span class="idiff">Pair</span>["C",0.2],<span class="idiff">Pair</span>["T",0.3],<span class="idiff right">Pair</span>["G",0.4]]]+x2</span>

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<td class="old_line diff-line-num new" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="xml">      <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>hky85[pi=List[<span class="idiff left">Tuple</span>["A",0.1],<span class="idiff">Tuple</span>["C",0.2],<span class="idiff">Tuple</span>["T",0.3],<span class="idiff right">Tuple</span>["G",0.4]]]+x2</span>

</pre>

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<pre style="margin: 0;"> <span id="LC1425" class="line" lang="xml"></span>

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<td class="old_line diff-line-num old" data-linenumber="1426" style="width: 35px; color: rgba(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="new_line diff-line-num old" data-linenumber="1426" style="width: 35px; color: rgba(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="LC1426" class="line" lang="xml">hky85_sym+x2_sym+f[pi=List[<span class="idiff left">Pair</span>["AA",0.01],<span class="idiff">Pair</span>["AC",0.01],<span class="idiff">Pair</span>["AG",0.01],<span class="idiff">Pair</span>["AU",0.22],<span class="idiff">Pair</span>["CA",0.01],<span class="idiff">Pair</span>["CC",0.01],<span class="idiff">Pair</span>["CG",0.22],<span class="idiff">Pair</span>["CU",0.01],<span class="idiff">Pair</span>["GA",0.01],<span class="idiff">Pair</span>["GC",0.22],<span class="idiff">Pair</span>["GG",0.01],<span class="idiff">Pair</span>["GU",0.01],<span class="idiff">Pair</span>["UA",0.22],<span class="idiff">Pair</span>["UC",0.01],<span class="idiff">Pair</span>["UG",0.01],<span class="idiff right">Pair</span>["UU",0.01]]]<span class="nt" style="color: #000080;"></programlisting></span></span>

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<pre style="margin: 0;">+<span id="LC1426" class="line" lang="xml">hky85_sym+x2_sym+f[pi=List[<span class="idiff left">Tuple</span>["AA",0.01],<span class="idiff">Tuple</span>["AC",0.01],<span class="idiff">Tuple</span>["AG",0.01],<span class="idiff">Tuple</span>["AU",0.22],<span class="idiff">Tuple</span>["CA",0.01],<span class="idiff">Tuple</span>["CC",0.01],<span class="idiff">Tuple</span>["CG",0.22],<span class="idiff">Tuple</span>["CU",0.01],<span class="idiff">Tuple</span>["GA",0.01],<span class="idiff">Tuple</span>["GC",0.22],<span class="idiff">Tuple</span>["GG",0.01],<span class="idiff">Tuple</span>["GU",0.01],<span class="idiff">Tuple</span>["UA",0.22],<span class="idiff">Tuple</span>["UC",0.01],<span class="idiff">Tuple</span>["UG",0.01],<span class="idiff right">Tuple</span>["UU",0.01]]]<span class="nt" style="color: #000080;"></programlisting></span></span>

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<pre style="margin: 0;"> <span id="LC1427" class="line" lang="xml"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1428" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Frequencies can also be specified using functions:<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1429" class="line" lang="xml">      <span class="c" style="color: #998; font-style: italic;"><!-- para></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); 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="1530" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1530,7 +1530,7 @@ hky85_sym+x2_sym+f[pi=List[Pair["AA",0.01],Pair["AC",0.01],Pair["AG",0.01],Pair[</td>

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<pre style="margin: 0;"> <span id="LC1530" class="line" lang="xml">      <span class="nt" style="color: #000080;"><info><title></span>Frequencies<span class="nt" style="color: #000080;"></title></info></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Frequencies are estimated by default.  Frequencies can be fixed by setting the <span class="nt" style="color: #000080;"><userinput></span>pi<span class="nt" style="color: #000080;"></userinput></span> parameter to a constant value, if the model allows unequal frequencies.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1532" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Constant frequencies are specified as a list of pairs that associates each letter with its frequency.<span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC1533" class="line" lang="xml">      <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>hky85[pi=List[<span class="idiff left">Pair</span>["A",0.1],<span class="idiff">Pair</span>["C",0.2],<span class="idiff">Pair</span>["T",0.3],<span class="idiff right">Pair</span>["G",0.4]]]+x3<span class="nt" style="color: #000080;"></programlisting></span></span>

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<td class="new_line diff-line-num new" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="xml">      <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>hky85[pi=List[<span class="idiff left">Tuple</span>["A",0.1],<span class="idiff">Tuple</span>["C",0.2],<span class="idiff">Tuple</span>["T",0.3],<span class="idiff right">Tuple</span>["G",0.4]]]+x3<span class="nt" style="color: #000080;"></programlisting></span></span>

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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Frequencies can also be specified using functions:<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;"> <span id="LC1535" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span></span>

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<pre style="margin: 0;"> <span id="LC1536" class="line" lang="xml"> <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>hky85_sym+x3_sym+f[pi=f1x4]            // nucleotide frequencies are estimated<span class="nt" style="color: #000080;"></programlisting></span></span>

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<pre style="margin: 0;"> <span id="LC1760" class="line" lang="xml">      <span class="nt" style="color: #000080;"><info><title></span>Frequencies<span class="nt" style="color: #000080;"></title></info></span></span>

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<pre style="margin: 0;"> <span id="LC1761" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Frequencies are estimated by default.  Frequencies can be fixed by setting the <span class="nt" style="color: #000080;"><userinput></span>pi<span class="nt" style="color: #000080;"></userinput></span> parameter to a constant value, if the model allows unequal frequencies.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;"> <span id="LC1762" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Constant frequencies are specified as a list of pairs that associates each letter with its frequency.<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;">-<span id="LC1763" class="line" lang="xml">      <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>gy94[pi=List[<span class="idiff left">Pair</span>["AAA",0.01],<span class="idiff right">Pair</span>["C",0.02],...]]</span>

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<pre style="margin: 0;">-<span id="LC1764" class="line" lang="xml">mg94[pi=List[<span class="idiff left">Pair</span>["A",0.1],<span class="idiff">Pair</span>["C",0.2],<span class="idiff">Pair</span>["T",0.3],<span class="idiff right">Pair</span>["G",0.4]]]</span>

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<pre style="margin: 0;">+<span id="LC1763" class="line" lang="xml">      <span class="nt" style="color: #000080;"><programlisting</span> <span class="na" style="color: #008080;">language=</span><span class="s" style="color: #d14;">"java"</span><span class="nt" style="color: #000080;">></span>gy94[pi=List[<span class="idiff left">Tuple</span>["AAA",0.01],<span class="idiff right">Tuple</span>["C",0.02],...]]</span>

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<pre style="margin: 0;">+<span id="LC1764" class="line" lang="xml">mg94[pi=List[<span class="idiff left">Tuple</span>["A",0.1],<span class="idiff">Tuple</span>["C",0.2],<span class="idiff">Tuple</span>["T",0.3],<span class="idiff right">Tuple</span>["G",0.4]]]</span>

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<pre style="margin: 0;"> <span id="LC1765" class="line" lang="xml"><span class="nt" style="color: #000080;"></programlisting></span></span>

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<pre style="margin: 0;"> <span id="LC1766" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>Frequencies can also be specified using functions:<span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;"> <span id="LC1767" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2277,7 +2277,7 @@ The <userinput>help</userinput> command can be used to determine the default val</td>

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<pre style="margin: 0;"> <span id="LC2277" class="line" lang="xml">  <span class="nt" style="color: #000080;"><para></span>Some types contain parameters.  For example <span class="nt" style="color: #000080;"><userinput></span>List[Int]<span class="nt" style="color: #000080;"></userinput></span> indicates a list of integers and <span class="nt" style="color: #000080;"><userinput></span>List[Double]<span class="nt" style="color: #000080;"></userinput></span> indicates a list of real numbers.  In order to indicate a list of unknown type, we use a <span class="nt" style="color: #000080;"><emphasis></span>type variable<span class="nt" style="color: #000080;"></emphasis></span> <span class="nt" style="color: #000080;"><userinput></span>a<span class="nt" style="color: #000080;"></userinput></span> and write <span class="nt" style="color: #000080;"><userinput></span>List[a]<span class="nt" style="color: #000080;"></userinput></span>.  Type variables always begin with a lower-case letter.  They are able to match any specific type, and their value is found by pattern-matching.  For example, the function <span class="nt" style="color: #000080;"><userinput></span>add[x,y]<span class="nt" style="color: #000080;"></userinput></span> takes two arguments of type <span class="nt" style="color: #000080;"><userinput></span>a<span class="nt" style="color: #000080;"></userinput></span> and has a result of type <span class="nt" style="color: #000080;"><userinput></span>a<span class="nt" style="color: #000080;"></userinput></span>.  Thus:</span>

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<pre style="margin: 0;"> <span id="LC2278" class="line" lang="xml"><span class="nt" style="color: #000080;"><programlisting></span>add[1,2]        // arguments are a=Int, so result is of type Int</span>

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<pre style="margin: 0;"> <span id="LC2279" class="line" lang="xml">add[1.0,2.0]    // arguments are a=Double, so result is of type Double<span class="nt" style="color: #000080;"></programlisting></span></span>

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<pre style="margin: 0;">-<span id="LC2280" class="line" lang="xml"><span class="nt" style="color: #000080;"><userinput></span><span class="idiff left">Pair</span>[a,b]<span class="nt" style="color: #000080;"></userinput></span> is a parameterized type that can be specialized to (for example) <span class="nt" style="color: #000080;"><userinput></span><span class="idiff">Pair</span>[String,Double]<span class="nt" style="color: #000080;"></userinput></span> and <span class="nt" style="color: #000080;"><userinput></span><span class="idiff right">Pair</span>[Int,Int]<span class="nt" style="color: #000080;"></userinput></span>.</span>

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<pre style="margin: 0;">+<span id="LC2280" class="line" lang="xml"><span class="nt" style="color: #000080;"><userinput></span><span class="idiff left">Tuple</span>[a,b]<span class="nt" style="color: #000080;"></userinput></span> is a parameterized type that can be specialized to (for example) <span class="nt" style="color: #000080;"><userinput></span><span class="idiff">Tuple</span>[String,Double]<span class="nt" style="color: #000080;"></userinput></span> and <span class="nt" style="color: #000080;"><userinput></span><span class="idiff right">Tuple</span>[Int,Int]<span class="nt" style="color: #000080;"></userinput></span>.</span>

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<pre style="margin: 0;"> <span id="LC2281" class="line" lang="xml">  <span class="nt" style="color: #000080;"></para></span></span>

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<pre style="margin: 0;"> <span id="LC2282" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC2283" class="line" lang="xml">  <span class="nt" style="color: #000080;"><para></span>Types for components of substitution models are often parameterized by type of the alphabet.  For example, hky85 has a result type of <span class="nt" style="color: #000080;"><userinput></span>RevCTMC[a]<span class="nt" style="color: #000080;"></userinput></span>, where <span class="nt" style="color: #000080;"><userinput></span>a<span class="nt" style="color: #000080;"></userinput></span> could be <span class="nt" style="color: #000080;"><userinput></span>DNA<span class="nt" style="color: #000080;"></userinput></span> or <span class="nt" style="color: #000080;"><userinput></span>RNA<span class="nt" style="color: #000080;"></userinput></span>.  The use of alphabet types in substitution models prevents combining substitution models with mismatched alphabets.</span>

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<pre style="margin: 0;"> <span id="LC2670" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC2671" class="line" lang="xml">      <span class="nt" style="color: #000080;"><section><info><title></span>ESS for split frequencies<span class="nt" style="color: #000080;"></title></info></span></span>

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<pre style="margin: 0;"> <span id="LC2672" class="line" lang="xml"> </span>

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<pre style="margin: 0;">-<span id="LC2673" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span><span class="idiff left right">To calculate the split ESS values, run</span>:</span>

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<pre style="margin: 0;">+<span id="LC2673" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span><span class="idiff left">As desribed in </span><span class="nt" style="color: #000080;"><span class="idiff"><link</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">xmlns:xlink=</span></span><span class="s" style="color: #d14;"><span class="idiff">"http://www.w3.org/1999/xlink"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">xlink:href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"https://doi.org/10.3852/10-120"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">Gaya et al (2011)</span><span class="nt" style="color: #000080;"><span class="idiff"></link></span></span><span class="idiff right">, we can also compute ESS values for splits on the tree</span>:</span>

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<pre style="margin: 0;"> <span id="LC2674" class="line" lang="xml"><span class="nt" style="color: #000080;"><screen><prompt></span>%<span class="nt" style="color: #000080;"></prompt></span> trees-bootstrap <span class="nt" style="color: #000080;"><replaceable></span>dir-1<span class="nt" style="color: #000080;"></replaceable></span>/C1.trees <span class="nt" style="color: #000080;"><replaceable></span>dir-2<span class="nt" style="color: #000080;"></replaceable></span>/C1.trees ... <span class="nt" style="color: #000080;"><replaceable></span>dir-n<span class="nt" style="color: #000080;"></replaceable></span>/C1.trees <span class="ni" style="color: #800080;">&gt;</span> partitions.bs<span class="nt" style="color: #000080;"></screen></span></span>

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<pre style="margin: 0;"> <span id="LC2675" class="line" lang="xml">      To compute the ESS for a split, we consider the presence or absence</span>

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<pre style="margin: 0;"> <span id="LC2676" class="line" lang="xml">      of a split in each iteration as a series of binary values.  We</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">@@ -2901,20 +2901,20 @@ The stabilization criterion is the same one described above for numerical values</td>

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<pre style="margin: 0;"> <span id="LC2901" class="line" lang="xml"></span>

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2902

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<pre style="margin: 0;"> <span id="LC2902" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>In order to compile BAli-Phy, you need</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2903

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<td class="new_line diff-line-num" data-linenumber="2903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2903

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<pre style="margin: 0;"> <span id="LC2903" class="line" lang="xml">    <span class="nt" style="color: #000080;"><itemizedlist></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2904

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<td class="new_line diff-line-num old" data-linenumber="2904" style="width: 35px; color: rgba(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="LC2904" class="line" lang="xml">      <span class="nt" style="color: #000080;"><listitem></span>a <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"https://en.wikipedia.org/wiki/C%2B%2B14"</span><span class="nt" style="color: #000080;">></span>C++1<span class="idiff left right">4</span><span class="nt" style="color: #000080;"></link></span> compiler<span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2905

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<td class="new_line diff-line-num old" data-linenumber="2904" style="width: 35px; color: rgba(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="LC2905" class="line" lang="xml">      <span class="nt" style="color: #000080;"><listitem><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://mesonbuild.com"</span><span class="nt" style="color: #000080;">></span>meson<span class="nt" style="color: #000080;"></link></span> (version >= 0.<span class="idiff left right">4</span>5)<span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2906" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2904

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<pre style="margin: 0;">+<span id="LC2904" class="line" lang="xml">      <span class="nt" style="color: #000080;"><listitem></span>a <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"https://en.wikipedia.org/wiki/C%2B%2B14"</span><span class="nt" style="color: #000080;">></span>C++1<span class="idiff left right">7</span><span class="nt" style="color: #000080;"></link></span> compiler<span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2906" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2905" class="line" lang="xml">      <span class="nt" style="color: #000080;"><listitem><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://mesonbuild.com"</span><span class="nt" style="color: #000080;">></span>meson<span class="nt" style="color: #000080;"></link></span> (version >= 0.5<span class="idiff left right">3</span>)<span class="nt" style="color: #000080;"></listitem></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2906

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<td class="new_line diff-line-num" data-linenumber="2906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2906

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<pre style="margin: 0;"> <span id="LC2906" class="line" lang="xml">    <span class="nt" style="color: #000080;"></itemizedlist></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2907

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<td class="new_line diff-line-num old" data-linenumber="2907" style="width: 35px; color: rgba(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="LC2907" class="line" lang="xml">    We recommend the GNU C++ Compiler (<span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://gcc.gnu.org"</span><span class="nt" style="color: #000080;">></span>GCC<span class="nt" style="color: #000080;"></link></span>) version <span class="idiff left">5</span>.0 (or higher) or the <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://clang.llvm.org"</span><span class="nt" style="color: #000080;">></span>Clang<span class="nt" style="color: #000080;"></link></span> compiler version <span class="idiff right">3.5.0</span> or higher. The <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://www.cairographics.org/"</span><span class="nt" style="color: #000080;">></span>Cairo<span class="nt" style="color: #000080;"></link></span> graphics library is optional, but if it is missing, the <span class="nt" style="color: #000080;"><command></span>drawtree<span class="nt" style="color: #000080;"></command></span> tool that is used to draw consensus trees won<span class="ni" style="color: #800080;">&apos;</span>t be built. See also <span class="nt" style="color: #000080;"><xref</span> <span class="na" style="color: #008080;">linkend=</span><span class="s" style="color: #d14;">"software_req"</span><span class="nt" style="color: #000080;">/></span>. <span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2908" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2907

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<pre style="margin: 0;">+<span id="LC2907" class="line" lang="xml">    We recommend the GNU C++ Compiler (<span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://gcc.gnu.org"</span><span class="nt" style="color: #000080;">></span>GCC<span class="nt" style="color: #000080;"></link></span>) version <span class="idiff left">9</span>.0 (or higher) or the <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://clang.llvm.org"</span><span class="nt" style="color: #000080;">></span>Clang<span class="nt" style="color: #000080;"></link></span> compiler version <span class="idiff right">8</span> or higher. The <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://www.cairographics.org/"</span><span class="nt" style="color: #000080;">></span>Cairo<span class="nt" style="color: #000080;"></link></span> graphics library is optional, but if it is missing, the <span class="nt" style="color: #000080;"><command></span>drawtree<span class="nt" style="color: #000080;"></command></span> tool that is used to draw consensus trees won<span class="ni" style="color: #800080;">&apos;</span>t be built. See also <span class="nt" style="color: #000080;"><xref</span> <span class="na" style="color: #008080;">linkend=</span><span class="s" style="color: #d14;">"software_req"</span><span class="nt" style="color: #000080;">/></span>. <span class="nt" style="color: #000080;"></para></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2908

</td>

<td class="new_line diff-line-num" data-linenumber="2908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2908

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

<pre style="margin: 0;"> <span id="LC2908" class="line" lang="xml"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2909

</td>

<td class="new_line diff-line-num" data-linenumber="2909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2909

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<pre style="margin: 0;"> <span id="LC2909" class="line" lang="xml">    <span class="nt" style="color: #000080;"><section><info><title></span>Linux<span class="nt" style="color: #000080;"></title></info></span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2910

</td>

<td class="new_line diff-line-num" data-linenumber="2910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2910

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<pre style="margin: 0;"> <span id="LC2910" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>On Debian and Ubuntu, you can type:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2911

</td>

<td class="new_line diff-line-num" data-linenumber="2911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2911

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<pre style="margin: 0;"> <span id="LC2911" class="line" lang="xml"><span class="nt" style="color: #000080;"><screen><prompt></span>%<span class="nt" style="color: #000080;"></prompt></span> <span class="nt" style="color: #000080;"><userinput></span>sudo apt-get install g++ git libcairo2-dev pandoc<span class="nt" style="color: #000080;"></userinput></screen></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2912

</td>

<td class="new_line diff-line-num" data-linenumber="2912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2912

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

<pre style="margin: 0;"> <span id="LC2912" class="line" lang="xml"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2913

</td>

<td class="new_line diff-line-num" data-linenumber="2913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2913

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<pre style="margin: 0;"> <span id="LC2913" class="line" lang="xml">    <span class="nt" style="color: #000080;"></para></span></span>

</pre>

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2914

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<td class="new_line diff-line-num old" data-linenumber="2914" style="width: 35px; color: rgba(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="LC2914" class="line" lang="xml">If your version of Debian or Ubuntu is recent enough to contain meson version 0.<span class="idiff left right">4</span>5 or higher, you can install meson with apt-get:</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2915" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2914" class="line" lang="xml">If your version of Debian or Ubuntu is recent enough to contain meson version 0.5<span class="idiff left right">3</span> or higher, you can install meson with apt-get:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2915

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<td class="new_line diff-line-num" data-linenumber="2915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2915

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<pre style="margin: 0;"> <span id="LC2915" class="line" lang="xml"><span class="nt" style="color: #000080;"><screen><prompt></span>%<span class="nt" style="color: #000080;"></prompt></span> <span class="nt" style="color: #000080;"><userinput></span>sudo apt-get install meson<span class="nt" style="color: #000080;"></userinput></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2916

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<td class="new_line diff-line-num" data-linenumber="2916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2916

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<pre style="margin: 0;"> <span id="LC2916" class="line" lang="xml"><span class="nt" style="color: #000080;"><prompt></span>%<span class="nt" style="color: #000080;"></prompt></span> <span class="nt" style="color: #000080;"><userinput></span>dpkg -s meson | grep Version<span class="nt" style="color: #000080;"></userinput></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2917

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<td class="new_line diff-line-num old" data-linenumber="2917" style="width: 35px; color: rgba(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="LC2917" class="line" lang="xml">Version: 0.<span class="idiff left right">45.1-2</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2918" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2917" class="line" lang="xml">Version: 0.<span class="idiff left right">53</span></span>

</pre>

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2918

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<td class="new_line diff-line-num" data-linenumber="2918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2918

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<pre style="margin: 0;"> <span id="LC2918" class="line" lang="xml"><span class="nt" style="color: #000080;"></screen></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2919

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<td class="new_line diff-line-num" data-linenumber="2919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2919

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<pre style="margin: 0;"> <span id="LC2919" class="line" lang="xml">Otherwise you can install meson through pip3:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2920

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<td class="new_line diff-line-num" data-linenumber="2920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2920

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<pre style="margin: 0;"> <span id="LC2920" class="line" lang="xml"><span class="nt" style="color: #000080;"><screen><prompt></span>%<span class="nt" style="color: #000080;"></prompt></span> <span class="nt" style="color: #000080;"><userinput></span>sudo apt-get install python3 python3-pip ninja<span class="nt" style="color: #000080;"></userinput></span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2926" style="width: 35px; color: rgba(0,0,0,0.3); 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="2926" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2926,7 +2926,7 @@ Otherwise you can install meson through pip3:</td>

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<td class="old_line diff-line-num" data-linenumber="2926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2926

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<td class="new_line diff-line-num" data-linenumber="2926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2926" class="line" lang="xml">    <span class="nt" style="color: #000080;"></section></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2927" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="2927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2927" class="line" lang="xml"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2928" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="2928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2928" class="line" lang="xml">    <span class="nt" style="color: #000080;"><section><info><title></span>Mac<span class="nt" style="color: #000080;"></title></info></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2929" style="width: 35px; color: rgba(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="new_line diff-line-num old" data-linenumber="2929" style="width: 35px; color: rgba(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="LC2929" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>On Mac OS X, the simplest way to get a compiler is to install <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"https://developer.apple.com/xcode/"</span><span class="nt" style="color: #000080;">></span>XCode<span class="nt" style="color: #000080;"></link></span> (version <span class="idiff left right">6</span> or newer) command line tools, which come with <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://clang.llvm.org"</span><span class="nt" style="color: #000080;">></span>clang<span class="nt" style="color: #000080;"></link></span>.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2929" class="line" lang="xml">    <span class="nt" style="color: #000080;"><para></span>On Mac OS X, the simplest way to get a compiler is to install <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"https://developer.apple.com/xcode/"</span><span class="nt" style="color: #000080;">></span>XCode<span class="nt" style="color: #000080;"></link></span> (version <span class="idiff left right">11</span> or newer) command line tools, which come with <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://clang.llvm.org"</span><span class="nt" style="color: #000080;">></span>clang<span class="nt" style="color: #000080;"></link></span>.</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2930

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<td class="new_line diff-line-num" data-linenumber="2930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2930

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<pre style="margin: 0;"> <span id="LC2930" class="line" lang="xml"> <span class="nt" style="color: #000080;"><screen><prompt></span>%<span class="nt" style="color: #000080;"></prompt></span> <span class="nt" style="color: #000080;"><userinput></span>xcode-select --install<span class="nt" style="color: #000080;"></userinput></screen></span>    To get the other tools, first install <span class="nt" style="color: #000080;"><link</span> <span class="na" style="color: #008080;">xmlns:xlink=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xlink"</span> <span class="na" style="color: #008080;">xlink:href=</span><span class="s" style="color: #d14;">"http://brew.sh/"</span><span class="nt" style="color: #000080;">></span>homebrew<span class="nt" style="color: #000080;"></link></span>, and then type:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2931

</td>

<td class="new_line diff-line-num" data-linenumber="2931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2931

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<pre style="margin: 0;"> <span id="LC2931" class="line" lang="xml"><span class="nt" style="color: #000080;"><screen><prompt></span>%<span class="nt" style="color: #000080;"></prompt></span> <span class="nt" style="color: #000080;"><userinput></span>brew install git meson cairo pandoc<span class="nt" style="color: #000080;"></userinput></screen></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2932" class="line" lang="xml">    <span class="nt" style="color: #000080;"></para></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">@@ -2981,8 +2981,8 @@ The command <command>bali-phy</command> and its associated tools should then be</td>

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<pre style="margin: 0;"> <span id="LC2981" class="line" lang="xml">    <span class="nt" style="color: #000080;"></section></span></span>

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<pre style="margin: 0;"> <span id="LC2982" class="line" lang="xml">      <span class="nt" style="color: #000080;"><section><info><title></span>Options: compiler and linker flags<span class="nt" style="color: #000080;"></title></info></span></span>

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<pre style="margin: 0;"> <span id="LC2983" class="line" lang="xml"> </span>

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<pre style="margin: 0;">-<span id="LC2984" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>You can select the C++ compiler by setting the CXX variable.  A useful example of this is to use <span class="nt" style="color: #000080;"><command></span>g++-<span class="idiff left right">8</span><span class="nt" style="color: #000080;"></command></span> on systems where <span class="nt" style="color: #000080;"><command></span>g++<span class="nt" style="color: #000080;"></command></span> invokes a compiler that is too old:</span>

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<pre style="margin: 0;">-<span id="LC2985" class="line" lang="xml"> <span class="nt" style="color: #000080;"><screen><prompt></span>%<span class="nt" style="color: #000080;"></prompt></span> <span class="nt" style="color: #000080;"><userinput></span>CXX=g++-<span class="idiff left right">8</span> meson build --prefix=<span class="ni" style="color: #800080;">&#36;</span>HOME/Applications/bali-phy-<span class="ni" style="color: #800080;">&version;</span> --buildtype=release<span class="nt" style="color: #000080;"></userinput></screen></span></span>

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<pre style="margin: 0;">+<span id="LC2984" class="line" lang="xml">      <span class="nt" style="color: #000080;"><para></span>You can select the C++ compiler by setting the CXX variable.  A useful example of this is to use <span class="nt" style="color: #000080;"><command></span>g++-<span class="idiff left right">9</span><span class="nt" style="color: #000080;"></command></span> on systems where <span class="nt" style="color: #000080;"><command></span>g++<span class="nt" style="color: #000080;"></command></span> invokes a compiler that is too old:</span>

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<pre style="margin: 0;">+<span id="LC2985" class="line" lang="xml"> <span class="nt" style="color: #000080;"><screen><prompt></span>%<span class="nt" style="color: #000080;"></prompt></span> <span class="nt" style="color: #000080;"><userinput></span>CXX=g++-<span class="idiff left right">9</span> meson build --prefix=<span class="ni" style="color: #800080;">&#36;</span>HOME/Applications/bali-phy-<span class="ni" style="color: #800080;">&version;</span> --buildtype=release<span class="nt" style="color: #000080;"></userinput></screen></span></span>

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<pre style="margin: 0;"> <span id="LC2986" class="line" lang="xml"> You may also set compiler and linker options using the CPPFLAGS, CXXFLAGS, and LDFLAGS variables.  For example, you can instruct the compiler to use all the features of your chip, instead of producing generic code that will run anywhere:</span>

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<pre style="margin: 0;"> <span id="LC2987" class="line" lang="xml"> <span class="nt" style="color: #000080;"><screen><prompt></span>%<span class="nt" style="color: #000080;"></prompt></span> <span class="nt" style="color: #000080;"><userinput></span>CXXFLAGS="-mtune=native -march=native" meson --prefix=<span class="ni" style="color: #800080;">&#36;</span>HOME/Applications/bali-phy-<span class="ni" style="color: #800080;">&version;</span><span class="nt" style="color: #000080;"></userinput></screen></span></span>

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<pre style="margin: 0;"> <span id="LC2988" class="line" lang="xml"></span>

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<br>

</li>

<li id="3e2daa08aea898322cb10bfdfae471974db4f198">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#3e2daa08aea898322cb10bfdfae471974db4f198"><strong>haskell/Probability/Distribution/Mixture.hs</strong></a>

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

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="haskell"><span class="n" style="color: #333;">mixtureRange</span> <span class="kr" style="font-weight: 600;">_</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ds</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distRange</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="haskell"><span class="n" style="color: #333;">mixture_density</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">ps</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">dist</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">dists</span><span class="p">)</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">doubleToLogDouble</span> <span class="n" style="color: #333;">p</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">density</span> <span class="n" style="color: #333;">dist</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">mixture_density</span> <span class="n" style="color: #333;">ps</span> <span class="n" style="color: #333;">dists</span> <span class="n" style="color: #333;">x</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="haskell"><span class="n" style="color: #333;">mixture_density</span> <span class="kt" style="color: #458; font-weight: 600;">[]</span> <span class="kr" style="font-weight: 600;">_</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">doubleToLogDouble</span> <span class="mf" style="color: #099;"><span class="idiff left right">0</span>.0</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="haskell"><span class="n" style="color: #333;">mixture_density</span> <span class="kt" style="color: #458; font-weight: 600;">[]</span> <span class="kr" style="font-weight: 600;">_</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">doubleToLogDouble</span> <span class="mf" style="color: #099;"><span class="idiff left right">1</span>.0</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="haskell"><span class="n" style="color: #333;">sample_mixture</span> <span class="n" style="color: #333;">weights</span> <span class="n" style="color: #333;">dists</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">cat</span> <span class="o" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">categorical</span> <span class="n" style="color: #333;">weights</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="haskell">                                  <span class="n" style="color: #333;">dists</span><span class="o" style="font-weight: 600;">!!</span><span class="n" style="color: #333;">cat</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="haskell"></span>

</pre>

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<br>

</li>

<li id="0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa"><strong>meson.build</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">project('bali-phy', ['cpp','c'],</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">        version: '3.6.<span class="idiff left right">0</span>',</span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">        version: '3.6.<span class="idiff left right">1</span>',</span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">        default_options : [</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">          'cpp_std=c++17',</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">          'warning_level=3',</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">          'cpp_std=c++17'</span>

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">          'b_ndebug=if-release'</span>

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">        meson_version: '>= 0.53',</span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">        license: 'GPLv2')</span>

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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>

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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">@@ -29,15 +31,32 @@ configure_file(output : 'config.h', configuration : conf_data)</td>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">root_inc = include_directories('.','src')</span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">add_project_arguments('-DHAVE_CONFIG_H', language : 'cpp')</span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"></span>

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

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"># 3. Set compiler flags</span>

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

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"># 3.1 Set warning flags</span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">warn_flags = ['-Wno-sign-compare','-Wno-maybe-uninitialized','-Woverloaded-virtual','-Wstrict-aliasing','-Wno-unknown-pragmas', '-fdiagnostics-show-template-tree']</span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">add_project_arguments(cpp.get_supported_arguments(warn_flags), language : 'cpp')</span>

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

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"># 3.2 Set optimization flags</span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">if get_option('optimization') == '2' or get_option('optimization') == '3'</span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">  opt_flags = ['-funroll-loops','-fno-math-errno','-fno-signed-zeros']</span>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">  add_project_arguments(['-DNDEBUG','-DNDEBUG_DP']+cpp.get_supported_arguments(opt_flags), language : 'cpp')</span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">  add_project_arguments(cpp.get_supported_arguments(opt_flags), language : 'cpp')</span>

</pre>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">endif</span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"># 3.3 Enable/Disable extra debugging for dynamic programming</span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">assertions_off = get_option('b_ndebug') == 'true' or (get_option('b_ndebug') == 'if-release' and</span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">                                                      (get_option('buildtype') == 'release' or</span>

</pre>

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<td class="new_line diff-line-num new" 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="plaintext">                                                       get_option('buildtype') == 'plain')</span>

</pre>

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

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

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

</pre>

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

<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">  add_project_arguments('-DNDEBUG_DP', language : 'cpp')</span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

56

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

</pre>

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<td class="old_line diff-line-num" 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">

40

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<td class="new_line diff-line-num" 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">

57

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

<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"></span>

</pre>

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

<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"># 4. Dependencies</span>

</pre>

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

59

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

<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="new_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">threads = dependency('threads')</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">if host_machine.system() == 'darwin'</span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,18 +71,6 @@ else</td>

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<td class="old_line diff-line-num" 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="LC71" class="line" lang="plaintext">  used_cairo = 'system'</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext">endif</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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

<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

55

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(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="LC55" class="line" lang="plaintext">install_data('scripts/bp-analyze', install_mode: 'rwxr-xr-x', install_dir: 'bin')</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(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="LC56" class="line" lang="plaintext">install_data('scripts/bali-phy-pkg', install_mode: 'rwxr-xr-x', install_dir: 'bin')</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">install_data(['scripts/compare-runs.R', 'scripts/compare-runs2.R',</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

58

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">              'scripts/tree-plot.R', 'scripts/tree-plot-3D.R'],</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

59

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">             install_dir:'lib/bali-phy/libexec')</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

60

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

61

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(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="LC61" class="line" lang="plaintext">## we need to build libdl if we are on windows (cygwin or mingw64, and then find the library</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(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="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">install_subdir('haskell', install_dir: 'lib/bali-phy')</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

63

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(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="LC63" class="line" lang="plaintext">install_subdir('bindings', install_dir: 'lib/bali-phy')</span>

</pre>

</td>

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64

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">install_subdir('help', install_dir: 'lib/bali-phy')</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

65

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">install_subdir('examples', install_dir: get_option('datadir')/'doc/bali-phy')</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

66

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

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

</pre>

</td>

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

67

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<td class="new_line diff-line-num" 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">

74

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

<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">if get_option('with-mpi')</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

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

<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">  mpi = dependency('mpi', language='cpp')</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

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<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

76

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

<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">endif</span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -174,6 +181,21 @@ test('bali-phy testsuite',</td>

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<td class="old_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

174

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<td class="new_line diff-line-num" 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">

181

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

<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext">     workdir: meson.source_root()/'tests',</span>

</pre>

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<td class="old_line diff-line-num" 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">

175

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<td class="new_line diff-line-num" 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">

182

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

<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext">     args:[baliphy.full_path(), packagepath])</span>

</pre>

</td>

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<td class="old_line diff-line-num" 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">

176

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<td class="new_line diff-line-num" 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">

183

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

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

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"># Install non-executable files</span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">install_data('scripts/bp-analyze', install_mode: 'rwxr-xr-x', install_dir: 'bin')</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">install_data('scripts/bali-phy-pkg', install_mode: 'rwxr-xr-x', install_dir: 'bin')</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">install_data(['scripts/compare-runs.R', 'scripts/compare-runs2.R',</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">              'scripts/tree-plot.R', 'scripts/tree-plot-3D.R'],</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

190

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

<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">             install_dir:'lib/bali-phy/libexec')</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">install_subdir('haskell', install_dir: 'lib/bali-phy')</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">install_subdir('bindings', install_dir: 'lib/bali-phy')</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">install_subdir('help', install_dir: 'lib/bali-phy')</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="plaintext">install_subdir('examples', install_dir: get_option('datadir')/'doc/bali-phy')</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"># Print a summary of the configuration</span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

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

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

</pre>

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<td class="old_line diff-line-num" 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">

177

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<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

199

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

<pre style="margin: 0;"> <span id="LC199" class="line" lang="plaintext">summary({'host': host_machine.system()</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

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<td class="new_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

200

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="plaintext">        }, section: 'Architecture')</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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<td class="new_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -187,7 +209,12 @@ summary({'BOOST': used_boost,</td>

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<td class="old_line diff-line-num" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

187

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<td class="new_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

209

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

<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext">summary({'prefix': get_option('prefix'),</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

188

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<td class="new_line diff-line-num" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

210

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

<pre style="margin: 0;"> <span id="LC210" class="line" lang="plaintext">        },section: 'Directories')</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

189

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<td class="new_line diff-line-num" 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">

211

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

<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">assertions_enabled = 'enabled'</span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">if assertions_off</span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

214

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

<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">  assertions_enabled = 'disabled'</span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">endif</span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

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

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

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

190

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<td class="new_line diff-line-num" 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">

217

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

<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext">summary({'optimization': get_option('optimization'),</span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

191

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<td class="new_line diff-line-num old" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext">         'b_ndebug': get_option('b_ndebug'),</span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

192

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<td class="new_line diff-line-num" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

218

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

<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext">         'debug': get_option('debug'),</span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

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

219

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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="LC219" class="line" lang="plaintext">         'assertions': assertions_enabled,</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

193

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<td class="new_line diff-line-num" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

220

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

<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext">        },section: 'Configuration')</span></pre>

</td>

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</table>

<br>

</li>

<li id="fd745eb42b76be12f9ba032d71f67c2001677e3b">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#fd745eb42b76be12f9ba032d71f67c2001677e3b"><strong>src/alignment/load.H</strong></a>

<hr>

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

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,7 +54,7 @@ class alignment_reader: public file_reader<std::string></td>

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<td class="old_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">current</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"><span class="nl">public:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC57" 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;">read</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">current</span><span class="p">;}</span></span>

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<pre style="margin: 0;">+<span id="LC57" 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;">read</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="n" style="color: #333;"><span class="idiff left">assert</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">done</span></span><span class="p"><span class="idiff">());</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">current</span><span class="p">;}</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">next</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">    <span class="n" style="color: #333;">alignment_reader</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="p">);</span></span>

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<br>

</li>

<li id="f9c02f01207d5d200fc0360acaea4b488f711119">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#f9c02f01207d5d200fc0360acaea4b488f711119"><strong>src/alignment/load.cc</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); 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="424" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -424,6 +424,8 @@ alignment find_last_alignment(std::istream& ifile, const string& alph_name)</td>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">A</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// After reading the alignment, we will have</span></span>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// `not file` if there is not a blank line.</span></span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="nf" style="color: #900; font-weight: 600;">read_next_alignment</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;">file</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"><span class="p">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">alignment_string</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -434,8 +436,13 @@ string read_next_alignment(std::istream& file)</td>

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<pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp">        <span class="n" style="color: #333;">alignment_string</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp">    <span class="p">}</span></span>

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

</pre>

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<pre style="margin: 0;">-<span id="LC437" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">alignment_string</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">alignment_string</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC438" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">alignment_string</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">)</span></span>

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

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp">        <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">alignment_string</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">alignment_string</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">alignment_string</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC445" 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="LC446" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp"></span>

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<br>

</li>

<li id="865ca7a790386f7472962bf795f41805aaea8cc2">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#865ca7a790386f7472962bf795f41805aaea8cc2"><strong>src/bali-phy/A-T-model.cc</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); 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="871" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -871,8 +871,8 @@ owned_ptr<Model> create_A_and_T_model(const Rules& R, variables_map& args, const</td>

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<pre style="margin: 0;"> <span id="LC871" class="line" lang="cpp">    <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">probability</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC872" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//-------- Set the alignments for variable partitions ---------//</span></span>

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<pre style="margin: 0;"> <span id="LC873" 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;">P</span><span class="p">.</span><span class="n" style="color: #333;">n_data_partitions</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC874" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">not</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">unalign</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">get_data_partition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">has_IModel</span><span class="p">())</span></span>

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<td class="old_line diff-line-num old" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

875

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<pre style="margin: 0;">-<span id="LC875" class="line" lang="cpp">            <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">get_data_partition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">set_alignment</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC874" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unalign</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">get_data_partition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">has_IModel</span><span class="p">())</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp">            <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">get_data_partition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">set_alignment</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">unalign_A</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">A</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])<span class="idiff right">)</span>;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC876" class="line" lang="cpp">    <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">probability</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC877" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC878" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// If the tree has any foreground branch attributes, then set the corresponding branch to foreground, here.</span></span>

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<br>

</li>

<li id="2179cd1191f1302041c0cd85304a3b27ece2d66c">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#2179cd1191f1302041c0cd85304a3b27ece2d66c"><strong>src/bali-phy/bali-phy.cc</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); 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="348" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -348,7 +348,7 @@ std::string generate_print_program(const model_t& print, const expression_ref& a</td>

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

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

</pre>

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<td class="old_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">print</span><span class="p">.</span><span class="n" style="color: #333;">code</span><span class="p">.</span><span class="n" style="color: #333;">is_action</span><span class="p">())</span></span>

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<td class="old_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(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="new_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(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="LC351" class="line" lang="cpp">        <span class="n" style="color: #333;">program_file</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"  result <- run_lazy (<span class="idiff left right">print_model alphabet</span>)</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="old_line diff-line-num new" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp">        <span class="n" style="color: #333;">program_file</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"  result <- run_lazy (<span class="idiff left">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="n" style="color: #333;"><span class="idiff">E</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span>)</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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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp">        <span class="n" style="color: #333;">program_file</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"  let result = "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">E</span><span class="o" style="font-weight: 600;"><<</span><span class="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="old_line diff-line-num" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -446,12 +446,11 @@ int main(int argc,char* argv[])</td>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="cpp">    <span class="n" style="color: #333;">owned_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Model</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">M</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Declare early so we can reference from catch block.</span></span>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC449" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC450" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(HAVE_FEENABLEEXCEPT) && <span class="idiff left">!</span>defined(<span class="idiff right">N</span>DEBUG)</span></span>

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This should probably be a run-time switch.</span></span>

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(HAVE_FEENABLEEXCEPT) && defined(DEBUG<span class="idiff left right">_FPE</span>)</span></span>

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp">        <span class="n" style="color: #333;">feenableexcept</span><span class="p">(</span><span class="n" style="color: #333;">FE_DIVBYZERO</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">FE_OVERFLOW</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">FE_INVALID</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC452" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//    feclearexcept(FE_DIVBYZERO|FE_OVERFLOW|FE_INVALID);</span></span>

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">-<span id="LC454" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(HAVE_CLEAREXCEPT) && defined(<span class="idiff left right">N</span>DEBUG)</span></span>

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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(HAVE_CLEAREXCEPT) && <span class="idiff left">!</span>defined(DEBUG<span class="idiff right">_FPE</span>)</span></span>

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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp">        <span class="n" style="color: #333;">feclearexcept</span><span class="p">(</span><span class="n" style="color: #333;">FE_DIVBYZERO</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">FE_OVERFLOW</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">FE_INVALID</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp">        <span class="n" style="color: #333;">fp_scale</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>

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<br>

</li>

<li id="238e374095867defed8cf9bfefbd51d3028da46b">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#238e374095867defed8cf9bfefbd51d3028da46b"><strong>src/builtins/PopGen.cc</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,6 +9,7 @@</td>

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9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "util/string/split.H"</span></span>

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10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "util/string/strip.H"</span></span>

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11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "util/log-level.H"</span></span>

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<td class="old_line diff-line-num new" 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 "math/logprod.H"</span></span>

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12

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13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>

</pre>

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13

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

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</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="p">;</span></span>

</pre>

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14

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<td class="new_line diff-line-num" 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">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optional</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -534,17 +535,10 @@ extern "C" closure builtin_function_ewens_diploid_probability(OperationArgs& Arg</td>

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534

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535

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="cpp">    <span class="n" style="color: #333;">n</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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535

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<td class="new_line diff-line-num" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

536

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">I</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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536

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<td class="new_line diff-line-num" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

537

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<pre style="margin: 0;"> <span id="LC537" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

537

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<td class="new_line diff-line-num old" data-linenumber="538" style="width: 35px; color: rgba(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="LC537" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Pr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

538

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<td class="new_line diff-line-num old" data-linenumber="538" style="width: 35px; color: rgba(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="LC538" class="line" lang="cpp">    <span class="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">Pr2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

538

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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp">    <span class="n" style="color: #333;">log_prod_underoverflow</span> <span class="n" style="color: #333;">Pr</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

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<td class="new_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

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

<pre style="margin: 0;"> <span id="LC539" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n_theta_pow</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="old_line diff-line-num" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

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<td class="new_line diff-line-num" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

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

<pre style="margin: 0;"> <span id="LC540" 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;">total</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;">n</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

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<td class="new_line diff-line-num" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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542

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<td class="new_line diff-line-num old" data-linenumber="542" style="width: 35px; color: rgba(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="LC542" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Pr</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0e-30</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

543

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<td class="new_line diff-line-num old" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC543" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

544

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<td class="new_line diff-line-num old" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC544" class="line" lang="cpp">      <span class="n" style="color: #333;">Pr2</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">Pr</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

545

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<td class="new_line diff-line-num old" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC545" class="line" lang="cpp">      <span class="n" style="color: #333;">Pr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

546

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<td class="new_line diff-line-num old" data-linenumber="542" style="width: 35px; color: rgba(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="LC546" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

547

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<td class="new_line diff-line-num old" data-linenumber="542" style="width: 35px; color: rgba(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="LC547" class="line" lang="cpp"></span>

</pre>

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548

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542

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alleles</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">as_int</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

549

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<td class="new_line diff-line-num" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

543

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alleles</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">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;">as_int</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

550

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<td class="new_line diff-line-num" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

544

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

<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -568,7 +562,7 @@ extern "C" closure builtin_function_ewens_diploid_probability(OperationArgs& Arg</td>

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<td class="old_line diff-line-num" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

568

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<td class="new_line diff-line-num" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

562

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<pre style="margin: 0;"> <span id="LC562" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Heterozygotes coalesce before outbreeding with probability 0.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

569

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<td class="new_line diff-line-num" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

563

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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">heterozygote</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">coalesced</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

570

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<td class="new_line diff-line-num" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

564

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<pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp">      <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

571

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<td class="new_line diff-line-num old" data-linenumber="565" style="width: 35px; color: rgba(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="LC571" class="line" lang="cpp">          <span class="n" style="color: #333;">Pr<span class="idiff left right">2</span></span> <span class="o" style="font-weight: 600;">*=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// This accumulates zeros, in order to penalize them.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="572" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

565

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<pre style="margin: 0;">+<span id="LC565" class="line" lang="cpp">          <span class="n" style="color: #333;">Pr</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// This accumulates zeros, in order to penalize them.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

572

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<td class="new_line diff-line-num" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

566

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

573

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<td class="new_line diff-line-num" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

567

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<pre style="margin: 0;"> <span id="LC567" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

574

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<td class="new_line diff-line-num" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

568

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

<pre style="margin: 0;"> <span id="LC568" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); 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="575" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -581,12 +575,9 @@ extern "C" closure builtin_function_ewens_diploid_probability(OperationArgs& Arg</td>

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<td class="old_line diff-line-num" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

581

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<td class="new_line diff-line-num" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

575

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

582

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<td class="new_line diff-line-num" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

576

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<pre style="margin: 0;"> <span id="LC576" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

583

</td>

<td class="new_line diff-line-num" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

577

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

<pre style="margin: 0;"> <span id="LC577" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

584

</td>

<td class="new_line diff-line-num old" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC584" class="line" lang="cpp">    <span class="n" style="color: #333;">Pr2</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">Pr</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;">log_double_t</span><span class="p">(</span><span class="n" style="color: #333;">theta</span><span class="p">),</span> <span class="n" style="color: #333;">n_theta_pow</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

585

</td>

<td class="new_line diff-line-num old" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC585" class="line" lang="cpp">  </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

586

</td>

<td class="new_line diff-line-num old" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC586" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">Pr</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC587" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//  assert(Pr2 > 0.0);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp">    <span class="n" style="color: #333;">Pr</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;">log_double_t</span><span class="p">(</span><span class="n" style="color: #333;">theta</span><span class="p">),</span> <span class="n" style="color: #333;">n_theta_pow</span><span class="p">);</span></span>

</pre>

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579

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<pre style="margin: 0;"> <span id="LC579" class="line" lang="cpp">  </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

589

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<td class="new_line diff-line-num old" data-linenumber="580" style="width: 35px; color: rgba(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="LC589" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span><span class="n" style="color: #333;">Pr<span class="idiff left right">2</span></span><span class="p">};</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">expression_ref</span></span><span class="p">{</span><span class="n" style="color: #333;">Pr</span><span class="p">};</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC582" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC583" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Pr(I|s) = \sum_t=0^\infty s^t (1-s) (1/2^t)^(L-n) (1-(1/2^t))^n</span></span>

</pre>

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<br>

</li>

<li id="0a7e2430f68ad463d640bc16eec3fbd5401c0878">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#0a7e2430f68ad463d640bc16eec3fbd5401c0878"><strong>src/computation/expression/expression_ref.H</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -55,6 +55,8 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">return</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;">E2</span><span class="p">.</span><span class="n" style="color: #333;">as_index_var</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC56" 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="old_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp">       <span class="nl">default:</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ptr</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">E2</span><span class="p">.</span><span class="n" style="color: #333;">ptr</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>

</pre>

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ptr</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;">E2</span><span class="p">.</span><span class="n" style="color: #333;">ptr</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp">       <span class="p">}</span></span>

</pre>

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

</pre>

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<br>

</li>

<li id="cf54d7ede176936d89260818c8d70ee19d32cbe9">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#cf54d7ede176936d89260818c8d70ee19d32cbe9"><strong>src/computation/optimization/float-out.cc</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -198,7 +198,12 @@ float_lets(expression_ref& E, int level)</td>

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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="old_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

199

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<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

199

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// 1. Var</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

200

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<td class="new_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_var</span><span class="p">(</span><span class="n" style="color: #333;">E</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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 class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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;">auto</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">E</span><span class="p">.</span><span class="n" style="color: #333;">as_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">var</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strip_level</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp">        <span class="n" style="color: #333;">E</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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201

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<td class="new_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="p">{};</span></span>

</pre>

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

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<td class="old_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

202

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<td class="new_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

207

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

203

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<td class="new_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

208

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// 2. Constant</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">E</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span></span>

</pre>

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<br>

</li>

<li id="cd6d57441fe89247b6e6a9e74d810778209c4f42">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#cd6d57441fe89247b6e6a9e74d810778209c4f42"><strong>src/dp/alignment-sums.H</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>

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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">@@ -29,8 +29,9 @@</td>

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29

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <memory></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(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="new_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(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="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <memory>                  // for shared_ptr</span></span>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector>                  // for vector</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <memory>                  // for std::shared_ptr</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector>                  // for std::vector</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <optional>                // for std::optional</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "dp-engine.H"             // for DPengine</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "util/math/log-double.H"  // for log_double_t</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>

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<br>

</li>

<li id="535235710e10492b72a1f4ed649df7d4a5736803">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#535235710e10492b72a1f4ed649df7d4a5736803"><strong>src/math/exponential.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">@@ -86,11 +86,11 @@ Matrix expm1(const EigenValues& solution,double t)</td>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp">       <span class="n" style="color: #333;">E</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;">temp</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp">   </span>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>

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<pre style="margin: 0;">-<span id="LC90" 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;">E</span><span class="p">.</span><span class="n" style="color: #333;">size1</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC91" 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;">E</span><span class="p">.</span><span class="n" style="color: #333;">size2</span><span class="p">();</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp">       <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">E</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="p">((</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">j</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span><span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">:</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0e-10</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>#ifndef NDEBUG</span></span>

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<td class="new_line diff-line-num new" 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="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>    for(int i=0;i<E.size1();i++)</span></span>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span> for(int j=0;j<E.size2();j++)</span></span>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>     assert(E(i,j) + ((i==j)?1.0:0.0) >= -1.0e-10);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>#endif</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">E</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC96" 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="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -117,11 +117,11 @@ Matrix exp(const EigenValues& solution,double t)</td>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp">      <span class="n" style="color: #333;">E</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;">temp</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp">  <span class="p">}</span></span>

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

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>

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<pre style="margin: 0;">-<span id="LC121" 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;">E</span><span class="p">.</span><span class="n" style="color: #333;">size1</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC122" 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;">E</span><span class="p">.</span><span class="n" style="color: #333;">size2</span><span class="p">();</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp">      <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">E</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="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0e-10</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>#ifndef NDEBUG</span></span>

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<td class="new_line diff-line-num new" 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="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>    for(int i=0;i<E.size1();i++)</span></span>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>        for(int j=0;j<E.size2();j++)</span></span>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>            assert(E(i,j) >= -1.0e-10);</span></span>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>#endif</span></span>

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

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">E</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -185,13 +185,16 @@ Matrix exp(const EigenValues& eigensystem, const vector<double>& pi, const doubl</td>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sum</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="LC187" 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;">E</span><span class="p">.</span><span class="n" style="color: #333;">size2</span><span class="p">();</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="cpp">      <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">E</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="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0e-10</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// assert(E(i,j) >= -1.0e-10);</span></span>

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

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// Force positive</span></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp">            <span class="n" style="color: #333;">E</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;">max</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">E</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp">            <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">E</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">);</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// assert(t > 10 or std::abs(sum - 1.0) < 1.0e-10*E.size1());</span></span>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Renormalize rows</span></span>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="cpp">        <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">10</span> <span class="n" style="color: #333;">or</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0e-10</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">E</span><span class="p">.</span><span class="n" style="color: #333;">size1</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">factor</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;">sum</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">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;">E</span><span class="p">.</span><span class="n" style="color: #333;">size2</span><span class="p">();</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp">            <span class="n" style="color: #333;">E</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;">factor</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="f784e669c8f7b7c916e62bab68d5fc49d8247850">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#f784e669c8f7b7c916e62bab68d5fc49d8247850"><strong>src/math/logprod.H</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,6 +22,7 @@</td>

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

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cmath></span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "util/assert.hh"</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="cp" style="color: #999; font-weight: 600;">#include "util/math/log-double.H"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">log_prod_underflow</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -95,6 +96,110 @@ struct log_prod_underflow</td>

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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">constexpr</span> <span class="n" style="color: #333;">log_prod_underflow</span><span class="p">()</span> <span class="p">{}</span></span>

</pre>

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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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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">log_prod_underoverflow</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp">    <span class="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">accum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">prod</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num new" 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;">log_prod_underoverflow</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;">log_double_t</span> <span class="n" style="color: #333;">x</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp">  <span class="n" style="color: #333;">accum</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">;</span></span>

</pre>

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="new_line diff-line-num new" 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="c1" style="color: #998; font-style: italic;">// NOTE: by not using the smallest/largest possible values, we avoid FPE exceptions on underflow / overflow (mostly).</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">max_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">115792089237316195423570985008687907853269984665640564039457584007913129639936e0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// static constexpr double min_value = std::numeric_limits<double>::min();</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">min_value</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;">max_value</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="new_line diff-line-num new" 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;">log_prod_underoverflow</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="p">{</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">was_zero</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_zero</span><span class="p">();</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mult</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prod</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// keep the larger of {prod,x} in the "prod" slot.</span></span>

</pre>

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123

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prod</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">x</span><span class="p">)</span></span>

</pre>

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124

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

</pre>

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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

125

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp">                <span class="n" style="color: #333;">accum</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">prod</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

126

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp">                <span class="n" style="color: #333;">prod</span> <span class="o" style="font-weight: 600;">=</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="LC127" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

128

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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129

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp">                <span class="n" style="color: #333;">accum</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

130

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

131

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mult</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_value</span><span class="p">)</span></span>

</pre>

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132

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// keep the smaller of {prod,x} in the "prod" slot.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prod</span> <span class="o" style="font-weight: 600;">></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="LC135" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp">                <span class="n" style="color: #333;">accum</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">prod</span><span class="p">;</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp">                <span class="n" style="color: #333;">prod</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp">                <span class="n" style="color: #333;">accum</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>

</pre>

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

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

</pre>

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

142

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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

143

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp">      <span class="n" style="color: #333;">prod</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mult</span><span class="p">;</span></span>

</pre>

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

144

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

145

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

146

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp">  <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_zero</span><span class="p">()</span> <span class="n" style="color: #333;">or</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="n" style="color: #333;">or</span> <span class="n" style="color: #333;">was_zero</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

147

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

148

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

150

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp">    <span class="n" style="color: #333;">log_prod_underoverflow</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mult_with_count</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;">int</span> <span class="n" style="color: #333;">c</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

152

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp">  <span class="n" style="color: #333;">assert</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>

</pre>

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<td class="new_line diff-line-num new" 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 class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">prod</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="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

154

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

155

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count_limit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

156

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

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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 class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">was_zero</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_zero</span><span class="p">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

158

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp">  <span 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="n" style="color: #333;">count_limit</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp">      <span class="n" style="color: #333;">accum</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;">log_double_t</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">),</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

161

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

162

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

163

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<pre style="margin: 0;">+<span id="LC163" 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;">x</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

164

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<pre style="margin: 0;">+<span id="LC164" 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;">c</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

165

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp">          <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

166

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mult</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prod</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="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

168

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mult</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_value</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

169

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// keep the larger of {prod,x} in the "prod" slot.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prod</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">x</span><span class="p">)</span></span>

</pre>

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

172

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

</pre>

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<td class="new_line diff-line-num new" 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;">accum</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">prod</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="n" style="color: #333;">prod</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="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp">                    <span class="n" style="color: #333;">accum</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;">log_double_t</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">),</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>

</pre>

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

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

</pre>

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<td class="new_line diff-line-num new" 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;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mult</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_value</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" 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;">prod</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">x</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="n" style="color: #333;">accum</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">prod</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

184

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp">                    <span class="n" style="color: #333;">prod</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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185

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp">                <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="new_line diff-line-num new" 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;">accum</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;">log_double_t</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">),</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>

</pre>

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188

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" 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 class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

190

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

</pre>

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

</pre>

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

</pre>

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<td class="new_line diff-line-num new" 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 class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_zero</span><span class="p">()</span> <span class="n" style="color: #333;">or</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="n" style="color: #333;">or</span> <span class="n" style="color: #333;">was_zero</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" 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;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">;</span></span>

</pre>

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

</pre>

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">value</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">accum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">prod</span><span class="p">;}</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">operator</span> <span class="n" style="color: #333;">log_double_t</span> <span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span><span class="p">();}</span></span>

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<td class="new_line diff-line-num new" 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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">is_zero</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;}</span></span>

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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">constexpr</span> <span class="n" style="color: #333;">log_prod_underoverflow</span><span class="p">()</span> <span class="p">{}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">log_prod_rescale</span></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"><span class="p">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale_factor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">115792089237316195423570985008687907853269984665640564039457584007913129639936e0</span><span class="p">;</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,6 +220,11 @@ struct log_prod_rescale</td>

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

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp">      <span class="n" style="color: #333;">prod</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale_factor</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" 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="LC221" class="line" lang="cpp">      <span class="n" style="color: #333;">scale</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp">  <span class="p">}</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prod</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">scale_factor</span><span class="p">)</span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp">            <span class="n" style="color: #333;">prod</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale_min</span><span class="p">;</span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp">            <span class="n" style="color: #333;">scale</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>

</pre>

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

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

</pre>

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

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<td class="new_line diff-line-num" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp">  <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_zero</span><span class="p">()</span> <span class="n" style="color: #333;">or</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="n" style="color: #333;">or</span> <span class="n" style="color: #333;">was_zero</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="b56bfbbf69bb94c0e10814775ed402a5732685f0">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#b56bfbbf69bb94c0e10814775ed402a5732685f0"><strong>src/probability/choose.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">@@ -26,11 +26,20 @@ using std::vector;</td>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">choose2</span><span class="p">(</span><span class="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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 class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">log_double_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Pr</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp">  <span class="n" style="color: #333;">Pr</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;">x</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(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="new_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp">  <span class="n" style="color: #333;">Pr</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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;">auto</span> <span class="n" style="color: #333;">sum0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">sum1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">choose_scratch</span><span class="p">(</span><span class="n" style="color: #333;">Pr</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log_double_t</span><span class="p">(</span><span class="n" style="color: #333;">uniform</span><span class="p">())</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sum1</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sum0</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sum1</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</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="LC38" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="n" style="color: #333;">choose_exception</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">log_double_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">c</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</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>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp">    <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">prepend</span><span class="p">(</span><span class="s" style="color: #d14;">":</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp">    <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">prepend</span><span class="p">(</span><span class="n" style="color: #333;">__PRETTY_FUNCTION__</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>

</pre>

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34

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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35

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" 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">

36

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="p">></span> <span class="n" style="color: #333;">choose_exception</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">log_double_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">choose_exception</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="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;">log_double_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">V</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="074bf1d6d3874f73c6d0fc2b177af772a6934be8">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#074bf1d6d3874f73c6d0fc2b177af772a6934be8"><strong>src/sequence/sequence-format.H</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">  <span class="idiff left right"> </span>Copyright (C) 2004-2005,2007,2009 Benjamin Redelings</span></span>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">  Copyright (C) 2004-2005,2007,2009<span class="idiff left right">,2012</span> Benjamin Redelings</span></span>

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3

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">This file is part of BAli-Phy.</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span>This file is part of BAli-Phy.</span></span>

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5

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

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

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">BAli-Phy is free software; you can redistribute it and/or modify it under</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">the terms of the GNU General Public License as published by the Free</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">Software Foundation; either version 2, or (at your option) any later</span></span>

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9

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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">version.</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

6

</td>

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span>BAli-Phy is free software; you can redistribute it and/or modify it under</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span>the terms of the GNU General Public License as published by the Free</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span>Software Foundation; either version 2, or (at your option) any later</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span>version.</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" 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

</td>

<td class="new_line diff-line-num" 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

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">BAli-Phy is distributed in the hope that it will be useful, but WITHOUT ANY</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">WARRANTY; without even the implied warranty of MERCHANTABILITY or</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">for more details.</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

11

</td>

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span>BAli-Phy is distributed in the hope that it will be useful, but WITHOUT ANY</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

12

</td>

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span>WARRANTY; without even the implied warranty of MERCHANTABILITY or</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span>FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

14

</td>

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

<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span>for more details.</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" 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">

15

</td>

<td class="new_line diff-line-num" 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">

15

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="new_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">You should have received a copy of the GNU General Public License</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

</td>

<td class="new_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">along with BAli-Phy; see the file COPYING.  If not see</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num 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">

18

</td>

<td class="new_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><http://www.gnu.org/licenses/>.  */</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span>You should have received a copy of the GNU General Public License</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span>along with BAli-Phy; see the file COPYING.  If not see</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">  </span><http://www.gnu.org/licenses/>.  */</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @file sequence-format.H</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,39 +33,39 @@ along with BAli-Phy; see the file COPYING.  If not see</td>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">/// A namespace containing functions for parsing and writing sequence formats</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">sequence_format</span> </span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">/// A typedef for functions that reads sequences from a file</span></span>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">typedef</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;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">loader_t</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;">file</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"><span class="idiff left right">  </span>  <span class="c1" style="color: #998; font-style: italic;">/// A typedef for functions that reads sequences from a file</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"><span class="idiff left right">  </span>  <span class="k" style="font-weight: 600;">typedef</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;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">loader_t</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;">file</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in phylip format</span></span>

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<pre style="margin: 0;">-<span id="LC40" 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;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">read_guess</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;">file</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" 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="LC39" class="line" lang="cpp"><span class="idiff left right">  </span>  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in phylip format</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"><span class="idiff left right">  </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;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">read_guess</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;">file</span><span class="p">);</span></span>

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

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in phylip format</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(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="LC43" 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;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">read_phylip</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;">file</span><span class="p">);</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="idiff left right">  </span>  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in phylip format</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="idiff left right">  </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;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">read_phylip</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;">file</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp">  </span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in fasta format</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC46" 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;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">read_fasta</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;">file</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="idiff left right">  </span>  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in fasta format</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="idiff left right">  </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;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">read_fasta</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;">file</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in fasta format</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">read_fasta_entire_file</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;">file</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="idiff left right">  </span>  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in fasta format</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="idiff left right">  </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;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">read_fasta_entire_file</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;">file</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(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="new_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(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="LC51" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">/// A typedef for functions that write sequences to a file</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(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="LC52" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="n" style="color: #333;">dumper_t</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="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;">sequence</span><span class="o" style="font-weight: 600;">>&</span><span class="p">);</span></span>

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<td class="new_line diff-line-num new" 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="idiff left right">  </span>  <span class="c1" style="color: #998; font-style: italic;">/// A typedef for functions that write sequences to a file</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="idiff left right">  </span>  <span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="n" style="color: #333;">dumper_t</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="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;">sequence</span><span class="o" style="font-weight: 600;">>&</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(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="LC54" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in phylip format</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_phylip</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;">file</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;">sequence</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">sequences</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="idiff left right">  </span>  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in phylip format</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="idiff left right">  </span>  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_phylip</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;">file</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;">sequence</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">sequences</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in fasta format</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_fasta</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;">file</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;">sequence</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">sequences</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="idiff left right">  </span>  <span class="c1" style="color: #998; font-style: italic;">/// Read an alignments letters and names from a file in fasta format</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="idiff left right">  </span>  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_fasta</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;">file</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;">sequence</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">sequences</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"></span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">/// load a format from a file with name filename</span></span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">load_from_file</span><span class="p">(</span><span class="n" style="color: #333;">loader_t</span> <span class="n" style="color: #333;">loader</span><span class="p">,</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"><span class="idiff left right">  </span>  <span class="c1" style="color: #998; font-style: italic;">/// load a format from a file with name filename</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"><span class="idiff left right">  </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;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">load_from_file</span><span class="p">(</span><span class="n" style="color: #333;">loader_t</span> <span class="n" style="color: #333;">loader</span><span class="p">,</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">/// load a format from a file with name filename</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">load_from_file</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"><span class="idiff left right">  </span>  <span class="c1" style="color: #998; font-style: italic;">/// load a format from a file with name filename</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"><span class="idiff left right">  </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;">sequence</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">load_from_file</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">/// write a format to a file.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_to_file</span><span class="p">(</span><span class="n" style="color: #333;">loader_t</span> <span class="n" style="color: #333;">loader</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;">sequence</span><span class="o" style="font-weight: 600;">>&</span><span class="p">,</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"><span class="idiff left right">  </span>  <span class="c1" style="color: #998; font-style: italic;">/// write a format to a file.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"><span class="idiff left right">  </span>  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_to_file</span><span class="p">(</span><span class="n" style="color: #333;">loader_t</span> <span class="n" style="color: #333;">loader</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;">sequence</span><span class="o" style="font-weight: 600;">>&</span><span class="p">,</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>

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<br>

</li>

<li id="2b49d788b7727bf59b6addf9630d6185b61b3a73">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#2b49d788b7727bf59b6addf9630d6185b61b3a73"><strong>src/sequence/sequence-format.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">@@ -110,7 +110,7 @@ namespace sequence_format {</td>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp">              <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp">          <span class="p">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(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="LC113" class="line" lang="cpp"><span class="idiff left right">   </span></span>

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<td class="old_line diff-line-num new" 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="LC113" class="line" lang="cpp"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// add the letters in</span></span>

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

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp">          <span class="n" style="color: #333;">letters</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" 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="LC116" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="d40956e0ef89c695ee758deaa21c1d0a996c2cbc">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#d40956e0ef89c695ee758deaa21c1d0a996c2cbc"><strong>src/tools/pickout.cc</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,6 +17,7 @@</td>

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17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">  along with BAli-Phy; see the file COPYING.  If not see</span></span>

</pre>

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<td class="old_line diff-line-num" 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="cm" style="color: #998; font-style: italic;">  <http://www.gnu.org/licenses/>.  */</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <optional></span></span>

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<td class="old_line diff-line-num" 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="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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 <string></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>

</pre>

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</li>

<li id="b7018a0aaa166740c68039b579041123634699f3">

<a href="https://salsa.debian.org/med-team/bali-phy/-/compare/34bb7b4040446b77d436078c1d724a5d0216593d...9cc015b75d097fe2400f47cd6232d4e150f6a950#b7018a0aaa166740c68039b579041123634699f3"><strong>src/util/include/util/math/log-double.H</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,7 +43,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">operator</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);}</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">constexpr</span> <span class="n" style="color: #333;">log_double_t</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp">   <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp">   <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">isnan</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">or</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">y</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp">       <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log_0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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